Transcriptomic hallmarks of bone remodeling revealed by RNA-seq profiling in blood of Arabian horses during racing training regime
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ABSTRACT:
PROVIDER: PRJNA419260 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6311470.fastq.gz | Fastqsanger.gz | |||
| SRR6311461.fastq.gz | Fastqsanger.gz | |||
| SRR6311462.fastq.gz | Fastqsanger.gz | |||
| SRR6311463.fastq.gz | Fastqsanger.gz | |||
| SRR6311464.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: RNA-seq method was used to identify differentially expressed genes in whole blood involved in bone remodelling during racing training in young Arabian horses. Methods: The comparisons of transcriptomes of whole blood between GI (6 untrained horses) and GII (4 horses after 24 weeks of flat racing training) has been performed. The RNA was isolated using MagMAX™-96 Total RNA Isolation Kit and 400ng were directed to cDNA libraries construction Illumina deep sequencing (75 single-end cycles on Illumina HiScan SQ platform). The bioinformatics analysis include the RSEM and STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes were detected by DESeq2.The validation of RNA-seq results were performed by qPCR. Results: After comparison of whole blood transcriptomes from control and trained horses, we identified 1290 training induced genes. Among significant deregulated molecules we recognized twelve genes potentially involved in metabolism of bone (BGLAP, CTSK, TYROBP, PDLIM7, SLC9B2, TWSG1, NOTCH2, IL6ST, VAV3, NFATC1, CLEC5A, TXLNG). Within significantly deregulated pathways one from the most overrepresented was associated with osteoclast differentiation. Conclusions: In the presented study, we identified a panel of DEGs which should be evaluated as candidate biomarkers for bone homeostasis indicators in Arabians performed racetrack. In our results, we pinpointed that intense training has itself effect on immature skeletal system. Thus, further studies are essential to establish biomarkers which could be used in assessment of bone remodelling state during training for race track competition.
2017-11-24 | GSE107197 | GEO
Project description:Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with exercise adaptation in Arabian horses. Methods: Whole transcriptome profiling of blood was performed for untrained horses and horses from which samples were collected during at 3 different periods of training procedure (T1-during intense training period - March, T2- before starts - May and T3 -after flat racing season - October). The muscle transcriptome sequencing was performed for 37 blood samples using Illumina HiScan SQ in 75 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes in blood tissue were detected by DESeq2. The RNA-seq results were validated using by qPCR. Results: The increase of the number of DEGs between subsequent training periods has been observed and the highest amount of DEGs was detected between untrained horses (T0) and horses at the end of the racing season (T3) â 440. The comparison of transcriptome of T2 vs T3 and T0 vs T3 showed a significant advantage of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in T3 period compared T2 and T0; respectively). Our results showed that the largest number of identified genes encoded transcription factors, nucleic acid binding proteins and G-protein modulators, which mainly were transcriptional activated at the last training phase (T3) . Moreover, in the T3 period the identified DEGs represented genes coded for cytoskeletal proteins including actin cytoskeletal proteins and kinases. The most abundant exercise-upregulated genes were involved in pathways important in regulating the cell cycle (PI3K-Akt signaling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis as well as immunity processes (Jak-STAT signaling pathway). We also observed exercise induced expression of genes related in regulation of actin cytoskeleton, gluconeogenesis (FoxO signaling pathway; Insulin signaling pathway), glycerophospholipid metabolism and calcium signaling. Conclusions: TOur results allow to identify changes in genes expression profile following training schedule in Arabian horses. Based on comparison analysis of blood transcriptomes, several exercise-regulated pathways and genes most affected by exercise were detected. We pinpointed overrepresented molecular pathways and genes essential for exercise adaptive response via maintaining of body homeostasis. The observed transcriptional activation of such gene as LPGAT1, AGPAT5, PIK3CG, GPD2, FOXN2, FOXO3, ACVR1B and ACVR2A can be a base for further research in order to identify genes potentially associated with race performance in Arabian horses. Such markers will be essential to choice the training type, and could result in differences in racing performance specific to various breeds. The blood transcriptome sequencing was performed for 37 samples collected form Arabian horses using Illumina HiScan SQ in75 single-end cycles and in 3-4 technical repetitions.repetitions.
2016-06-16 | E-GEOD-83404 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) was used to select genes potentially associated with exercise adaptation in Arabian horses. Methods: Whole transcriptome profiling of blood was performed for untrained horses and horses from which samples were collected during at 3 different periods of training procedure (T1-during intense training period - March, T2- before starts - May and T3 -after flat racing season - October). The muscle transcriptome sequencing was performed for 37 blood samples using Illumina HiScan SQ in 75 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes in blood tissue were detected by DESeq2. The RNA-seq results were validated using by qPCR. Results: The increase of the number of DEGs between subsequent training periods has been observed and the highest amount of DEGs was detected between untrained horses (T0) and horses at the end of the racing season (T3) – 440. The comparison of transcriptome of T2 vs T3 and T0 vs T3 showed a significant advantage of up-regulated genes during long-term exercise (up-regulation of 266 and 389 DEGs in T3 period compared T2 and T0; respectively). Our results showed that the largest number of identified genes encoded transcription factors, nucleic acid binding proteins and G-protein modulators, which mainly were transcriptional activated at the last training phase (T3) . Moreover, in the T3 period the identified DEGs represented genes coded for cytoskeletal proteins including actin cytoskeletal proteins and kinases. The most abundant exercise-upregulated genes were involved in pathways important in regulating the cell cycle (PI3K-Akt signaling pathway), cell communication (cAMP-dependent pathway), proliferation, differentiation and apoptosis as well as immunity processes (Jak-STAT signaling pathway). We also observed exercise induced expression of genes related in regulation of actin cytoskeleton, gluconeogenesis (FoxO signaling pathway; Insulin signaling pathway), glycerophospholipid metabolism and calcium signaling. Conclusions: TOur results allow to identify changes in genes expression profile following training schedule in Arabian horses. Based on comparison analysis of blood transcriptomes, several exercise-regulated pathways and genes most affected by exercise were detected. We pinpointed overrepresented molecular pathways and genes essential for exercise adaptive response via maintaining of body homeostasis. The observed transcriptional activation of such gene as LPGAT1, AGPAT5, PIK3CG, GPD2, FOXN2, FOXO3, ACVR1B and ACVR2A can be a base for further research in order to identify genes potentially associated with race performance in Arabian horses. Such markers will be essential to choice the training type, and could result in differences in racing performance specific to various breeds.
2016-06-16 | GSE83404 | GEO
Project description:Report transcritpome analysis of Arabian horses before and after exercise
2019-01-23 | GSE104388 | GEO
Project description:Purpose: RNA-seq method was used to select genes expressed in muscle tissue and are potentially associated with exercise adaptation in Arabian horses. Methods: Whole transcriptomes between three time points of muscle tissue collection were compared: T0 (untrained horses), T1 (horses after intense gallop phase) and T2 (at the end of the racing season), in total 23 samples. The biopsy of gluteus medius muscle was performed by using minimally invasive ProMag™ Ultra Automatic Biopsy Instrument with a 2 mm diameter biopsy needle. The total RNA was isolated using by TriReagent and 300ng was used to cDNA libraries preparation. The NGS sequencing was performed on HiScan SQ (Illumina). The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Equus caballus reference genome. Differentially expressed genes were detected by DESeq2. The RNA-seq results were validated using by qPCR. Results: To detected differentially expressed genes during training preparing to the flat racing, whole transcriptomes between three time points of muscle tissue collection were compared: T0 (untrained horses), T1 (horses after intense gallop phase) and T2 (at the end of the racing season). We identified 1168 DEGs between T0 vs T1; 1593 between T1 vs T2 and 763 between T2 vs T0. The analysis for all DEGs allow to detect 11 pathways which ale significant over represented between at last two training periods. The numerous group of exercise-regulated DEGs was related with muscle cell structure and signaling (‘focal adhesion’, ‘adherens juntion’ and ‘PI3-ATK signaling’) and included insulin-like growth factor 1 receptor (IGF1R); insulin receptor (INSR); transforming growth factor beta receptors 1 and 2 (TGFBR1; TGFBR2); vascular endothelial growth factor B (VEGFB); epidermal growth factor (EGF); hepatocyte growth factor (HGF) and vascular endothelial growth factor D (FIGF). Our results showed that in Arabian horses exercise modified the expression of genes belonging to the ‘PPAR signaling pathway’ (e.g. PPARA; PPARD; PLIN2); ‘calcium signaling pathway’ (e.g. PLN; PLCD1; TNNC1; TNNC2) as well as pathways associated with metabolism processes - ‘oxidative phosphorylation’; ‘fatty acid metabolism’; ‘glycolysis/gluconeogenesis’ and ‘citrate cycle’. Conclusions: Our research allowed to identify the group of exercise-regulated genes which was related with muscle cell structure as well as signaling and pinpointed the significant metabolic processes critical for adaptive response during training. We confirmed that in Arabians, the exercise switch energy generation towards fatty acid utilization, enhance glycogen transport and calcium signaling. The sequencing of skeletal muscle transcriptome allowed to propose the panel of new candidate genes (such as SLC16A1; ME3; ACTN3; PPARα; SH3RF2; TPM3; TNNC1; TNNI3; TGFBR1; TGFBR2; FABP3) potentially related with body homeostasis maintenance and race performance in Arabian horse.
2016-10-21 | GSE88951 | GEO
Project description:Purpose: RNA-sequencing (RNA-seq) was used to identify the changes in gene expression profile to describe the metabolism adaptation at the whole transcriptome of blood to endurance effort. Samples from ten Arabian horses were taken before and after a 120km long endurance ride.
2023-04-04 | GSE226819 | GEO
Project description:The currently known homing pigeon is a result of a sharp one-sided selection for flight characteristics focused on speed, endurance, and spatial orientation. This has led to extremely well-adapted athletic phenotypes in racing birds. Here, we identify genes and pathways contributing to exercise adaptation in sport pigeons by applying next-generation transcriptome sequencing of m.pectoralis muscle samples, collected before and after a 300 km competition flight. The analysis of differentially expressed genes pictured the central role of pathways involved in fuel selection and muscle maintenance during flight, with a core set of genes: ARTN, NREP, CAV3, SLC25A30, SLC2A11. Variations in these genes may therefore be exploited for genetic improvement of the racing pigeon population towards specific categories of competition flights.
2023-01-15 | GSE222537 | GEO
Project description:Development of an anti-inflammatory state during physical training has been postulated in both human and equine athletes, but it is not completely understood. The aim of this study was to investigate whether endurance training changes pro- and anti-inflammatory cytokine profiles within a 20-week training season in young inexperienced endurance horses. Nine Arabian horses were examined in this prospective 20-week follow-up study. Blood samples were analysed 5 times monthly, at rest and after training sessions. Routine haematological examinations were performed. Cytokine patterns including IL-1?, IL-6, TNF-?, IL-10 mRNA expression using Real Time-PCR, and serum concentrations of IL-1?, IL-2, IL-4, IL-6, IL-17, INF?, TNF-?, and IL-10 by ELISA test were determined. During endurance training, the most significant decrease in post-exercise cytokine type 1 levels (TNF? and IL-?) occurred within 20 weeks, beginning from the 3rd month of training. IL-6 serum level decreased after the 4th month. The results suggest that endurance training can induce advanced overall anti-inflammatory response as an adaptation to increasing workload.
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