Identification of Novel lncRNA and Differentially Expressed Genes (DEGs) of Testicular Tissues among Cattle, Yak, and Cattle-Yak Associated with Male Infertility

Comparative Analysis of mRNA and lncRNA Expression Profiles in Testicular Tissue of Sexually Immature and Sexually Mature Mongolian Horses

Testicular development and spermatogenesis are tightly regulated by both coding and non-coding genes, with mRNA and lncRNA playing crucial roles in post-transcriptional gene expression regulation. However, there are significant differences in regulatory mechanisms before and after sexual maturity. Nevertheless, the mRNAs and lncRNAs in the testes of Mongolian horses have not been systematically identified. In this study, we first identified the testicular tissues of sexually immature and sexually mature Mongolian horses at the tissue and protein levels, and comprehensively analyzed the expression profiles of mRNA and lncRNA in the testes of 1-year-old (12 months, n = 3) and 10-year-old (n = 3) Mongolian horses using RNA sequencing technology. Through gene expression analysis, we identified 16,582 mRNAs and 2128 unknown lncRNAs that are commonly expressed in both sexually immature and sexually mature Mongolian horses. Meanwhile, 9217 mRNAs (p < 0.05) and 2191 unknown lncRNAs (p < 0.05) were identified as differentially expressed between the two stages, which were further validated by real-time fluorescent quantitative PCR and analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The analysis results showed that genes in the sexually immature stage were mainly enriched in terms related to cellular infrastructure, while genes in the sexually mature stage were enriched in terms associated with hormones, metabolism, and spermatogenesis. In summary, the findings of this study provide valuable resources for a deeper understanding of the molecular mechanisms underlying testicular development and spermatogenesis in Mongolian horses and offer new perspectives for future related research.

Single-cell RNA sequencing and UPHLC-MS/MS targeted metabolomics offer new insights into the etiological basis for male cattle-yak sterility

The variety of species can be efficiently increased by interspecific hybridization. However, because the males in the hybrid progeny are usually sterile, this heterosis cannot be employed when other cattle and yaks are hybridized. While some system-level studies have sought to explore the etiological basis for male cattle-yak sterility, no systematic cellular analyses of this phenomenon have yet been performed. Here, single-cell RNA sequencing and UPHLC-MS/MS targeted metabolomics methods were used to study the differences in testicular tissue between 4-year-old male yak and 4-year-old male cattle-yak, providing new and comprehensive insights into the causes of male cattle-yak sterility. Cattle-yak testes samples detected 6 somatic cell types and one mixed germ cell type. Comparisons of these cell types revealed the more significant differences in Sertoli cells (SCs) and [Leydig cells and myoid cells (LCs_MCs)] between yak and cattle-yak samples compared to other somatic cell clusters. Even though the LCs and MCs from yaks and cattle-yaks were derived from the differentiation of the same progenitor cells, a high degree of overlap between LCs and MCs was observed in yak samples. Still, only a small overlap between LCs and MCs was observed in cattle-yak samples. Functional enrichment analyses revealed that genes down-regulated in cattle-yak SCs were primarily enriched in biological activity, whereas up-regulated genes in these cells were enriched for apoptotic activity. Furthermore, the genes of up-regulated in LCs_MCs of cattle-yak were significantly enriched in enzyme inhibitor and molecular function inhibitor activity. On the other hand, the genes of down-regulated in these cells were enriched for signal receptor binding, molecular function regulation, positive regulation of biological processes, and regulation of cell communication activity. The most significant annotated differences between yak and cattle-yak LCs_MCs were associated with cell-to-cell communication. While yak LCs_MCs regulated spermatogenic cells at spermatogonia, spermatocyte, and spermatid levels, no such relationships were found between cattle-yak LCs_MCs and germ cells. This may suggest that the somatic niche in male cattle-yak testes is a microenvironment that is ultimately not favorable for spermatogenesis.

Characteristic flavor fingerprint disclosure of dzo beef in Tibet by applying SAFE-GC-O-MS and HS-GC-IMS technology

To understand the overall flavor of the dzo beef, fatty acids, volatile compounds and aroma profiles of dzo beef samples (raw beef (RB), broth (BT) and cooked beef (CB)) were investigated by head-space-gas chromatography-ion mobility spectrometry (HS-GC-IMS) and gas chromatography-mass spectrometry (GC-MS). The fatty acid analysis showed a decrease in the ratio of polyunsaturated fatty acids, such as linoleic acid, which decreased from 2.60 % in RB to 0.51 % in CB. The principal component analysis (PCA) showed that HS-GC-IMS was able to distinguish different samples. A total of 19 characteristic compounds with odor activity value (OAV) > 1 were identified by gas chromatography-olfactometry (GC-O). Fruity, caramellic, fatty and fermented attributes were enhanced after stewing. Butyric acid and 4-methylphenol were responsible for the stronger off-odor in RB. 3-Hydroxy-2-butanone and 2,5-dimethyl-4-hydroxy-3(2H)-furanone with buttery and caramellic attributes were dominated in BT, while (E)-2-nonenal, (E,E)-2,4-decadienal and (E,E)-2,4-nonadienal prominently conferred fatty attribute on CB. Furthermore, anethole with anisic aroma was first identified in beef, which may be one of the typical chemical markers that distinguish dzo beef from other varieties.

MAEL gene contributes to bovine testicular development through the m5C-mediated splicing

Knowledge of RNA molecules regulating testicular development and spermatogenesis in bulls is essential for elite bull selection and an ideal breeding program. Herein, we performed direct RNA sequencing (DRS) to explore the functional characterization of RNA molecules produced in the testicles of 9 healthy Simmental bulls at three testicular development stages (prepuberty, puberty, and postpuberty). We identified 5,043 differentially expressed genes associated with testicular weight. These genes exhibited more alternative splicing at sexual maturity, particularly alternative 3' (A3) and 5' (A5) splice sites usage and exon skipping (SE). The expression of hub genes in testicular developmental stages was also affected by both m6A and m5C RNA modifications. We found m5C-mediated splicing events significantly (p < 0.05) increased MAEL gene expression at the isoform level, likely promoting spermatogenesis. Our findings highlight the complexity of RNA processing and expression as well as the regulation of transcripts involved in testicular development and spermatogenesis.

The exploration of miRNAs and mRNA profiles revealed the molecular mechanisms of cattle-yak male infertility

Cattle-yak, the first-generation offspring of cattle and yak, inherited many excellent characteristics from their parents. However, F1 male hybrid infertility restricts the utilization of heterosis greatly. In this study, we first compared the testicular tissue histological characteristics of three cattle, three yaks, and three cattle-yak. Then we explored the miRNA profiles and the target functions of nine samples with RNA-seq technology. We further analyzed the function of DE gene sets of mRNA profiles identified previously with GSEA. Testicular histology indicated that the seminiferous tubules became vacuolated and few active germ cells can be seen. RNA-seq results showed 47 up-regulated and 34 down-regulated, 16 up-regulated and 21 down-regulated miRNAs in cattle and yaks compared with cattle-yak, respectively. From the intersection of DE miRNAs, we identified that bta-miR-7 in cattle-yak is down-regulated. Target prediction indicated that the filtered genes especially MYRFL, FANCA, INSL3, USP9X, and SHF of bta-miR-7 may play crucial roles in the reproductive process. With further network analysis and GSEA, we screened such hub genes and function terms, we also found some DE gene sets that enriched in ATP binding, DNA binding, and reproduction processes. We concluded that bta-miR-7 may play an important role in influencing fecundity. Our study provides new insights for explaining the molecular mechanism of cattle-yak infertility.

Whole-Genome Profile of Greek Patients with Teratozοοspermia: Identification of Candidate Variants and Genes

Male infertility is a global health problem that affects a large number of couples worldwide. It can be categorized into specific subtypes, including teratozoospermia. The present study aimed to identify new variants associated with teratozoospermia in the Greek population and to explore the role of genes on which these were identified. For this reason, whole-genome sequencing (WGS) was performed on normozoospermic and teratozoospermic individuals, and after selecting only variants found in teratozoospermic men, these were further prioritized using a wide range of tools, functional and predictive algorithms, etc. An average of 600,000 variants were identified, and of them, 61 were characterized as high impact and 153 as moderate impact. Many of these are mapped in genes previously associated with male infertility, yet others are related for the first time to teratozoospermia. Furthermore, pathway enrichment analysis and Gene ontology (GO) analyses revealed the important role of the extracellular matrix in teratozoospermia. Therefore, the present study confirms the contribution of genes studied in the past to male infertility and sheds light on new molecular mechanisms by providing a list of variants and candidate genes associated with teratozoospermia in the Greek population.

Characterization of N6-methyladenosine in cattle-yak testis tissue

N⁶-methyladenosine (m⁶A) is the most common form of eukaryotic mRNA modification, and it has been shown to exhibit broad regulatory activity in yeast, plants, and mammals. The specific role of m⁶A methylation as a regulator of spermatogenesis, however, has yet to be established. In this experiment, through a series of preliminary studies and methylated RNA immunoprecipitation sequencing, the m⁶A map of cattle-yak testicular tissue was established as a means of exploring how m⁶A modification affects cattle-yak male infertility. Cattle-yak testis tissues used in this study were found to contain sertoli cells and spermatogonia. Relative to sexually mature yak samples, those isolated from cattle-yak testis exhibited slightly reduced levels of overall methylation, although these levels were significantly higher than those in samples from pre-sexually mature yaks. Annotation analyses revealed that differentially methylated peaks were most concentrated in exonic regions, with progressively lower levels of concentration in the 3'-untranslated region (UTR) and 5'-UTR regions. To further explore the role of such m⁶A modification, enrichment analyses were performed on differentially methylated and differentially expressed genes in these samples. For the cattle-yaks vs. 18-months-old yaks group comparisons, differentially methylated genes were found to be associated with spermatogenesis-related GO terms related to the cytoskeleton and actin-binding, as well as with KEGG terms related to the regulation of the actin cytoskeleton and the MAPK signaling pathway. Similarly, enrichment analyses performed for the cattle-yaks vs. 5-years-old yaks comparison revealed differentially methylated genes to be associated with GO terms related to protein ubiquitination, ubiquitin ligase complexes, ubiquitin-dependent protein catabolism, and endocytotic activity, as well as with KEGG terms related to apoptosis and the Fanconi anemia pathway. Overall, enrichment analyses for the cattle-yaks vs. 18-months-old yaks comparison were primarily associated with spermatogenesis, whereas those for the cattle-yaks vs. 5-years-old yaks comparison were primarily associated with apoptosis.

RNA-Seq reveals the functional specificity of epididymal caput, corpus, and cauda genes of cattleyak

The first filial generation of the cattleyaks demonstrates hybrid vigor; however, the male cattleyaks are infertile and restrict productivity and breeding. The discovery of genes in a segment-specific approach offers valuable information and understanding concerning fertility status, yet the biology of cattleyak epididymis is still progressing. Comparative transcriptome analysis was performed on segment pairs of cattleyak epididymis. The caput versus corpus epididymis provided the highest (57.8%) differentially expressed genes (DEGs), corpus versus cauda (25.1%) followed, whereas caput versus cauda pair (17.1%) had the least DEGs. The expression levels of genes coding EPHB6, TLR1, MUC20, MT3, INHBB, TRPV5, EI24, PAOX, KIF12, DEPDC5, and KRT25, which might have the potentials to regulate the homeostasis, innate immunity, differentiation, motility, transport, and sperm maturation-related function in epididymal cells, were downregulated in the distal segment of epididymis. Top enriched KEGG pathways included mTOR, axon guidance, and taste transduction signaling pathways. EIF4B, EPHB6, and TAS2R42 were enriched in the pathways, respectively. Identifying key, new, and unexplored DEGs among the epididymal segments and further analyzing them could boost cattleyak fertility by maximizing sperm quality from genetically better sires and also facilitate better understanding of the epididymal biology.

RNA sequencing reveals novel LncRNA/mRNAs co-expression network associated with puerarin-mediated inhibition of cardiac hypertrophy in mice

Background

Evidence has demonstrated that puerarin is a potential medicine for the treatment of cardiac hypertrophy. However, the precise underlying molecular mechanisms of the protective effect of puerarin are still unclear. Here, we aimed to explore the regulatory mechanisms of lncRNAs/mRNAs co-expression network in a cardiac hypertrophy mouse model after puerarin treatment.

Methods

A mouse model of cardiac hypertrophy was established by transverse aortic constriction (TAC). The echocardiography, tissue staining and western blot were used to examine the protective effect of puerarin. Then RNA sequencing (RNA-seq) was carried out to analyze systematically mRNAs and lncRNAs expression. The target lncRNA were confirmed using qRT-PCR. Moreover, a coding/non-coding gene co-expression network were established to find the interaction of lncRNA and mRNAs. The biological process, cellular component, molecular function and pathways of different expression mRNAs targeted by lncRNA were explored using Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis.

Results

Puerarin exhibited an obvious inhibitory effect in cardiac hypertrophy in TAC model. RNA-seq analysis was performed to investigate the lncRNAs and mRNAs expression patterns of cardiomyocytes in sham and TAC groups treated with or without puerarin. RNA-seq identified that TAC downregulated four lncRNAs, which could be revised by puerarin treatment (|log2 Fold change| > 2 and FDR < 0.05). Among them, expression alterations of lncRNA Airn (antisense of Igf2r non-protein coding RNA) was confirmed by qRT-PCR. Pearson's correlation coefficients of co-expression levels suggested that there was an interactive relationship between Airn and 2,387 mRNAs (r > 0.95 or r < -0.95). Those co-expressed mRNAs were enriched in some important biological processes such as translational initiation, cell proliferation, insulin-like growth factor binding and poly(A) RNA binding. KEGG analyses suggested that those Airn-interacted mRNAs were enriched in endocytosis, signaling pathways regulating pluripotency of stem cells and the Jak-STAT pathway.

Conclusion

Puerarin may exert beneficial effects on cardiac hypertrophy through regulating the lncRNAs/mRNAs co-expression network.

Single-Cell Sequencing Revealed Pivotal Genes Related to Prognosis of Myocardial Infarction Patients

Objectives

Myocardial infarction (MI) is a common cardiovascular disease. Histopathology is a main molecular characteristic of MI, but often, differences between various cell subsets have been neglected. Under this premise, MI-related molecular biomarkers were screened using single-cell sequencing.

Methods

This work examined immune cell abundance in normal and MI samples from GSE109048 and determined differences in the activated mast cells and activated CD4 memory T cells, resting mast cells. Weighted gene coexpression network analysis (WGCNA) demonstrated that activated CD4 memory T cells were the most closely related to the turquoise module, and 10 hub genes were screened. Single-cell sequencing data (scRNA-seq) of MI were examined. We used t-distributed stochastic neighbor embedding (t-SNE) for cell clustering.

Results

We obtained 8 cell subpopulations, each of which had different marker genes. 7 out of the 10 hub genes were detected by single-cell sequencing analysis. The expression quantity and proportion of the 7 genes were different in 8 cell clusters.

Conclusion

In general, our study revealed the immune characteristics and determined 7 prognostic markers for MI at the single-cell level, providing a new understanding of the molecular characteristics and mechanism of MI.