Integrated analysis of miRNA and mRNA expression profiles in testes of Landrace and Hezuo boars

Cellulase activity and age-based variation of intestinal microbiota in Hezuo pigs

Introduction

To examine the fiber-degrading enzyme activity and the changes of intestinal microbiota in Hezuo pigs across different age stages.

Methods

Fecal samples from 36 semi-grazed Hezuo pigs across five growth stages were collected for cellulase activity and 16S rRNA gene sequencing analysis.

Results

The results showed that the cellobiase activity in adult Hezuo pigs was markedly higher than in other groups (p < 0.01). The intestinal microbiota of Hezuo pigs was predominantly composed of Firmicutes and Bacteroidetes. The prevalence of Proteobacteria of nursing piglets was significantly higher compared to other stages (p < 0.05), which might be related to protein degradation. Prevotella_NK3B31_group was a shared dominant genus across at all age stages, while Ruminococcaceae_UCG-005 dominated during the weaning, growth, fattening and adult stages. Its cellulose-degrading enzyme secretion capacity enhanced with age to meet the high-fiber dietary demands of Hezuo pigs. Functional prediction of intestinal microbiota in adjacent age groups using PICRUSt revealed that the differences between lactating piglets and weaned piglets were primarily due to the enrichment of various metabolic pathways functional genes, while differences between fattening pigs and adult sows were negligible. Adult boars showed significant enrichment in amino acid metabolism, energy metabolism, and nucleotide metabolism pathways compared to fattening piglets.

Discussion

These results reveal the age-related dynamic development of intestinal microbiota in Hezuo pigs, providing novel insights into the mechanism of their roughage tolerance.

CircRNA profiling reveals the regulatory role of circPAN3 in Hezuo boars Sertoli cell growth

BACKGROUND

The Hezuo (HZ) pig, a famous indigenous breed in China, is characterized by precocious puberty compared with foreign-introduced pig breeds. Sexual maturation is a complex physiological process, and in recent years, circular RNAs (circRNAs), a new class of noncoding RNAs with endogenous regulatory functions, have been shown to play important roles in regulating sexual maturation. However, the dynamic expression and regulatory mechanism of circRNAs during sexual maturation in HZ pigs remain unclear. In this study, we performed RNA sequencing and bioinformatics analysis to reveal circRNA expression patterns in the testes of HZ boars at 30 days (sexual immaturity; Ha) and 120 days (sexual maturity; Hb), with Landrace (LC) boars of the same age (La and Lb) as controls. Subsequently, an abundant circ_005678 (circPAN3) transcribed from the PAN3 gene, was functionally investigated by RT-qPCR, Western Blot, CCK-8, and flow cytometry.

RESULTS

We identified 31,134 circRNAs in 12 samples, and 2,562, 2,401, 749, and 831 differentially expressed (DE) circRNAs were identified in the Ha-vs-Hb, La-vs-Lb, Ha-vs-La, and Hb-vs-Lb groups, respectively. The results of functional enrichment analyses indicated that these source genes of the DE circRNAs were involved mainly in testicular development and spermatogenesis. Furthermore, we constructed a circRNA-miRNA-mRNA interaction network and functionally analyzed the target genes. GO functional annotation of the target genes suggested that they were mainly involved in biological processes such as gland development, cell proliferation, and reproduction. KEGG pathway analysis further revealed that these genes were enriched mainly in signaling pathways involved in testicular development and spermatogenesis, including the PI3K-Akt and MAPK signaling pathways. Cellular assays revealed that circPAN3 promoted proliferation and inhibited apoptosis in immature Sertoli cells, whereas opposite changes were observed by circPAN3 knockdown.

CONCLUSIONS

This study revealed the dynamic expression profiles and regulatory mechanisms of circRNAs during sexual maturation in HZ pigs. Further functional studies demonstrated that circPAN3 promoted the proliferation and inhibited the apoptosis of immature Sertoli cells, suggesting that circPAN3 may be closely related to the characteristics of precocious puberty in HZ boars. These findings provide a new perspective for exploring the regulatory mechanism of circRNAs in precocious puberty in HZ pigs.

Transcriptional Profiling of Testis Development in Pre-Sexually-Mature Hezuo Pig

Spermatogenesis is an advanced biological process, relying on intricate interactions between somatic and germ cells in testes. Investigating various cell types is challenging because of cellular heterogeneity. Single-cell RNA sequencing (scRNA-seq) offers a method to analyze cellular heterogeneity. In this research, we performed 10× Genomics scRNA-seq to conduct an unbiased single-cell transcriptomic analysis in Hezuo pig (HZP) testis at one month of age during prepuberty. We collected 14,276 cells and identified 8 cell types (including 2 germ cells types and 6 somatic cell types). Pseudo-timing analysis demonstrated that Leydig cells (LCs) and myoid cells (MCs) originated from a shared progenitor cell lineage. Moreover, the functional enrichment analyses showed that the genes of differential expression were enriched in spermatogonia (SPG) and were enriched in the cell cycle, reproduction, and spermatogenesis. Expressed genes in spermatocytes (SPCs) were enriched in the cAMP, cell cycle, male gamete generation, reproductive system development, and sexual reproduction, while growth hormone synthesis, gamete generation, reproductive process, and spermine synthase activity were enriched in Sertoli cells (SCs). Additionally, chemokine, B cell receptor, activation of immune response, and enzyme binding were enriched in macrophages. Our study investigated transcriptional alterations across different cell types during spermatogenesis, yielding new understandings of spermatogenic processes and cell development. This research delivers an exploration of spermatogenesis and testicular cell biology in HZP, establishing the groundwork for upcoming breeding initiatives.

Single-Cell RNA Sequencing Reveals an Atlas of Hezuo Pig Testis Cells

Spermatogenesis is a complex biological process crucial for male reproduction and is characterized by intricate interactions between testicular somatic cells and germ cells. Due to the cellular heterogeneity of the testes, investigating different cell types across developmental stages has been challenging. Single-cell RNA sequencing (scRNA-seq) has emerged as a valuable approach for addressing this limitation. Here, we conducted an unbiased transcriptomic study of spermatogenesis in sexually mature 4-month-old Hezuo pigs using 10× Genomics-based scRNA-seq. A total of 16,082 cells were collected from Hezuo pig testes, including germ cells (spermatogonia (SPG), spermatocytes (SPCs), spermatids (SPTs), and sperm (SP)) and somatic cells (Sertoli cells (SCs), Leydig cells (LCs), myoid cells (MCs), endothelial cells (ECs), and natural killer (NK) cells/macrophages). Pseudo-time analysis revealed that LCs and MCs originated from common progenitors in the Hezuo pig. Functional enrichment analysis indicated that the differentially expressed genes (DEGs) in the different types of testicular germ cells were enriched in the PI3K-AKT, Wnt, HIF-1, and adherens junction signaling pathways, while the DEGs in testicular somatic cells were enriched in ECM-receptor interaction and antigen processing and presentation. Moreover, genes related to spermatogenesis, male gamete generation, sperm part, sperm flagellum, and peptide biosynthesis were expressed throughout spermatogenesis. Using immunohistochemistry, we verified several stage-specific marker genes (such as UCHL1, WT1, SOX9, and ACTA2) for SPG, SCs, and MCs. By exploring the changes in the transcription patterns of various cell types during spermatogenesis, our study provided novel insights into spermatogenesis and testicular cells in the Hezuo pig, thereby laying the foundation for the breeding and preservation of this breed.

Causal association between mTOR-dependent circulating protein levels and central precocious puberty: a Mendelian randomization study

Background

The mechanistic target of rapamycin (mTOR) signaling pathway has a significant effect on central precocious puberty (CPP). However, the causality between mTOR-dependent circulating protein levels and CPP is still unclear. Our aim is to assess the effects of seven mTOR-dependent circulating protein levels on CPP using Mendelian randomization (MR).

Methods

Instrumental variables (IVs) for mTOR-dependent circulating protein levels were retrieved from the proteomics-GWAS INTERVAL study and eQTLGen. The summary-level genetic datasets for CPP outcome were obtained from the FinnGen Consortium. Inverse-variance weighted (IVW) was used as the primary method and the pleiotropy, heterogeneity and robustness of the analyses were detected as sensitivity analysis. Positive exposures in the discovery cohort would be revalidated in the validation cohort.

Results

This two-sample MR study revealed a causal association between eIF4G level in plasma and CPP in both discovery cohort (IVW: OR = 0.45, 95% CI = 0.22-0.91, p = 0.026) and validation cohort (IVW: OR = 0.45, 95% CI = 0.24-0.85, p = 0.014).

Conclusions

There was a causal association between eIF4G level in plasma and CPP. Whether eIF4G can be used for the prevention or treatment of CPP needs to be explored in further studies.

Integrated analysis of lncRNA, miRNA and mRNA expression profiles reveals regulatory pathways associated with pig testis function

Long noncoding RNA (lncRNA) and microRNA (miRNA) are known to play pivotal roles in mammalian testicular function and spermatogenesis. However, their impact on porcine male reproduction has yet to be well unraveled. Here, we sequenced and identified lncRNA and miRNA expressed in the testes of Chinese indigenous Banna mini-pig inbred line (BMI) and introduced Western Duroc (DU) and Large White (LW) pigs. By pairwise comparison (BMI vs DU, BMI vs LW, and DU vs LW), we found the gene expression differences in the testes between Chinese local pigs and introduced Western commercial breeds were more striking than those between introduced commercial breeds. Furthermore, we found 1622 co-differentially expressed genes (co-DEGs), 122 co-differentially expressed lncRNAs (co-DELs), 39 co-differentially expressed miRNAs (co-DEMs) in BMI vs introduced commercial breeds (DU and LW). Functional analysis revealed that these co-DEGs and co-DELs/co-DEMs target genes were enriched in male sexual function pathways, including MAPK, AMPK, TGF-β/Smad, Hippo, NF-kappa B, and PI3K/Akt signaling pathways. Additionally, we established 10,536 lncRNA-mRNA, 11,248 miRNA-mRNA pairs, and 62 ceRNA (lncRNA-miRNA-mRNA) networks. The ssc-miR-1343 had the most interactive factors in the ceRNA network, including 20 mRNAs and 3 lncRNAs, consisting of 56 ceRNA pairs. These factors played extremely important roles in the regulation of testis function as key nodes in the interactive regulatory network. Our results provide insight into the functional roles of lncRNAs and miRNAs in porcine testis and offer a valuable resource for understanding the differences between Chinese indigenous and introduced Western pigs.

Effects of Whole-Plant Corn Silage on Growth Performance, Serum Biochemical Indices, and Fecal Microorganisms in Hezuo Pigs

In this study, we investigated the effects of the dietary inclusion of different proportions of whole-plant corn silage on growth performance, serum biochemical indexes, and intestinal microorganisms in Hezuo pigs. Thirty-two two-month-old Hezuo pigs (body weight: 7.88 ± 0.81 kg) were randomly divided into four groups of eight pigs (half male, half female) each. The control (CON) group received a basal diet, while the three experimental groups were fed the basal diet, part of which had been replaced with 5%, 10%, and 15% whole-plant corn silage, respectively. The experiment lasted for 127 days, including 7 days of pre-testing and 120 days of formal testing. At the end of the experiment, blood and fecal samples were collected. Compared with the CON group, the feed-to-gain ratio was significantly lower in the 10% test group (p < 0.05), whereas the total protein, albumin, triglyceride, and glucose contents were significantly higher (p < 0.05). No significant differences in total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, creatinine, urea, aspartate aminotransferase, and alanine aminotransferase were observed among the groups (p > 0.05). The addition of whole-plant corn silage to the diet significantly increased alpha diversity in the pig gut based on 16S rRNA gene sequencing. The principal coordinate analysis results showed significant clustering of the different groups (p < 0.05). At the phylum level, the addition of whole-plant corn silage to the diet significantly decreased (p < 0.05) the relative abundance of Firmicutes and significantly increased (p < 0.05) that of Bacteroidetes. At the genus level, the relative abundance of Streptococcus significantly decreased (p < 0.05) with increasing silage supplementation levels, whereas species diversity significantly increased (p < 0.05). In conclusion, 10% is the recommended inclusion ratio for whole-plant corn silage in the diets of pigs.

Seasonal patterns of miRNA and mRNA expression profiles in the testes of plateau zokors (Eospalax baileyi)

The gonads of seasonal breeding animals undergo periodic annual changes in morphology, physiological hormones, and gene expression levels. To clarify the regulatory mechanism of miRNAs in the seasonal testicular development and spermatogenesis of plateau zokors, the miRNA expression profiles in their testicles during breeding and non-breeding seasons were analyzed. In total, 447 miRNAs, including 366, 81, and 167 known, novel, and differentially expressed (DE) miRNAs, respectively, were determined in the testes. Compared to the non-breeding season, 90 DE miRNAs were upregulated and 77 DE miRNAs were downregulated during the breeding season. By analysing the miRNA and mRNA expression profiles, we predicted 2096 significant target mRNAs. According to the miRNA-mRNA interaction network, target mRNAs with DE miRNAs were related to testicular development and spermatogenesis. GO indicated that target mRNAs were enriched in spermatogenesis, cell differentiation, multicellular biological development, and flagellated sperm movement and were associated with regulating testicular development and spermatogenesis. KEGG suggested that target mRNAs were enriched in lipid and fructose metabolism and provided energy and material for spermatogenesis. The target mRNA of rno-miR-24-3p was determined to be Polyubiquitin-B (UBB). Our results provide a reference for revealing the mechanism by which miRNAs regulate testicular development and spermatogenesis in plateau zokors, which has important implications for understanding the regulation of seasonal reproduction in animals.

Integrative transcriptomic profiling of mRNA, miRNA, circRNA, and lncRNA in alveolar macrophages isolated from PRRSV-infected porcine

Introduction

The porcine reproductive and respiratory syndrome virus (PRRSV) continues to pose a significant threat to the global swine industry, attributed largely to its immunosuppressive properties and the chronic nature of its infection. The absence of effective vaccines and therapeutics amplifies the urgency to deepen our comprehension of PRRSV's intricate pathogenic mechanisms. Previous transcriptomic studies, although informative, are partially constrained by their predominant reliance on in vitro models or lack of long-term infections. Moreover, the role of circular RNAs (circRNAs) during PRRSV invasion is yet to be elucidated.

Methods

In this study, we employed an in vivo approach, exposing piglets to a PRRSV challenge over varied durations of 3, 7, or 21 days. Subsequently, porcine alveolar macrophages were isolated for a comprehensive transcriptomic investigation, examining the expression patterns of mRNAs, miRNAs, circRNAs, and long non-coding RNAs (lncRNAs).

Results

Differentially expressed RNAs from all four categories were identified, underscoring the dynamic interplay among these RNA species during PRRSV infection. Functional enrichment analyses indicate that these differentially expressed RNAs, as well as their target genes, play a pivotal role in immune related pathways. For the first time, we integrated circRNAs into the lncRNA-miRNA-mRNA relationship, constructing a competitive endogenous RNA (ceRNA) network. Our findings highlight the immune-related genes, CTLA4 and SAMHD1, as well as their associated miRNAs, lncRNAs, and circRNAs, suggesting potential therapeutic targets for PRRS. Importantly, we corroborated the expression patterns of selected RNAs through RT-qPCR, ensuring consistency with our transcriptomic sequencing data.

Discussion

This study sheds lights on the intricate RNA interplay during PRRSV infection and provides a solid foundation for future therapeutic strategizing.

Comparative analysis of microRNA and messengerRNA expression profiles in plateau zokor testicular cells under reproductive suppression

Introduction

Reproductive suppression is an adaptive strategy that affects the success rate and reproductive efficiency in animals, which in turn affects population continuation and evolution. However, no studies on the miRNAs in testicular development and spermatogenesis regulatory mechanisms under reproductive suppression have been reported.

Methods

In this study, the differentially expressed (DE) miRNAs, miRNA-mRNA interaction network and function of the plateau zokor testicular cells of non-breeders and breeders during the breeding season were comprehensively analyzed by transcriptomics.

Results

In total, 381 known and 94 novel miRNAs were determined. Compared with that in the breeders, 70 downregulated and 68 upregulated DE miRNAs were identified in the non-breeders. We predicted 1670 significant target mRNAs by analyzing the miRNA and mRNA expression profiles. According to the miRNA-mRNA interaction network, the target mRNAs of the DE miRNAs were related to testicular development and spermatogenesis. GO indicate that the target mRNAs were related to testicular development and spermatogenesis. KEGG indicate that pathways of target mRNAs enrichment related to testicular development, spermatogenesis, and energy metabolism. PROK2 was determined as the target mRNA of rno-miR-143-3p.

Discussion

Our study offers a basis for the regulatory mechanisms of miRNAs in testicular development and spermatogenesis in plateau zokor under reproductive suppression and offers a reference for reproductive regulation.