1
|
Cortes S, Farhat E, Talarico G, Mennigen JA. The dynamic transcriptomic response of the goldfish brain under chronic hypoxia. Comp Biochem Physiol Part D Genomics Proteomics 2024; 50:101233. [PMID: 38608489 DOI: 10.1016/j.cbd.2024.101233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
Oxygen is essential to fuel aerobic metabolism. Some species evolved mechanisms to tolerate periods of severe hypoxia and even anoxia in their environment. Among them, goldfish (Carassius auratus) are unique, in that they do not enter a comatose state under severely hypoxic conditions. There is thus significant interest in the field of comparative physiology to uncover the mechanistic basis underlying hypoxia tolerance in goldfish, with a particular focus on the brain. Taking advantage of the recently published and annotated goldfish genome, we profile the transcriptomic response of the goldfish brain under normoxic (21 kPa oxygen saturation) and, following gradual reduction, constant hypoxic conditions after 1 and 4 weeks (2.1 kPa oxygen saturation). In addition to analyzing differentially expressed protein-coding genes and enriched pathways, we also profile differentially expressed microRNAs (miRs). Using in silico approaches, we identify possible miR-mRNA relationships. Differentially expressed transcripts compared to normoxia were either common to both timepoints of hypoxia exposure (n = 174 mRNAs; n = 6 miRs), or exclusive to 1-week (n = 441 mRNAs; n = 23 miRs) or 4-week hypoxia exposure (n = 491 mRNAs; n = 34 miRs). Under chronic hypoxia, an increasing number of transcripts, including those of paralogous genes, was downregulated over time, suggesting a decrease in transcription. GO-terms related to the vascular system, oxidative stress, stress signalling, oxidoreductase activity, nucleotide- and intermediary metabolism, and mRNA posttranscriptional regulation were found to be enriched under chronic hypoxia. Known 'hypoxamiRs', such as miR-210-3p/5p, and miRs such as miR-29b-3p likely contribute to posttranscriptional regulation of these pathways under chronic hypoxia in the goldfish brain.
Collapse
Affiliation(s)
- S Cortes
- Department of Biology, University of Ottawa, K1N6N5 20 Marie Curie, Ottawa, ON, Canada; Laboratorio de Oncogenómica, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico
| | - E Farhat
- Department of Biology, University of Ottawa, K1N6N5 20 Marie Curie, Ottawa, ON, Canada; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0371 Oslo, Norway
| | - Ggm Talarico
- Department of Biology, University of Ottawa, K1N6N5 20 Marie Curie, Ottawa, ON, Canada
| | - J A Mennigen
- Department of Biology, University of Ottawa, K1N6N5 20 Marie Curie, Ottawa, ON, Canada.
| |
Collapse
|
2
|
Houdelet C, Blondeau-Bidet E, Estevez-Villar M, Mialhe X, Hermet S, Ruelle F, Dutto G, Bajek A, Bobe J, Geffroy B. Circulating MicroRNAs Indicative of Sex and Stress in the European Seabass (Dicentrarchus labrax): Toward the Identification of New Biomarkers. Mar Biotechnol (NY) 2023; 25:749-762. [PMID: 37581865 DOI: 10.1007/s10126-023-10237-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/01/2023] [Indexed: 08/16/2023]
Abstract
MicroRNAs (miRNAs) constitute a new category of biomarkers. Studies on miRNAs in non-mammalian species have drastically increased in the last few years. Here, we explored the use of miRNAs as potential, poorly invasive markers, to identify sex and characterize acute stress in fish. The European seabass (Dicentrarchus labrax) was chosen as a model because of its rapid response to stress and its specific sex determination system, devoid of sexual chromosomes. We performed a small RNA-sequencing analysis in the blood plasma of male and female European seabass (mature and immature) as well as in the blood plasma of juveniles submitted to an acute stress and sampled throughout the recovery period (at 0 h, 0.5 h, 1.5 h and 6 h). In immature individuals, both miR-1388-3p and miR-7132a-5p were up-regulated in females, while miR-499a-5p was more abundant in males. However, no miRNAs were found to be differentially expressed between sexes in the blood plasma of mature individuals. For the acute stress analysis, five miRNAs (miR-155-5p, miR-200a-3p, miR-205-1-5p, miR-143-3p, and miR-223-3p) followed cortisol production over time. All miRNAs identified were tested and validated by RT-qPCR on sequenced samples. A complementary analysis on the 3'UTR sequences of the European seabass allowed to predict potential mRNA targets, some of them being particularly relevant regarding stress regulation, e.g., the glucocorticoid receptor 1 and the mineralocorticoid receptor. The present study provides new avenues and recommendations on the use of miRNAs as biomarkers of sex or stress of the European seabass, with potential application on other fish species.
Collapse
Affiliation(s)
- Camille Houdelet
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | | | | | - Xavier Mialhe
- MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Sophie Hermet
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - François Ruelle
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Gilbert Dutto
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Aline Bajek
- Ecloserie Marine de Gravelines-Ichtus, Voie des Enrochements, F-59820, Gravelines, France
| | - Julien Bobe
- INRAE, UR1037, Fish Physiology and Genomic laboratory, F-35000, Rennes, France
| | - Benjamin Geffroy
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France.
| |
Collapse
|
3
|
Blödorn EB, Domingues WB, Martins AWS, Dellagostin EN, Komninou ER, Remião MH, Silveira TLR, Collares GL, Giongo JL, Vaucher RA, Campos VF. MicroRNA qPCR normalization in Nile tilapia (Oreochromis niloticus): Effects of acute cold stress on potential reference targets. Fish Physiol Biochem 2023; 49:409-423. [PMID: 37074474 DOI: 10.1007/s10695-023-01190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
The Nile tilapia (Oreochromis niloticus) is one of the most important cultured fish worldwide, but tilapia culture is largely affected by low temperatures. Recent studies suggest that microRNAs (miRNAs) regulate cold tolerance traits in fish. In general, qPCR-based methods are the simplest and most accurate forms of miRNA quantification. However, qPCR data heavily depends on appropriate normalization. Therefore, the aim of the present study is to determine whether the expression of previously tested, stably expressed miRNAs are affected by acute cold stress in Nile tilapia. For this purpose, one small nuclear RNA (U6) and six candidate reference miRNAs (miR-23a, miR-25-3, Let-7a, miR-103, miR-99-5, and miR-455) were evaluated in four tissues (blood, brain, liver, and gills) under two experimental conditions (acute cold stress and control) in O. niloticus. The stability of the expression of each candidate reference miRNA was analyzed by four independent methods (the delta Ct method, geNorm, NormFinder, and BestKeeper). Further, consensual comprehensive ranking of stability was built with RefFinder. Overall, miR-103 was the most stable reference miRNA in this study, and miR-103 and Let-7a were the best combination of reference targets. Equally important, Let-7a, miR-23a, and miR-25-3 remained consistently stable across different tissues and experimental groups. Considering all variables, U6, miR-99-5, and miR-455 were the least stable candidates under acute cold stress. Most important, suitable reference miRNAs were validated in O. niloticus, facilitating further accurate miRNA quantification in this species.
Collapse
Affiliation(s)
- Eduardo B Blödorn
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - William B Domingues
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Amanda W S Martins
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eduardo N Dellagostin
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Eliza R Komninou
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Mariana H Remião
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Tony L R Silveira
- Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Gilberto L Collares
- Agência de Desenvolvimento da Bacia da Lagoa Mirim, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Janice L Giongo
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-Organismos, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Rodrigo A Vaucher
- Laboratório de Pesquisa em Bioquímica e Biologia Molecular de Micro-Organismos, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vinicius Farias Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
| |
Collapse
|