Identification of microRNA-Associated-ceRNA Networks Regulating Crop Milk Production in Pigeon (Columba livia)

Identification of miRNA Associated with Trichomonas gallinae Resistance in Pigeon (Columba livia)

Trichomonas gallinae (T. gallinae) has a great influence on the pigeon industry. Pigeons display different resistance abilities to T. gallinae, so the study of the molecular mechanism of resistance is necessary in breeding disease resistant lines. MiRNA plays important roles in the immune response, but there are still no reports of miRNA regulating trichomonosis resistance. We used small RNA sequencing technology to characterize miRNA profiles in different groups. T. gallinae was nasally inoculated in one day old squabs, and according to the infection status, the groups were divided into control (C), susceptible (S) and tolerant (T) groups. We identified 2429 miRNAs in total, including 1162 known miRNAs and 1267 new miRNAs. In a comparison among the C, S and T groups, the target genes of differentially expressed miRNAs were analyzed via GO and KEGG annotation. The results showed that the target genes were enriched in immune-response-related pathways. This indicated that the differentially expressed miRNAs had a critical influence on T. gallinae infection. Novel_miR_741, which could inhibit the expression of PRKCQ, was down-regulated in the T group compared to the C group. It was proven that a decreased novel_miR_741 expression would increase the expression of PRKCQ and increase the immune response. This study brings new insights into understanding the mechanism of trichomonosis resistance.

Pigeon during the Breeding Cycle: Behaviors, Composition and Formation of Crop Milk, and Physiological Adaptation

Pigeon is an important economic poultry species in many countries. As an altricial bird, its growth and development are largely reliant on pigeon milk produced by the crop tissue in the first week. During the breeding cycle, pigeons undergo a series of behavioral changes. Pigeon milk is generally characterized by having high concentrations of proteins and lipids, and a complicated regulatory network is involved in the milk formation. Hormones, especially prolactin, could promote the proliferation of crop epidermal cells and nutrient accumulation. The expression of target genes associated with these important biological processes in the crop epidermis is affected by non-coding RNAs. Meanwhile, signaling pathways, such as target of rapamycin (TOR), Janus kinase/signal transducer and activator of transcription proteins (JAK/STAT), protein kinase B (Akt), etc., influence the production of crop milk by either enhancing protein synthesis in crop cells or inducing apoptosis of crop epidermal cells. In order to adapt to the different breeding periods, pigeons are physiologically changed in their intestinal morphology and function and liver metabolism. This paper reviews the behaviors and physiological adaptations of pigeon during the breeding cycle, the composition of pigeon crop milk, and the mechanism of its formation, which is important for a better understanding of the physiology of altricial birds and the development of artificial crop milk.

Chemical Composition of Pigeon Crop Milk and Factors Affecting Its Production: A Review

Pigeons are important commercial poultry in addition to being ornamental birds. In 2021, more than 111 million pairs of breeding pigeons were kept in stock and 1.6 billion squabs were slaughtered for meat in China. However, in many countries, pigeons are not domestic birds; thus, it is necessary to elucidate the factors involved in their growth and feeding strategy due to their economic importance. Pigeons are altricial birds, so feedstuffs cannot be digested by squabs, which instead are fed a mediator named pigeon crop milk. During lactation, breeding pigeons (both female and male) ingest diets and generate crop milk to feed squabs. Thus, research on squab growth is more complex than that on chicken and other poultry. To date, research on the measurement of crop milk composition and estimation of the factors affecting its production has not ceased, and these results are worth reviewing to guide production. Moreover, some studies have focused on the formation mechanism of crop milk, reporting that the synthesis of crop milk is controlled by prolactin and insulin-activated pathways. Furthermore, the Janus kinase 2 (JAK2)-signal transducer and activator of transcription 5 (STAT5) pathway, target of rapamycin (TOR) pathway and AMP-activated protein kinase (AMPK) pathway were also reported to be involved in crop milk synthesis. Therefore, this review focuses on the chemical composition of pigeon crop milk and factors affecting its production during lactation. This work explores novel mechanisms and provides a theoretical reference for improving production in the pigeon industry, including for racing, ornamental purposes, and production of meat products.

Effects of Hydrogen Peroxide-Induced Oxidative Stress on Intestinal Morphology, Redox Status, and Related Molecules in Squabs

The purpose of this study was to evaluate the potential effect of oxidative stress on the intestine of squabs, and to explore the molecular mechanisms. A total of 360 1-day-old squabs were divided evenly into five different groups (n = 72/group): control, negative control, low, medium, and high dose groups. On the 3rd, 5th, and 7th days, squabs in the control group were not effectively treated and the negative control group were intraperitoneally injected with normal saline, whereas the H₂O₂ group was injected with H₂O₂ of 2.0, 2.5, and 3.0 mmol/kg BW respectively. On the 21st day, the serum and duodenum were collected for further analysis. The results indicated that, compared with the control group, H₂O₂ caused squabs weight loss and intestinal morphology damage, and these effects were enhanced with an increase in dose. Further examination revealed that the contents of oxidative stress markers in both the serum and duodenum of the H₂O₂ group were significantly enhanced as the dose was increased. In addition, H₂O₂ exposure also resulted in the lower mRNA expression of Occludin, ZO-1, Beclin1, Atg5, and Caspase-3, but the expression of Claudin2 and Bcl-2 was decreased in comparison to the control group. These findings suggested that duodenal oxidative damage was accompanied by weight loss, changes in intestinal morphology, redox status imbalance, apoptosis as well as autophagy of intestinal cells, with, effects of 3.0 mmol/kg BW of H₂O₂ being the most severe.

Analyses of circRNAs profiles of the lactating and nonlactating crops in pigeon (Columba livia)

Pigeon has the specific biological ability to produce pigeon milk (also known as crop milk) by its crop. Circular RNAs (circRNAs) are important noncoding RNAs acting as the sponges of miRNAs, but the molecular mechanism of circRNAs regulating crop milk production has not been reported in pigeon. We compared expression profiles of crops during lactating and nonlactating crops, and networks of competing endogenous RNAs (ceRNAs) were constructed. The results showed a total of 8,723 circRNAs were identified, and there were 770 differentially expressed circRNAs (DECs) between these two different periods of crops. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the host genes of DECs were enriched in GnRH, MAPK, Insulin, Wnt, and AMPK signaling pathways. Furthermore, gga_circ_0000300 interacted with miR-92-2-5p, which targeted genes participating in lactation and milk composition synthesis. Gga_circ_0003018, gga_circ_0003019 and gga_circ_0003020 could bind with let-7c-5p regulating SOCS3 in crop milk production. These findings provide the circRNAs expression profiles and facilitate the analysis of molecular mechanism of crop milk production in pigeon.

miR-193-5p negatively regulates PIK3CD to promote crop fibrocyte proliferation in pigeon (Columba livia)

The crop of pigeon has specific characteristics as producing crop milk in the lactating period. However, the exact mechanisms underlying the regulation of crop lactation remain unclear. miRNAs, the essential regulators of gene expression, are implicated in various physiological and biological activities. In this study, we discovered a new miRNA that regulated phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta (PIK3CD) and crop fibrocyte proliferation. Results of the luciferase reporter assay suggested that miR-193-5p suppressed PIK3CD expression by targeting a conserved binding site in the 3'-untranslated region (UTR) of PIK3CD mRNA. MiR-193-5p promoted crop fibrocyte proliferation and migration, whereas PIK3CD inhibited these effects. These findings suggested an important regulatory role of miR-193-5p in crop fibrocyte proliferation, suggesting that miR-193-5p and PIK3CD might be important regulators of crop milk production.

Identification of LARS as an essential gene for osteosarcoma proliferation through large-Scale CRISPR-Cas9 screening database and experimental verification

Background

Osteosarcoma is one of the most malignant tumors, and it occurs mostly in children and adolescents. Currently, surgery and chemotherapy are the main treatments. The recurrence rate is high and the prognosis is often poor. Finding an effective target gene therapy for osteosarcoma may effectively improve its prognosis.

Method

In this study, genes essential for the survival of osteosarcoma cells were identified by genome-wide screening of CRISPR-Cas9 based on the DepMap database. The expression of these essential genes in osteosarcoma patients’ tissues and normal tissues was identified in the GSE19276 database. Functional pathway enrichment analysis, protein interaction network construction, and LASSO were performed to construct a prognostic risk model based on these essential genes. CCK8 assay was used to detect the effect of essential gene-LARS (Leucyl-TRNA Synthetase 1) on the proliferation of osteosarcoma.

Results

In this study, 785 genes critical for osteosarcoma cell proliferation were identified from the DepMap. Among these 785 essential genes, 59 DEGs were identified in osteosarcoma tissues. In the functional enrichment analysis, these 59 essential genes were mainly enriched in cell cycle-related signaling pathways. Furthermore, we established a risk score module, including LARS and DNAJC17, screened from these 59 genes, and this module could divide osteosarcoma patients into the low-risk and high-risk groups. In addition, knockdown of LARS expression inhibited the proliferative ability of osteosarcoma cells. A significant correlation was found between LARS expression and Monocytic lineage, T cells, and Fibroblasts.

Conclusion

In conclusion, LARS was identified as an essential gene for survival in osteosarcoma based on the DepMap database. Knockdown of LARS expression significantly inhibited the proliferation of osteosarcoma cells, suggesting that it is involved in the formation and development of osteosarcoma. The results are useful as a foundation for further studies to elucidate a potential osteosarcoma diagnostic index and therapeutic targets.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-022-03571-9.

Whole transcriptome RNA Sequencing Reveals the Global Molecular Responses and circRNA/lncRNA-miRNA-mRNA ceRNA Regulatory Network in Chicken Fat Deposition

Fat deposition is a vital factor affecting the economics of poultry production. Numerous studies on fat deposition have been done. However, the molecular regulatory mechanism is still unclear. In the present study, the whole-transcriptome RNA sequencing in abdominal fat, back skin, and liver both high- and low-abdominal fat groups was used to uncover the competitive endogenous RNA (ceRNA) regulation network related to chicken fat deposition. The results showed that differentially expressed (DE) genes in abdominal fat, back skin, liver were 1207(784 mRNAs, 330 lncRNAs, 41 circRNAs, 52 miRNAs), 860 (607 mRNAs, 166 lncRNAs, 26 circRNAs, 61 miRNAs), and 923 (501 mRNAs, 262 lncRNAs, 15 circRNAs, 145 miRNAs), respectively. The ceRNA regulatory network analysis indicated that the fatty acid metabolic process, monocarboxylic acid metabolic process, carboxylic acid metabolic process, glycerolipid metabolism, fatty acid metabolism, and peroxisome proliferator-activated receptor (PPAR) signaling pathway took part in chicken fat deposition. Meanwhile, we scan the important genes, FADS2, HSD17B12, ELOVL5, AKR1E2, DGKQ, GPAM, PLIN2, which were regulated by gga-miR-460b-5p, gga-miR-199-5p, gga-miR-7470-3p, gga-miR-6595-5p, gga-miR-101-2-5p. While these miRNAs were competitive combined by lncRNAs including MSTRG.18043, MSTRG.7738, MSTRG.21310, MSTRG.19577, and circRNAs including novel_circ_PTPN2, novel_circ_CTNNA1, novel_circ_PTPRD. This finding provides new insights into the regulatory mechanism of mRNA, miRNA, lncRNA, and circRNA in chicken fat deposition.

Dietary Supplementation of Chitosan Oligosaccharide–Clostridium butyricum Synbiotic Relieved Early-Weaned Stress by Improving Intestinal Health on Pigeon Squabs (Columba livia)

According to a previous study, we had found that early weaning causes harm to growth performance, intestinal morphology, activity of digestive enzymes, and antioxidant status in pigeon squabs (Columba livia). Chitosan oligosaccharides (COS) and Clostridium butyricum have been reported to have great potential to improve the growth performance and intestinal health of early-weaned animals. Therefore, the aim of this study is to explore whether dietary supplementation with COS-C. butyricum synbiotic could relieve early-weaned stress by evaluating its effects on growth performance and intestinal health in pigeon squabs. A total of 160 squabs (weaned at 7 days of age) were randomly divided into 5 groups: the control group, fed with artificial crop milk; the COS supplementation group, fed with artificial crop milk + 150 mg/kg COS; and three synbiotic supplementation groups, fed with artificial crop milk + 150 mg/kg COS + 200, 300, and 400 mg/kg C. butyricum. The results showed that a diet supplemented with COS-C. butyricum synbiotic benefitted the growth performance of early-weaned squabs; even so the differences were not significant among the five groups (p > 0.05). In addition, dietary supplementation of 150 mg/kg COS + 300~400 mg/kg C. butyricum significantly improved the intestinal morphology (especially villus surface area and the ratio of villus height to crypt depth), the activity of digestive enzymes (lipase, trypsin, and leucine aminopeptidase) in duodenum contents, and the production of total short-chain fatty acids and acetic acid in ileum content (p < 0.05). Additionally, dietary supplementation of 150 mg/kg COS + 400 mg/kg C. butyricum benefitted gut health by improving the antioxidant capacity (glutathione peroxidase and total antioxidant capacity) and cytokine status (IL-4 and IL-10) (p < 0.05), as well as by improving the intestinal microbiota diversity. In conclusion, our results revealed that dietary supplementation with synbiotic (150 mg/kg COS + 300~400 mg/kg C. butyricum) could relieve early-weaned stress by maintaining intestinal health in pigeon squabs.

Effects of early weaning on intestinal morphology, digestive enzyme activity, antioxidant status, and cytokine status in domestic pigeon squabs (Columba livia)

The aim of this study was to explore the effects of early weaning on growth performance, intestinal morphology, digestive enzyme activity, antioxidant status, and cytokine status in domestic pigeon squabs (Columba livia). The conclusion is based on body weight (BW) and average daily gain (ADG), length index and weight index of small intestine, small intestinal morphology, activity of digestive enzymes in duodenum content, the concentrations of jejunal antioxidant status and cytokines. A completely randomized design with 2 treatments, the control group (CON) and early weaning (EW) group, was utilized. Eight squabs per treatment were sampled at the age of 25 d. The results showed that early weaning reduced BW (P < 0.05), ADG (P < 0.05), ileac length index (P < 0.05), and weight index (P < 0.01). Compared with the CON group, small intestinal morphology was altered in the EW group. Ileac crypt depth (CD) increased significantly (P < 0.01). The villus area was decreased in the duodenum (P < 0.05), jejunum (P < 0.01), and ileum (P < 0.05). The ileac ratio of villus height to crypt depth (VCR) in the EW group was lower than the ileac ratio of villus height to VCR in the CON group (P < 0.01). The activity of trypsin (P < 0.05), sucrase (P < 0.01) and aminopeptidase-N (APN) (P < 0.01) in the duodenum was reduced. Jejunal malondialdehyde (MDA) (P < 0.01) was increased and total superoxide dismutase (T-SOD) (P < 0.01) was reduced significantly. Early weaning decreased the concentrations of interferon-γ (IFN-γ) (P < 0.01), interleukin-4 (IL-4) (P < 0.05) and interleukin-10 (IL-10) (P < 0.01) but induced significant upregulation of interleukin-2 (IL-2) (P < 0.05). In conclusion, our results suggested that early weaning did harm the BW and ADG, intestinal length index and weight index, intestinal morphology, activity of digestive enzymes, and antioxidant and cytokine status.

LncRNAs in domesticated animals: from dog to livestock species

Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

Exploration of Proteomics Analysis of Crop Milk in Pigeons (Columba livia) during the Lactation Period

Pigeon milk is a curdlike substance separated from the mature crop epithelium of breeders, associated with the rapid growth and development of squabs. The aim of this study was to investigate in detail the variations in the content of several important ingredients in crop milk. In this study, we utilized proteomic techniques to investigate the composition and changing pattern of crop milk protein of squabs on days 1 (D1), 3 (D3), and 7 (D7). Our results indicated that the crude protein contents in crop milk decreased with age, and they were up to 50% during the first 3 days. The proteomic data showed that a total of 2558 proteins were identified in all samples from three stages, and the top 15% crop milk proteins were ribosomal protein, keratin, peroxiredoxin, annexin, heat shock protein, and eukaryotic translation protein based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and normalized spectral abundance factors (NSAFs) calculation. Furthermore, the compositions of crop milk protein between D1 and D3 were quite similar [51 differentially expressed proteins (DEPs)], while great proteomic differences were observed between D1/D3 and D7 (more than 240 DEPs). Additionally, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that up-regulated DEPs mainly participate in immune response, while down-regulated DEPs were involved in cell differentiation and development as well as tRNA aminoacylation biosynthesis. In conclusion, DEPs were mainly related to protein synthesis, immunity, and antioxidation, which provided effective information for the development of artificial squab milk products in the future.