Abstract
Piscirickettsiosis is the most important bacterial disease in the Chilean salmon industry, which has borne major economic losses due to failure to control it. Cells use extracellular vesicles (EVs) as an inter-cellular communicators to deliver several factors (e.g., microRNAs) that may regulate the responses of other cells. However, there is limited knowledge about the identification and characterization of EV-miRNAs in salmonids or the effect of infections on these. In this study, Illumina sequencing technology was used to identify Coho salmon plasma EV-miRNAs upon Piscirickettsia salmonis infection at four different time points. A total of 118 novels and 188 known EV-miRNAs, including key immune teleost miRNAs families (e.g., miR-146, miR-122), were identified. A total of 245 EV-miRNAs were detected as differentially expressed (FDR < 5%) in terms of control, with a clear down-regulation pattern throughout the disease. KEGG enrichment results of EV-miRNAs target genes showed that they were grouped mainly in cellular, stress, inflammation and immune responses. Therefore, it is hypothesized that P. salmonis could potentially benefit from unbalanced modulation response of Coho salmon EV-miRNAs in order to promote a hyper-inflammatory and compromised immune response through the suppression of different key immune host miRNAs during the course of the infection, as indicated by the results of this study.
Similar content being viewed by others
Availability of data and material
Sequence data file has been deposited in the Sequence Read Archive (SRA), accession number National Center for Biotechnology Information (NCBI) SRA# PRJNA627938.
References
Abels ER, Breakefield XO (2016) Introduction to extracellular vesicles: biogenesis, RNA cargo selection, content, release, and uptake. Front Immunol 36:301–312
Abu-Jamous B, Kelly S (2018) Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data. Genome Biol 19:172
Andreassen R, Høyheim B (2017) miRNAs associated with immune response in teleost fish. Dev Comp Immunol 75:77–85
Barría A, Christensen KA, Yoshida GM, Correa K, Jedlicki A, Lhorente JP, et al. (2018) Genomic predictions and genome-wide association study of resistance against Piscirickettsia salmonis in Coho salmon (Oncorhynchus kisutch) using ddRAD sequencing. G3 8:1183-1194
Barría A, Doeschl-Wilson AB, Lhorente JP, Houston RD, Yáñez JM (2019) Novel insights into the genetic relationship between growth and disease resistance in an aquaculture strain of Coho salmon (Oncorhynchus kisutch). Aquaculture 511:734207
Bhatnagar S, Schorey JS (2007) Exosomes released from infected macrophages contain Mycobacterium avium glycopeptidolipids and are proinflammatory. J Biol Chem 282:25779–25789
Bravo S, Midtlyng PJ (2007) The use of fish vaccines in the Chilean salmon industry 1999–2003. Aquaculture 270:36–42
Campoy E, Colombo MI (2009) Autophagy in intracellular bacterial infection. Bba-Mol Cell Res 1793:1465–1477
Cassat JE, Skaar EP (2013) Iron in infection and immunity. Cell Host Microbe 13:509–519
Chan PP, Lowe TM (2016) GtRNAdb 2.0: An expanded database of transfer RNA genes identified in complete and draft genomes. Nucl Acids Res 44:D184–D189
Chandan K, Gupta M, Sarwat M (2020) Role of host and pathogen-derived MicroRNAs in immune regulation during infectious and inflammatory diseases. Front Immunol 10:3081
Chatterjee A, Roy D, Patnaik E, Nongthomba U (2016) Muscles provide protection during microbial infection by activating innate immune response pathways in Drosophila and zebrafish. Dis Model Mech 9:697–705
Chu Q, Sun Y, Cui J, Xu T (2017) Inducible microRNA-214 contributes to the suppression of NF-κB-mediated inflammatory response via targeting myd88 gene in fish. J Biol Chem 292:5282–5290
Chu Q, Yan X, Liu L, Xu T (2019) The inducible microRNA-21 negatively modulates the inflammatory response in teleost fish via targeting IRAK4. Front Immunol 10:1623
Cui L, Hu H, Wei W, Wang W, Liu H (2016) Identification and characterization of MicroRNAs in the liver of blunt snout bream (Megalobrama amblycephala) infected by Aeromonas hydrophila. Int J Mol Sci 17:1972
Das K, Garnica O, Dhandayuthapani S (2016) Modulation of host miRNAs by intracellular bacterial pathogens. Front Cell Infect Microbio 6:79
da Silva Duran BO, Fernandez GJ, Mareco EA, Moraes LN, Salomão RAS, Gutierrez De Paula T et al (2015) Differential microRNA expression in fast- and slow-twitch skeletal muscle of Piaractus mesopotamicus during growth. PLoS One 10:e0141967
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS (2003) MicroRNA targets in Drosophila. Genome Biol 5:R1
Evensen Ø (2016) Immunization strategies against Piscirickettsia salmonis infections: review of vaccination approaches and modalities and their associated immune response profiles. Front Immunol 7:482
Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S et al (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26:407–415
Fryer JL, Hedrick RP (2003) Piscirickettsia salmonis: A Gram-negative intracellular bacterial pathogen of fish. J Fish Dis 26:251–262
Gao K, Jin J, Huang C, Li J, Luo H, Li L et al (2019) Exosomes derived from septic mouse serum modulate immune responses via exosome-associated cytokines. Front Immunol 10:1560
Hartjes TA, Mytnyk S, Jenster GW, van Steijn V, van Royen ME (2019) Extracellular vesicle quantification and characterization: common methods and emerging approaches. Bioengineering 6:7
Herkenhoff ME, Oliveira AC, Nachtigall PG, Costa JM, Campos VF, Hilsdorf AWS et al (2018) Fishing into the microRNA transcriptome. Front Genet 9:88
Hu Y hua, Zhang B cun, Zhou H zhen, Guan X lu, Sun L (2017) Edwardsiella tarda-induced miRNAs in a teleost host: global profile and role in bacterial infection as revealed by integrative miRNA–mRNA analysis. Virulence 8:1457–1464
Huang Y, Shen X-J, Zou Q, Wang S, Tang S, Zhang G (2010) Biological functions of microRNAs: a review. J Physiol Biochem 67:129–139
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110:462–467
Kang JY, Park H, Kim H, Mun D, Park H, Yun N et al (2019) Human peripheral blood-derived exosomes for microRNA delivery. Int J Mol Med 43:2319–2328
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39:1278–1284
Kirschner MB, Edelman JJB, Kao SCH, Vallely MP, Van Zandwijk N, Reid G (2013) The impact of hemolysis on cell-free microRNA biomarkers. Front Genet 4:94
Lagos L, Tandberg J, Kashulin-Bekkelund A, Colquhoun DJ, Sørum H, Winther-Larsen HC (2017) Isolation and characterization of serum extracellular vesicles (EVs) from Atlantic salmon infected with Piscirickettsia salmonis. Proteomes 5:34
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
Leiva F, Rojas M, Reyes D, Bravo S, Garcia K, Moya J, Vidal R (2020) Identification and characterization of miRNAs and lncRNAs of Coho salmon (Oncorhynchus kisutch) in normal immune organs. Genomics 112:45–54
Lhorente JP, Gallardo JA, Villanueva B, Carabaño MJ, Neira R (2014) Disease resistance in Atlantic salmon (Salmo salar): coinfection of the intracellular bacterial pathogen Piscirickettsia salmonis and the sea louse Caligus rogercresseyi. PLoS One 9:e95397
Magnadóttir B, Uysal-Onganer P, Kraev I, Dodds A, Gudmundsdottir S, Lange S (2020) Extracellular vesicles, deiminated protein cargo and microRNAs are novel serum biomarkers for environmental rearing temperature in Atlantic cod (Gadus morhua L.). Aquac Rep (16):100245
Marshall SH, Tobar JA (2014). In: Gudding R, Lillehaug A, Øystein E (eds) Vaccination against piscirickettsiosis. Wiley-Blackwell, USA
Maudet C, Mano M, Eulalio A (2014) MicroRNAs in the interaction between host and bacterial pathogens. FEBS Lett 588:4140–4147
Mauel MJ, Miller DL (2002) Piscirickettsiosis and piscirickettsiosis-like infections in fish: a review. Vet Microbiol 87:279–289
Nachtigall PG, Dias MC, Carvalho RF, Martins C, Pinhal D (2015) MicroRNA-499 expression distinctively correlates to target genes sox6 and rod1 profiles to resolve the skeletal muscle phenotype in Nile tilapia. PLoS ONE 10:e0119804
Nahid MA, Yao B, Dominguez-Gutierrez PR, Kesavalu L, Satoh M, Chan EK (2013) Regulation of TLR2-mediated tolerance and cross-tolerance through IRAK4 modulation by miR-132 and miR-212. J Immunol 190:1250–1263
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR et al (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 43:D130–D137
Ni B, Rajaram MVS, Lafuse WP, Landes MB, Schlesinger LS (2014) Mycobacterium tuberculosis decreases human macrophage IFN-γ Responsiveness through miR-132 and miR-26a. Immunol 193:4537–4547
Olsen AB, Melby HP, Speilberg L, Evensen Håstein T (1997) Piscirickettsia salmonis infection in Atlantic salmon Salmo salar in Norway — epidemiological, pathological and microbiological findings. Dis Aquat Organ 31:35–48
Palazzo AF, Lee ES (2015) Non-coding RNA: What is functional and what is junk? Front Genet 6:2
Pulgar R, Hödar C, Travisany D, Zuñiga A, Domínguez C, Maass A et al (2015) Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system. BMC Genomics 16:495
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl Acids Res 41:D590–D596
Ramírez R, Gomez FA, Marshall SH (2015) The infection process of Piscirickettsia salmonis in fish macrophages is dependent upon interaction with host-cell clathrin and actin. FEMS Microbiol Lett 362:1–8
Ranganathan K, Subramanian K, Pachiappan P (2013) The multitudinous role of microRNAs in various biological systems. J Pharm Res 6:679–683
Rao X, Huang X, Zhou Z, Lin X (2013) An improvement of the 2ˆ(-delta delta CT) method for quantitative real-time polymerase chain reaction data analysis. Biostat Bioinforma Biomath 3:71–85
Roberts TC, Coenen-Stass AML, Wood MJA (2014) Assessment of RT-qPCR normalization strategies for accurate quantification of extracellular microRNAs in murine serum. PLoS One 9:e89237
Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140
Rodrigues M, Fan J, Lyon C, Wan M, Hu Y (2018) Role of extracellular vesicles in viral and bacterial infections: pathogenesis, diagnostics, and therapeutics. Theranostics 8:2709–2721
Rozas M, Enríquez R (2014) Piscirickettsiosis and Piscirickettsia salmonis in fish: a review. J Fish Dis 37:163–188
Rozas-Serri M, Peña A, Arriagada G, Enríquez R, Maldonado L (2018) Comparison of gene expression in post-smolt Atlantic salmon challenged by LF-89-like and EM-90-like Piscirickettsia salmonis. J Fish Dis 41:539–552
Rozas-Serri M, Peña A, Maldonado L (2018) Transcriptomic profiles of post-smolt Atlantic salmon challenged with Piscirickettsia salmonis reveal a strategy to evade the adaptive immune response and modify cell-autonomous immunity. Dev Comp Immunol 81:348–362
Samanta S, Rajasingh S, Drosos N, Zhou Z, Dawn B, Rajasingh J (2018) Exosomes: new molecular targets of diseases. Acta Pharmacol Sin 39:501–513
Schmieder R, Edwards R (2011) Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864
Schorey JS, Cheng Y, McManus WR (2021) Bacteria- and host-derived extracellular vesicles — two sides of the same coin? J Cell Sci 134:jcs256628
Sedgwick AE, D’Souza-Schorey C (2018) The biology of extracellular microvesicles. Traffic 19:319–327
Shabalina SA, Spiridonov NA (2004) The mammalian transcriptome and the function of non-coding DNA sequences. Genome Biol 5:105
Signore A (2013) About inflammation and infection. EJNMMI Res 3:8
Simeone P, Bologna G, Lanuti P, Pierdomenico L, Guagnano MT, Pieragostino D et al (2020) Extracellular vesicles as signaling mediators and disease biomarkers across biological barriers. Int J Mol Sci 21:2514
Sohel MH (2016) Extracellular/circulating microRNAs: release mechanisms, functions and challenges. Achiev Life Sci 10:175–186
Spies D, Renz PF, Beyer TA, Ciaudo C (2019) Comparative analysis of differential gene expression tools for RNA sequencing time course data. Brief Bioinform 20:288–298
Spencer N, Yeruva L (2021) Role of bacterial infections in extracellular vesicles release and impact on immune response. Biomed J 44:157–164
Storey JD, Xiao W, Leek JT, Tompkins RG, Davis RW (2005) Significance analysis of time course microarray experiments. Proc Natl Aca Sci USA 102:12837–1242
Tacchi L, Bron JE, Taggart JB, Secombes CJ, Bickerdike R, Adler MA et al (2011) Multiple tissue transcriptomic responses to Piscirickettsia salmonis in Atlantic salmon (Salmo salar). Physiol Genomics 43:1241–1254
Tahamtan A, Teymoori-Rad M, Nakstad B, Salimi V (2018) Anti-inflammatory microRNAs and their potential for inflammatory diseases treatment. Front Immunol 9:1377
Tam S, Tsao MS, McPherson JD (2015) Optimization of miRNA-seq data preprocessing. Brief Bioinform 16:950–963
Tancini B, Buratta S, Sagini K, Costanzi E, Delo F, Urbanelli L et al (2019) Insight into the role of extracellular vesicles in lysosomal storage disorders. Genes 10:510
Tidball JG, Villalta SA (2010) Regulatory interactions between muscle and the immune system during muscle regeneration. Am J Physiol Regul Integr Comp Physiol 298:R1173–R1187
Valenzuela-Miranda D, Gallardo-Escárate C (2016) Novel insights into the response of Atlantic salmon (Salmo salar) to Piscirickettsia salmonis: interplay of coding genes and lncRNAs during bacterial infection. Fish Shellfish Immunol 59:427–438
Valenzuela-Miranda D, Valenzuela-Muñoz V, Farlora R, Gallardo-Escárate C (2017) MicroRNA-based transcriptomic responses of Atlantic salmon during infection by the intracellular bacterium Piscirickettsia salmonis. Dev Comp Immunol 77:287–296
Wery M, Kwapisz M, Morillon A (2011) Noncoding RNAs in gene regulation. Wiley Interdiscip Rev Syst Biol Med 3:728–738
Xie W, Li M, Xu N, Lv Q, Huang N, He J et al (2013) miR-181a regulates inflammation responses in monocytes and macrophages. PLoS One 8:e58639
Xu L, Yang BF, Ai J (2013) MicroRNA transport: a new way in cell communication. J. Cell Physiol 228:1713–1719
Xu T, Chu Q, Cui J, Zhao X (2018) The inducible microRNA-203 in fish represses the inflammatory responses to Gram-negative bacteria by targeting IL-1 receptor-associated kinase 4. J Biol Chem 293:1386–1396
Yamamura S, Imai-Sumida M, Tanaka Y, Dahiya R (2018) Interaction and cross-talk between non-coding RNAs. Cell Mol Life Sci 75:467–484
Funding
This research was supported by CORFO-INNOVA Chile 12IDL2-16192 and DICYT 022043VS, Vicerrectoría de Investigación, Desarrollo e Innovacion. K.K.G thank the Fellowship USA 1899 from the Universidad de Santiago de Chile.
Author information
Authors and Affiliations
Contributions
F.L. and R.V designed research; S.B., K. K. G., and F.L., developed experimental protocols and bioinformatics pipelines; J.M. conducted the sampling; and R.V., F.L., and K. K. G, wrote the paper. All authors reviewed the manuscript.
Corresponding author
Ethics declarations
Ethics Approval
The totality of the animal experiments in this study performed in agreement with the Institutional Ethics Committee of the Universidad de Santiago (USCH-1) and AVMA- 2019 guidelines.
Competing Interests
The authors declare no competing interests. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Leiva, F., Bravo, S., Garcia, K.K. et al. Temporal Gene Expression Signature of Plasma Extracellular Vesicles-MicroRNAs from Post-Smolt Coho Salmon Challenged with Piscirickettsia salmonis. Mar Biotechnol 23, 602–614 (2021). https://doi.org/10.1007/s10126-021-10049-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10126-021-10049-0