Blood transcriptome analysis revealed the immune changes and immunological adaptation of wildness training giant pandas

Yang, Miao; Huang, Yan; Wu, Honglin; Li, Caiwu; Ling, Shanshan; Sun, Jie; Shen, Huan; Yue, Bisong; Zhang, Xiuyue

doi:10.1007/s00438-021-01841-7

Cited by 6 publications

(8 citation statements)

References 59 publications

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“…Six WGBS samples and twelve transcriptome sequencing (RNA-seq) samples were obtained from fifteen giant pandas (seven in the wild training group and eight in the captive group). Twelve RNA-seq samples have been described in our previous study ( Yang et al, 2022 ).…”

Section: Methodsmentioning

confidence: 99%

“…Library preparation, sequencing and data analysis of RNA-seq samples have been described in our previous study ( Yang et al, 2022 ). All RNA-seq data have been submitted to NCBI Sequence Read Archive with BioProject numbers PRJNA878951.…”

Section: Methodsmentioning

confidence: 99%

“…After identifying a set of genes undergoing methylation changes in promoter region between the wildness training and captive groups, we combined RNA-seq data from wildness training and captive pandas to assess the associated changes in gene expression and promoter methylation levels ( Yang et al, 2022 ). We investigated the correlation between changes in methylation levels of promoter region and gene expression levels by Spearman rank correlation analysis with a two-tailed t-test.…”

Section: Methodsmentioning

confidence: 99%

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Whole genome bisulfite sequencing reveals DNA methylation roles in the adaptive response of wildness training giant pandas to wild environment

Jie

Wu²,

Yang³

et al. 2022

Front. Genet.

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DNA methylation modification can regulate gene expression without changing the genome sequence, which helps organisms to rapidly adapt to new environments. However, few studies have been reported in non-model mammals. Giant panda (Ailuropoda melanoleuca) is a flagship species for global biodiversity conservation. Wildness and reintroduction of giant pandas are the important content of giant pandas’ protection. However, it is unclear how wildness training affects the epigenetics of giant pandas, and we lack the means to assess the adaptive capacity of wildness training giant pandas. We comparatively analyzed genome-level methylation differences in captive giant pandas with and without wildness training to determine whether methylation modification played a role in the adaptive response of wildness training pandas. The whole genome DNA methylation sequencing results showed that genomic cytosine methylation ratio of all samples was 5.35%–5.49%, and the methylation ratio of the CpG site was the highest. Differential methylation analysis identified 544 differentially methylated genes (DMGs). The results of KEGG pathway enrichment of DMGs showed that VAV3, PLCG2, TEC and PTPRC participated in multiple immune-related pathways, and may participate in the immune response of wildness training giant pandas by regulating adaptive immune cells. A large number of DMGs enriched in GO terms may also be related to the regulation of immune activation during wildness training of giant pandas. Promoter differentially methylation analysis identified 1,199 genes with differential methylation at promoter regions. Genes with low methylation level at promoter regions and high expression such as, CCL5, P2Y13, GZMA, ANP32A, VWF, MYOZ1, NME7, MRPS31 and TPM1 were important in environmental adaptation for wildness training giant pandas. The methylation and expression patterns of these genes indicated that wildness training giant pandas have strong immunity, blood coagulation, athletic abilities and disease resistance. The adaptive response of giant pandas undergoing wildness training may be regulated by their negatively related promoter methylation. We are the first to describe the DNA methylation profile of giant panda blood tissue and our results indicated methylation modification is involved in the adaptation of captive giant pandas when undergoing wildness training. Our study also provided potential monitoring indicators for the successful reintroduction of valuable and threatened animals to the wild.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Whole genome bisulfite sequencing reveals DNA methylation roles in the adaptive response of wildness training giant pandas to wild environment

Jie

Wu²,

Yang³

et al. 2022

Front. Genet.

Self Cite

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“…Peripheral blood mononuclear cells (PBMCs) undergo gene expression and participate in the immune regulatory network of blood and are therefore the primary cells involved in immune response. Interestingly, nine organs, including the brain, colon, heart, kidney, liver, lung, prostate, spleen, and stomach, share approximately 80% of their transcriptome with PBMCs [ 18 ]; therefore, the rapid turnover rate of PBMCs makes it possible that disease-related subtle changes within tissues may result in a differential expression of genes in blood cells [ 19 ]. Consequently, the immunological status of different organs and tissues as well as the general health status of the body can be reflected in the genetic expression of peripheral blood [ 16 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, RNA sequencing (RNA-Seq) and metabolomic studies are suitable methods for investigating the immune-related functions and health status of an individual [ 21 , 22 ]. Currently, blood RNA-Seq and serum metabolomics have been used to study disease mechanisms [ 23 , 24 , 25 ] and immunity [ 19 , 26 , 27 , 28 , 29 , 30 ], but there are only a few reports available related to the use of multi-omics to explore the immune function in dogs.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic and Metabolomic Changes Reveal the Immunomodulatory Function of Casein Phosphopeptide-Selenium Chelate in Beagle Dogs

Wang¹,

Xu²,

Cao

et al. 2023

Veterinary Sciences

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Casein phosphopeptide-selenium chelate (CPP-Se) is an organic compound produced by the chelation of casein phosphopeptide with selenium. This compound showed the ability to modulate canine immune response in our previous study; but its effect on the peripheral blood transcriptome and serum metabolome was unknown. This study aims to reveal the potential mechanism behind the immunomodulatory function of CPP-Se. We have identified 341 differentially expressed genes (DEGs) in CPP-Se groups as compared to the control group which comprised 110 up-regulated and 231 down-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis found that DEGs were mainly involved in immune-related signaling pathways. Moreover, the immune-related DEGs and hub genes were identified. Similarly, metabolomics identified 53 differentially expressed metabolites (DEMs) in the CPP-Se group, of which 17 were up-regulated and 36 were down-regulated. The pathways mainly enriched by DEMs were primary bile acid biosynthesis, tryptophan metabolism, and other amino acids metabolic pathways. Combined analysis of transcriptomic and metabolomic data showed that the DEGs and DEMs were commonly enriched in fatty acid biosynthesis, pyrimidine metabolism, glutathione metabolism, and glycerolipid metabolic pathways. Taken together, our findings provided a theoretical basis for further understanding of the immunomodulatory function of CPP-Se as well as a scientific reference for the future use of CPP-Se in pet foods as a dietary supplement to modulate the immunity.

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Integrated mRNA–miRNA transcriptome profiling of blood immune responses potentially related to pulmonary fibrosis in forest musk deer

Qi,

Hu,

et al. 2024

Front. Immunol.

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BackgroundForest musk deer (FMD, Moschus Berezovskii) is a critically endangered species world-widely, the death of which can be caused by pulmonary disease in the farm. Pulmonary fibrosis (PF) was a huge threat to the health and survival of captive FMD. MicroRNAs (miRNAs) and messenger RNAs (mRNAs) have been involved in the regulation of immune genes and disease development. However, the regulatory profiles of mRNAs and miRNAs involved in immune regulation of FMD are unclear.MethodsIn this study, mRNA-seq and miRNA-seq in blood were performed to constructed coexpression regulatory networks between PF and healthy groups of FMD. The hub immune- and apoptosis-related genes in the PF blood of FMD were explored through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Further, protein–protein interaction (PPI) network of immune-associated and apoptosis-associated key signaling pathways were constructed based on mRNA-miRNA in the PF blood of the FMD. Immune hub DEGs and immune hub DEmiRNAs were selected for experimental verification using RT-qPCR.ResultsA total of 2744 differentially expressed genes (DEGs) and 356 differentially expressed miRNAs (DEmiRNAs) were identified in the PF blood group compared to the healthy blood group. Among them, 42 DEmiRNAs were negatively correlated with 20 immune DEGs from a total of 57 correlations. The DEGs were significantly associated with pathways related to CD molecules, immune disease, immune system, cytokine receptors, T cell receptor signaling pathway, Th1 and Th2 cell differentiation, cytokine-cytokine receptor interaction, intestinal immune network for IgA production, and NOD-like receptor signaling pathway. There were 240 immune-related DEGs, in which 186 immune-related DEGs were up-regulated and 54 immune-related DEGs were down-regulated. In the protein-protein interaction (PPI) analysis of immune-related signaling pathway, TYK2, TLR2, TLR4, IL18, CSF1, CXCL13, LCK, ITGB2, PIK3CB, HCK, CD40, CD86, CCL3, CCR7, IL2RA, TLR3, and IL4R were identified as the hub immune genes. The mRNA-miRNA coregulation analysis showed that let-7d, miR-324-3p, miR-760, miR-185, miR-149, miR-149-5p, and miR-1842-5p are key miRNAs that target DEGs involved in immune disease, immune system and immunoregulation.ConclusionThe development and occurrence of PF were significantly influenced by the immune-related and apoptosis-related genes present in PF blood. mRNAs and miRNAs associated with the development and occurrence of PF in the FMD.

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Blood transcriptome analysis revealed the immune changes and immunological adaptation of wildness training giant pandas

Cited by 6 publications

References 59 publications

Whole genome bisulfite sequencing reveals DNA methylation roles in the adaptive response of wildness training giant pandas to wild environment

Whole genome bisulfite sequencing reveals DNA methylation roles in the adaptive response of wildness training giant pandas to wild environment

Transcriptomic and Metabolomic Changes Reveal the Immunomodulatory Function of Casein Phosphopeptide-Selenium Chelate in Beagle Dogs

Integrated mRNA–miRNA transcriptome profiling of blood immune responses potentially related to pulmonary fibrosis in forest musk deer

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