Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs

Cross-kingdom regulation of gene expression in giant pandas via plant-derived miRNA

Giant pandas (Ailuropoda melanoleuca) belong to the order Carnivora, but they mainly feed on bamboo, and their unique dietary adaptability has always been the focus of research. Recent research indicates that plant-derived microRNAs (miRNAs) can be delivered to animal organisms via exosomes and exert cross-kingdom regulatory effects on gene expression. To explore the role of plant-derived miRNAs in the dietary adaptation of giant pandas, we collected peripheral blood samples from three groups of pandas: juvenile females, adult females, and adult males-and extracted exosomes from the blood for small RNA sequencing. Additionally, three types of bamboo (shoots, stems, and leaves) consumed by the pandas were sampled for miRNA sequencing. Through comparative analysis, we identified 57 bamboo-derived miRNAs in the extracellular exosomes of giant panda peripheral blood. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses of the target genes for these miRNAs revealed their involvement in various pathways, including taste and olfactory signal transduction, digestion and absorption, and hormonal signal transduction. Furthermore, we found that plant-derived miRNAs can modulate dopamine metabolism in giant pandas, thereby influencing their food preferences. This study shows that plant-derived miRNAs can enter the bloodstream of giant pandas and exert cross-kingdom regulatory effects, potentially playing a vital role in their dietary adaptation process.

MicroRNA Expression Profile Analysis in Blood During Giant Panda (Ailuropoda melanoleuca) Growth and Development

BACKGROUND/OBJECTIVES

Blood is an essential component of the immune system. As post-transcriptional regulators, miRNAs, abundant in blood, are necessary aspects in blood's immune and physiological functions. However, there is limited knowledge about the expression and function of miRNAs in the blood of giant pandas.

METHODS

We comparatively analyzed miRNA expression profiles in the blood of giant pandas of different ages using small-RNA sequencing technology.

RESULTS

We identified 393 known miRNAs, 219 conserved miRNAs, and 71 novel miRNAs in the blood of giant pandas, and functional enrichment analysis showed that the genes regulated by DE (differentially expressed) miRNAs were mainly enriched in the regulation of enzyme-linked receptor protein signaling pathways and the signaling pathways of MAPK, Hippo, and FoXO.

CONCLUSIONS

Our study clarified giant pandas' blood miRNA expression profiles at different developmental stages, which will help elucidate the blood immunity and regulation of blood cell physiological functions in giant pandas.

MicroRNA expression profiles in plasma exosomes of late pregnant giant pandas

BACKGROUND

MicroRNAs can regulate various biological functions including cell proliferation, differentiation, embryo formation, and implantation. The giant panda exhibits embryonic diapause, with embryo development resuming in late pregnancy. However, the changes in microRNAs during late pregnancy remain poorly understand.

METHODS AND RESULTS

After mating, plasma samples were collected on day 40 of early pregnancy (EP; n = 3) and 30 days before delivery of late pregnancy (LP; n = 3). Following microRNAs screening, a total of 120 microRNAs were detected in the plasma exosomes of pregnant pandas. Nine differentially expressed microRNAs (DEmicroRNAs) were identified in LP compared to EP, including three that were upregulated and six that were downregulated. Notably, miR-25b and miR-47 were significantly downregulated in LP group. All DEmicroRNAs were predicted to target a total of 2,675 genes. Pathway enrichment analysis of these target genes revealed significant enrichment in the MAPK and Rap1 signaling pathways, which are closely related to cell proliferation, differentiation, and cell-cell and cell-matrix interactions. Analysis of protein-protein interaction networks showed that most of the hub genes (five out of eight), including Fgfr1, Fgf2, Fgf18, Erbb4, and Kras within the MAPK and Rap1 pathways are associated with the cell proliferation and differentiation. Significantly, Erbb4 was regulated by significantly differentially expressed miRNA-47.

CONCLUSIONS

We suggest that plasma exosomal microRNAs are involved in cell proliferation and differentiation during embryonic development by regulating key hub genes within MAPK and Rap1 pathways. These findings provided new insights into the development of giant panda embryos.

Assessment of stress levels and reproductive condition in giant pandas: insights from hair, faecal and saliva samples

Concerted conservation efforts have brought the giant panda (Ailuropoda melanoleuca) back from the brink of extinction, but pandas continue to face anthropogenic threats in the wild and breeding success in captivity remains low. Because stress can have detrimental impacts on reproduction, monitoring stress- and sex-steroid levels would help assess the effectiveness of conservation mitigation measures in panda populations as well as monitor the welfare and reproductive health of captive animals. In this proof-of-concept study, we used faecal sex steroid and cortisol concentrations (n = 867 samples collected from five males and five females at Beijing Zoo every 4 days over the course of 12 months) as a reference to investigate if testosterone, estradiol, progesterone and cortisol can be meaningfully measured in panda hair (n = 10) using radio-immuno-assays. Additionally, we calculated the ratio of testosterone to cortisol (T:C ratio) for each male, which can provide a biomarker of stress and physical performance. Our findings revealed distinct monthly variations in faecal sex-steroid and cortisol concentrations, reflecting reproductive seasonality and visitor-related stress among individual pandas. Notably, the oldest male had a significantly lower T:C ratio than other males. Our results confirm that the level of sex steroids and cortisol can be assayed by panda hair, and the hair cortisol concentrations correlate significantly with that in faeces with one month lag behind (r = 0.68, P = 0.03). However, the concentrations of hormones detected in saliva are lower than those in faeces by two orders of magnitude, making it difficult to ensure accuracy. By assessing the applicability of hair, faecal and salivary sampling, we can infer their utility in monitoring the reproductive status and acute and chronic stress levels of giant pandas, thereby providing a means to gauge the success of ongoing habitat restoration efforts and to discuss the feasibility of sample collection from wild populations.

Identification and characterization of miRNA expression profiles across five tissues in giant panda

microRNA (miRNA) is a small endogenous noncoding RNA molecule that plays multiple roles in regulating most biological processes. However, for China's national treasure giant panda, a world-famous rare and protected species, reports of its miRNA have been found only in blood and breast milk. To explore the miRNA expression differences between different giant panda tissues, here, we generated the miRNA profiles of five tissues (heart, liver, spleen, lung, and kidney) from four giant pandas with Illumina Hiseq 2500 platform, and filtered the differentially expressed miRNAs (DEmiRs) in each tissue, predicted the target genes of miRNA from each tissue based on the DEmiRs. Then, the GO and KEGG enrichment analysis were conducted using the target genes predicted from DEmiRs in each tissue. The RNA-seq generated an average of 0.718 GB base per sample. A total of 1,256 known miRNAs and 12 novel miRNAs were identified, and there were 215, 131, 185, 83, and 126 tissue-specific DEmiRs filtered in the heart, liver, spleen, lung, and kidney, respectively, including miR-1b-5p, miR-122-5p, miR-143, miR-126-5p, and miR-10b-5p, respectively. The predicted target genes, including MYL2, LRP5, MIF, CFD, and PEBP1 in the heart, liver, spleen, lung, and kidney, respectively, were closely associated with tissue-specific biological functions. The enrichment analysis results of target genes showed tissue-specific characteristics, such as the significantly enriched GO terms extracellular matrix in the heart and insulin-like growth factor binding in the liver. The miRNA profiles of the heart, liver, spleen, lung, and kidney of giant panda have been reported in this study, it reveals the miRNA expression differences between different tissues of the giant panda, and provides valuable genetic resources for the further related molecular genetic research of the rare and protected species giant panda and other mammals.

Transcriptome Profiling across Five Tissues of Giant Panda

Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log₂FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney's transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.