细粒棘球绦虫原头蚴、包囊壁和成虫circRNA差异表达分析

doi:10.11843/j.issn.0366-6964.2023.08.032

Abstract

Abstract: The purpose of this study was to analyze the expression profile of circRNA in protoscolex, hydatid cyst wall and adult of Echinococcus granulosus, and to provide theoretical basis for further elucidating the role of circRNA in the growth and development of Echinococcus granulosus.Total RNA was extracted from Echinococcus granulosus protoscoleces, hydatid cyst wall and adult worms, and the circRNA, miRNA and mRNA libraries were constructed.The differentially expressed circRNA were screened by bioinformatics analysis and functional prediction, and then were analyzed by the GO, KEGG and ceRNA regulatory networks. The differentially expressed circRNA were validated by real-time fluorescent quantitative PCR (qRT-PCR).In this study, 636 circRNA molecules were identified from protoscolex, cyst wall and adult of Echinococcus Granulosus, of which 140 were differentially expressed.The specific expression of circRNA was 44, 2 and 0 in protoscolex, cyst wall and adult worms, respectively.The results of the GO analysis showed that compared with protoscolices and cyst walls, the differentially expressed circRNA molecules in the adult worms were mainly concentrated in the biological processes of sexual reproduction, spermatogenesis, male gametogenesis, axogenesis, neurogenesis and differentiation.The results of KEGG analysis showed that the differentially expressed circRNA was significantly enriched in Notch, tricarboxylic acid cycle, phosphatidylinositol, riboflavin metabolic pathway and fatty acid synthesis and degradation pathway. The differentially expressed circRNA in cyst wall and protoscolices were significantly enriched in dorsal-ventral axis formation, Notch, wnt and FoxO signaling pathway.The differentially expressed circRNA in cyst wall and adult worms were significantly enriched in Notch, carbon metabolism, tricarboxylic acid cycle and glycolysis/gluconeogenesis pathway.Targeted prediction of circRNA-miRNA-mRNA regulatory networks showed that 164 up-down-up circRNA-miRNA-mRNA regulatory networks were formed by 24 differentially expressed circRNAs, 14 miRNAs and 54 mRNAs, 36 down-up-down circRNA-miRNA-mRNA regulatory networks were composed of 13 differentially expressed circRNAs, 7 miRNAs and 16 mRNAs.The results of qRT-PCR for some circRNA molecules showed that the mRNA transcription level was consistent with the RNA-sequencing results.In conclusion, this study is the first to systematically analyze the differential expression profiles of circRNA in protoscolex, cyst wall and adult Echinococcus granulosus, the potential regulatory network of circRNA-miRNA-mRNA of differentially expressed circRNA was predicted, the high expression and specific expression circRNA molecules in protoscolex, cyst wall and adult worms were also screened, this study lays a foundation for further research on the role of circRNA in the growth and development of Echinococcus granulosus.

Key words: Echinococcus granulosus, circRNA, protoscolex, adult worm, cyst wall, expression profiles

CLC Number:

S852.734

WANG Zhengrong, MA Xun, ZHANG Yanyan, SUN Yan, MENG Jimeng, BO Xinwen. Differential Expression Profile of CircRNA in Protoscolex, Hydatid Cyst Wall and Adult of Echinococcus granulosus[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3474-3489.

References 56

[1]	SIRACUSANO A, DELUNARDO F, TEGGI A, et al.Host-parasite relationship in cystic echinococcosis:an evolving story[J].Clin Dev Immunol, 2012, 2012:639362.
[2]	SAVIOLI L, DAUMERIE D.Working to overcome the global impact of neglected tropical diseases-Summary[J].Wkly Epidemiol Rec, 2011, 86(13):113-120.
[3]	汪天平, 操治国.中国棘球蚴病防控进展及其存在的问题[J].中国寄生虫学与寄生虫病杂志, 2018, 36(3):291-296.WANG T P, CAO Z G.Current status of echinococcosis control in China and the existing challenges[J].Chinese Journal of Parasitology and Parasitic Diseases, 2018, 36(3):291-296.(in Chinese)
[4]	MCMANUS D P, ZHANG W B, LI J, et al.Echinococcosis[J].Lancet, 2003, 362(9392):1295-1304.
[5]	ZHENG H J, ZHANG W B, ZHANG L, et al.The genome of the hydatid tapeworm Echinococcus granulosus[J].Nat Genet, 2013, 45(10):1168-1175.
[6]	MEMCZAK S, JENS M, ELEFSINIOTI A, et al.Circular RNAs are a large class of animal RNAs with regulatory potency[J].Nature, 2013, 495(7441):333-338.
[7]	EBBESEN K K, HANSEN T B, KJEMS J.Insights into circular RNA biology[J].RNA Biol, 2017, 14(8):1035-1045.
[8]	BOWLES J, BLAIR D, MCMANUS D P.Genetic variants within the genus Echinococcus identified by mitochondrial DNA sequencing[J].Mol Biochem Parasitol, 1992, 54(2):165-173.
[9]	KECHIN A, BOYARSKIKH U, KEL A, et al.cutPrimers:a new tool for accurate cutting of primers from reads of targeted next generation sequencing[J].J Comput Biol, 2017, 24(11):1138-1143.
[10]	LANGMEAD B, SALZBERG S L.Fast gapped-read alignment with Bowtie 2[J].Nat Methods, 2012, 9(4):357-359.
[11]	KIM D, PERTEA G, TRAPNELL C, et al.TopHat2:accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions[J].Genome Biol, 2013, 14(4):R36.
[12]	MIHAELA P, PERTEA G M, ANTONESCU C M, et al.StringTie enables improved reconstruction of a transcriptome from RNA-seq reads[J].Nat Biotechnol, 2015, 33(3):290-295.
[13]	FRAZEE A C, GEO P, JAFFE A E, et al.Ballgown bridges the gap between transcriptome assembly and expression analysis[J].Nat Biotechnol, 2015, 33(3):243-246.
[14]	ANDERS S, HUBER W.Differential expression analysis for sequence count data[J].Genome Biol, 2010, 11(10):R106.
[15]	KIM D, SALZBERG S L.TopHat-Fusion:an algorithm for discovery of novel fusion transcripts[J].Genome Biol, 2011, 12(8):R72.
[16]	ZHANG X O, WANG H B, ZHANG Y, et al.Complementary sequence-mediated exon circularization[J].Cell, 2014, 159(1):134-147.
[17]	ASHWAL-FLUSS R, MEYER M, PAMUDURTI N R, et al.circRNA biogenesis competes with Pre-mRNA splicing[J].Mol Cell, 2014, 56(1):55-66.
[18]	CAMON E, MAGRANE M, BARRELL D, et al.The gene ontology annotation (GOA) database:sharing knowledge in uniprot with gene ontology[J].Nucleic Acids Res, 2004, 32(S1):D262-D266.
[19]	KANEHISA M, ARAKI M, GOTO S, et al.KEGG for linking genomes to life and the environment[J].Nucleic Acids Res, 2008, 36(S1):D480-D484.
[20]	LIVAK K J, SCHMITTGEN T D.Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method[J].Methods, 2001, 25(4):402-408.
[21]	MEMCZAK S, JENS M, ELEFSINIOTI A, et al.Circular RNAs are a large class of animal RNAs with regulatory potency[J].Nature, 2013, 495(7441):333-338.
[22]	EBBESEN K K, HANSEN T B, KJEMS J.Insights into circular RNA biology[J].RNA Biol, 2017, 14(8):1035-1045.
[23]	SANGER H L, KLOTZ G, RIESNER D, et al.Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures[J].Proc Natl Acad Sci U S A, 1976, 73(11):3852-3856.
[24]	CAPEL B, SWAIN A, NICOLIS S, et al.Circular transcripts of the testis-determining gene Sry in adult mouse testis[J].Cell, 1993, 73(5):1019-1030.
[25]	ABDELMOHSEN K, PANDA A C, DE S, et al.Circular RNAs in monkey muscle:age-dependent changes[J].Aging (Albany NY), 2015, 7(11):903-910.
[26]	VENØ M T, HANSEN T B, VENØ S T, et al.Spatio-temporal regulation of circular RNA expression during porcine embryonic brain development[J].Genome Biol, 2015, 16:245.
[27]	BURD C E, JECK W R, LIU Y, et al.Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk[J].PLoS Genet, 2010, 6(12):e1001233.
[28]	WANG P L, BAO Y, YEE M C, et al.Circular RNA is expressed across the eukaryotic tree of life[J].PLoS One, 2014, 9(6):e90859.
[29]	ZHANG X O, WANG H B, ZHANG Y, et al.Complementary sequence-mediated exon circularization[J].Cell, 2014, 159(1):134-147.
[30]	ZHANG Y, ZHANG X O, CHEN T, et al.Circular intronic long noncoding RNAs[J].Mol Cell, 2013, 51(6):792-806.
[31]	LI Z Y, HUANG C, BAO C, et al.Exon-intron circular RNAs regulate transcription in the nucleus[J].Nat Struct Mol Biol, 2015, 22(3):256-264.
[32]	HANSEN T B, JENSEN T I, CLAUSEN B H, et al.Natural RNA circles function as efficient microRNA sponges[J].Nature, 2013, 495(7441):384-388.
[33]	WANG Y, WANG Z F.Efficient backsplicing produces translatable circular mRNAs[J].RNA, 2015, 21(2):172-179.
[34]	JECK W R, SHARPLESS N E.Detecting and characterizing circular RNAs[J].Nat Biotechnol, 2014, 32(5):453-461.
[35]	BROADBENT K M, BROADBENT J C, RIBACKE U, et al.Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA[J].BMC Genomics, 2015, 16(1):454.
[36]	ZHOU C X, ZHANG Y, WU S M, et al.Genome-wide Identification of circRNAs of infective larvae and adult worms of parasitic nematode, Haemonchus contortus[J].Front Cell Infect Microbiol, 2021, 11:764089.
[37]	REN G J, FAN X C, LIU T L, et al.Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infection[J].BMC Genomics, 2018, 19(1):356.
[38]	ZHOU C X, AI K, HUANG C Q, et al.miRNA and circRNA expression patterns in mouse brain during toxoplasmosis development[J].BMC Genomics, 2020, 21(1):46.
[39]	YU H L, MI C H, WANG Q, et al.Comprehensive analyses of circRNA expression profiles and function prediction in chicken cecums after Eimeria tenella infection[J].Front Cell Infect Microbiol, 2021, 11:628667.
[40]	KALIFU B, MAITISEYITI A, GE X H, et al.Expression profile of circular RNAs in cystic echinococcosis pericystic tissue[J].J Clin Lab Anal, 2021, 35(3):e23687.
[41]	LIU T L, WANG L Q, LI H, et al.circRNA expression pattern and circRNA-miRNA-mRNA network in HCs, HSCs, and KCs of murine liver after Echinococcus multilocularis infection[J].Front Vet Sci, 2022, 9:825307.
[42]	ZHANG X F, GONG W C, CAO S K, et al.Comprehensive analysis of Non-coding RNA profiles of exosome-like vesicles from the protoscoleces and hydatid cyst fluid of Echinococcus granulosus[J].Front Cell Infect Microbiol, 2020, 10:316.
[43]	PALUDO G P, THOMPSON C E, MIYAMOTO K N, et al.Cestode strobilation:prediction of developmental genes and pathways[J].BMC Genomics, 2020, 21(1):487.
[44]	NADEAU S, HEIN P, FERNANDES K J L, et al.A transcriptional role for C/EBP β in the neuronal response to axonal injury[J].Mol Cell Neurosci, 2005, 29(4):525-535.
[45]	STERNECK E, PAYLOR R, JACKSON-LEWIS V, et al.Selectively enhanced contextual fear conditioning in mice lacking the transcriptional regulator CCAAT/enhancer binding protein δ[J].Proc Natl Acad Sci U S A, 1998, 95(18):10908-10913.
[46]	TAUBENFELD S M, WIIG K A, MONTI B, et al.Fornix-dependent induction of hippocampal CCAAT enhancer-binding proteinβ and δ Co-localizes with phosphorylated cAMP response element-binding protein and accompanies long-term memory consolidation[J].J Neurosci, 2001, 21(1):84-91.
[47]	ALBERINI C M, GHIRARDL M, METZ R, et al.C/EBP is an immediate-early gene required for the consolidation of long-term facilitation in Aplysia[J].Cell, 1994, 76(6):1099-1114.
[48]	CORTÉS-CANTELI M, PIGNATELLI M, SANTOS A, et al.CCAAT/enhancer-binding protein β plays a regulatory role in differentiation and apoptosis of neuroblastoma cells[J].J Biol Chem, 2002, 277(7):5460-5467.
[49]	MÉNARD C, HEIN P, PAQUIN A, et al.An essential role for a MEK-C/EBP pathway during growth factor-regulated cortical neurogenesis[J].Neuron, 2002, 36(4):597-610.
[50]	CORTES-CANTELI M, AGUILAR-MORANTE D, SANZ-SANCRISTOBAL M, et al.Role of C/EBPβ transcription factor in adult hippocampal neurogenesis[J].PLoS One, 2011, 6(10):e24842.
[51]	L'HÔTE D, SERRES C, LAISSUE P, et al.Centimorgan-range one-step mapping of fertility traits using interspecific recombinant congenic mice[J].Genetics, 2007, 176(3):1907-1921.
[52]	JIANG J Q, BENSON E, BAUSEK N, et al.Tombola, a tesmin/TSO1-family protein, regulates transcriptional activation in the Drosophila male germline and physically interacts with Always early[J].Development, 2007, 134(8):1549-1559.
[53]	International Helminth Genomes Consortium.Comparative genomics of the major parasitic worms[J].Nat Genet, 2019, 51(1):163-174.
[54]	COAKLEY G, MAIZELS R M, BUCK A H.Exosomes and other extracellular vesicles:the new communicators in parasite infections[J].Trends Parasitol, 2015, 31(10):477-489.
[55]	WU C, CAI P F, CHANG Q C, et al.Mapping the binding between the tetraspanin molecule (Sjc23) of Schistosoma japonicum and human non-immune IgG[J].PLoS One, 2011, 6(4):e19112.
[56]	KRAUTZ-PETERSON G, DEBATIS M, TREMBLAY J M, et al.Schistosoma mansoni infection of mice, rats and humans elicits a strong antibody response to a limited number of reduction-sensitive epitopes on five major tegumental membrane proteins[J].PLoS Negl Trop Dis, 2017, 11(1):e0005306.

Differential Expression Profile of CircRNA in Protoscolex, Hydatid Cyst Wall and Adult of Echinococcus granulosus

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 56

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	LIU Weiye, HUANG Xuewei. Research Progress of Non-coding RNA in Infectious Bursal Disease Virus Infection [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1488-1498.
[2]	AN Zongqi, ZHAN Siyuan, LI Li, ZHANG Hongping. ceRNA-mediated Function of CircRNA on Critical Economic Traits in Animals [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2215-2222.
[3]	DU Xiaodi, HOU Wei, SU Zhonghua, MA Qingmei, HE Xue, HUA Ruiqi, YANG Aiguo, YANG Guangyou. Bioinformatics and Expression Analysis of Ubiquitin-conjugating Enzyme Gene Family of Echinococcus granulosus [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2605-2618.
[4]	QIN Xue, SHA Yiwen, YANG Menghao, CAI Rui, PANG Weijun. Advances in Regulation of Non-coding RNA on Mammalian Endometrial Receptivity and Decidualization [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1347-1358.
[5]	LUO Ju, MAO Jiani, XIA Yinzhao, YANG Zhenguo. Regulation of circRNAs on Mammalian Intestinal Barrier Function [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4439-4448.
[6]	JIANG Shengqiang, HU Jing, CHEN Hongying. Expression Analysis of CircRNAs in A549 Cells Infected with H1N1 Influenza A Virus [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4724-4734.
[7]	YANG Zhimei, LIANG Chengcheng, ZHANG Dianqi, LI Xuefeng, ZAN Linsen. Research Progress on the Regulation of circRNA by m⁶A Modification [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4016-4027.
[8]	WANG Yiqun, LIU Zupei, LI Yating, ZHANG Haisen, LI Dan, JIN Yaping, CHEN Huatao. The Dairy Cow NR1D1 Gene’s Eukaryotic Expression Vector Construction, Expression Profile and Its Ovarian Localization [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(1): 133-145.
[9]	HE Xue, WANG Ning, HUA Ruiqi, DU Xiaodi, YANG Guangyou. Cloning, Expression of Echinococcus granulosus BAG3 and EB1 and Their Roles in the Apoptosis of Protoscoleces [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(5): 1562-1575.
[10]	FENG Xue, ZHAO Jinhui, WANG Shuzhe, HUANG Jieping, WEI Xuefeng, SHI Yuangang, MA Yun. Overexpression of circNMT1 Promotes Adipogenic Differentiation of Buffalo Adipocytes [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(4): 1077-1088.
[11]	WANG Zhengrong, MA Xun, ZHANG Yanyan, MENG Jimeng, BO Xinwen. Analysis of Genes Related to Immune Interaction between Protoscolices of Echinococcus granulosus and Macrophage RAW264.7 by Transcriptome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 3975-3988.
[12]	YIN Yanling, HUANG Shuang, YAO Qian, WU Jiangping, GUO Haochen, YANG Xin, SONG Junke, ZHAO Guanghui. The Mechanisms of Circular RNA ciRS-7 Affecting the Propagation of Cryptosporidium parvum in HCT-8 Cells via Targeting miR-219a-5p [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 3989-3999.
[13]	HUANG Xiaoyu, YANG Qiaoli, YAN Zunqiang, WANG Pengfei, SHI Hairen, GUN Shuangbao. Characterization of circRNA Expression Profiles Involved in Intestines of Clostridium Perfringens Type C-infected Diarrheal Piglet [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(11): 4058-4070.
[14]	WANG Zhengrong, MA Xun, ZHANG Yanyan, MENG Jimeng, BO Xinwen. Study on the Expression Profile of Th1/Th2 Immune Response-related Genes in Macrophage RAW264.7 in Response to the Stimulation of Echinococcus granulosus Protoscoleces [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(1): 250-262.
[15]	ZOU Yang, ZHENG Wenbin, ZHANG Jinpeng, LU Yixin, ZHU Xingquan. CircRNAs Expression Patterns in the Liver of Beagle Dogs at Different Stages of Toxocara canis Infection [J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(12): 3524-3534.