Single-Cell RNA Sequencing Reveals Atlas of Yak Testis Cells

Isoform-resolution single-cell RNA sequencing reveals the transcriptional panorama of adult Baoshan pig testis cells

BACKGROUND

As the primary organ of the male reproductive system, the testis facilitates spermatogenesis and androgen secretion. Due to the complexity of spermatogenesis, elucidating cellular heterogeneity and gene expression dynamics within the porcine testis is critical for advancing reproductive biology. Nevertheless, the cellular composition and regulatory mechanisms of porcine testes remain insufficiently characterized. In this study, we applied integrated long-read (Nanopore) and short-read (Illumina) scRNA-seq to Baoshan pig testes, establishing a comprehensive transcriptional profile to delineate cellular heterogeneity and molecular regulation.

RESULTS

Through systematic analysis of testicular architecture and the temporal progression of spermatogenesis, we characterized 11,520 single cells and 23,402 genes, delineating germ cell developmental stages: proliferative-phase spermatogonia (SPG), early-stage spermatocytes (Early SPC) and late-stage spermatocytes (Late SPC) during meiosis, and spermiogenic-phase round spermatids (RS) followed by elongating/elongated spermatids (ES), culminating in mature spermatozoa (Sperm). We further identified nine distinct testicular cell types, with germ cells spanning all developmental stages and somatic components comprising Sertoli cells, macrophages, and peritubular myoid cells as microenvironmental constituents, revealing the cellular heterogeneity of testicular tissue and dynamic characteristics of spermatogenesis. We obtained the dynamic expression changes of 16 vital marker genes during spermatogenesis and performed immunofluorescence validation on 7 marker genes. Gene ontology analysis revealed that germ cells at various stages were involved in specific biological processes, while cell communication networks highlighted eight pivotal signaling pathways, including MIF, NRG, WNT, VEGF, BMP, CCL, PARs, and ENHO pathways. Long-read sequencing further captured the full integrity and diversity of RNA transcripts, identifying 60% of the novel annotated isoforms and revealing that FSM isoforms exhibited longer transcript lengths, longer coding sequences, longer open reading frames, and a great number of exons, suggesting the complexity of isoforms within the testicular microenvironment.

CONCLUSIONS

Our results provide insight into the cellular heterogeneity, intercellular communication, and gene expression/transcript diversity in porcine testes, and offer a valuable resource for understanding the molecular mechanisms of porcine spermatogenesis.

Single-cell multiomic comparison of mouse and rat spermatogenesis reveals gene regulatory networks conserved for over 20 million years

Spermatogenesis is driven by dramatic changes in chromatin regulation, gene transcription, and protein expression. To assess the mechanistic bases for these developmental changes, we utilized multiomic single-cell/nucleus RNA sequencing (sc/snRNA-seq) and single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) to identify chromatin changes associated with transcription in adult mouse and rat testes. We characterized the relationships between the transcriptomes and chromatin of both species, including the divergent expression of Id4 in spermatogonial stem cells between species. Promoter accessibility and gene expression showed the greatest association during meiosis in both species. We mapped the cross-species conservation of putative regulatory regions for key spermatogenic genes, including Cd9 and Spam1, and investigated correlations and disconnects in chromatin accessibility, gene expression, and protein expression via antibody-derived tags. Using a gene regulatory network (GRN) model, we identified 40 core regulons conserved between mouse and rat germ cells, highlighting the relevance of chromatin-related factors in regulating the transcription of canonical genes across spermatogenesis.

Single-cell RNA sequencing of bone marrow reveals the immune response mechanisms of lymphocytes under avian leukosis virus subgroup J infection

Avian Leukosis Virus (ALV) can induce tumorigenesis and immune suppression by acting on lymphocytes in the bone marrow. In this study, single-cell RNA sequencing (scRNA-seq) was used to analyze chicken bone marrow lymphocytes under Avian Leukosis Virus subtype J (ALV-J) infection. Using subgroup-specific marker genes and cell state analysis, we identified 18 distinct cell clusters, including 8 T cell clusters, 2 B cell clusters, 5 tumor-like cell clusters, and 3 unidentified clusters. Gene expression analysis revealed that in the 10 T/B lymphocyte clusters, the differentially expressed genes in double-positive T cells, B1-like B cells, and cytotoxic T cells were highly enriched in pathways related to viral infection and immune response. These three cell populations exhibited high proportions and significant changes after infection, suggesting a strong immune response to ALV-J infection. Additionally, during ALV-J infection, the proportion of regulatory T cells and CTLA4 T cells increased, while immune suppressive factors TGFB1 and IL16 were highly expressed across the cell populations, indicating an immune-suppressive state in bone marrow lymphocytes. Moreover, ALV-J infected all cell populations; however, within the same cluster, only a fraction of the cells expressed ALV-J viral genes. Notably, in all cells expressing ALV-J viral genes, the "Rho family GTPase signaling pathway" associated with antiviral responses was activated. The Rho family, which is a key regulator of cytoskeletal reorganization and cell polarity, also plays a critical role in tumor cell proliferation and metastasis. Further analysis using Ingenuity Pathway Analysis (IPA) software predicted key upstream regulators of immune response, such as MYC and MCYN. In conclusion, this study identifies key genes and signaling pathways involved in immune responses of different lymphocyte subpopulations triggered by ALV-J infection in bone marrow. These findings contribute to a better understanding of the immune mechanisms in ALV-J-infected bone marrow lymphocytes and provide insights for discovering breeding loci for ALV-J resistance.

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

Mammalian spermatogenesis is a complex biological process that is regulated by multiple types of cells. The heterogeneity of these cells poses a challenge for analyzing different cell types at different developmental stages. To characterize the transcriptomic landscape of porcine spermatogenesis and identify potential marker genes for spermatogonia, an unbiased transcriptomic study of spermatogenesis in neonatal and sexually mature six-month-old Meihua pigs was performed using 10× Genomics single-cell RNA sequencing (scRNA-seq). Through the collection of scRNA-seq data from 13,839 cells from Meihua pig testes, three germ cells (spermatogonia, spermatocytes and spermatids) and eight somatic cells (Sertoli cells, Leydig cells, myoid/stromal cells, endothelial cells, T cells/macrophages and erythroblasts) were identified. Pseudo-timing analysis showed that myoid cells and stromal cells originated from common progenitors in Meihua pigs. Functional enrichment analysis revealed that the differentially expressed genes (DEGs) in testicular somatic cells were enriched in the pathways of Ribosome, Oxidative phosphorylation, Protein processing in endoplasmic reticulum, Retrograde endocannabinoid signaling, Cellular senescence and Insulin signaling. Meanwhile, in the three different germ cells, except for pathways which were the same as the first three pathways for somatic cells, DEGs were also enriched in the Spliceosome, Cell cycle, Autophagy and Mitophagy pathways. Furthermore, the candidate marker gene TKTL1 in spermatogonia was identified using immunohistochemistry and immunofluorescence. In conclusion, we collected transcription datasets and constructed single-cell developmental maps of germ cells and somatic cells during the testicular development of Meihua pigs, which provided new insights into the spermatogenesis of Meihua pigs and the development of various types of cells in their testes.

A Review and New Insights Into Spermatogenesis From Single-Cell RNA Sequencing

As the most primitive germ cells in the testis, spermatogonial stem cells (SSCs) not only constantly renew themselves to ensure their quantity, but also differentiate into mature sperm cells to complete spermatogenesis and transmit genetic information to the next generation. Successful spermatogenesis is inseparable from niche regulation, which provides factors that enhance the self-renewal of SSCs to maintain their numbers and directs the appropriate differentiation of spermatogonia. Some progress has been achieved in the definition and isolation of SSCs. However, a high degree of cellular heterogeneity is found in the testis, revealing a combination of various cell types at different developmental stages and a lack of specific molecular markers (especially in domestic animals) for fully screening and purifying SSCs. These factors have considerably hindered further research into the mechanisms of maintenance, self-renewal, and differentiation of SSCs, as well as limited their isolation, purification, and applications. Accumulated studies have recently successfully employed single-cell RNA sequencing (scRNA-seq) as a novel approach to detailing the classification of cell subsets, mining specifically expressed genes in different cell types, and accurate identification of specific cell types. This review summarises the progress of SSCs identification and offers new insights into the SSCs developmental trajectory from single-cell RNA sequencing.

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 the critical role of alternative splicing in cattle testicular spermatagonia

Spermatogonial stem cells (SSCs) form haploid gametes through the precisely regulated process of spermatogenesis. Within the testis, SSCs undergo self-renewal through mitosis, differentiation, and then enter meiosis to generate mature spermatids. This study utilized single-cell RNA sequencing on 26,888 testicular cells obtained from five Holstein bull testes, revealing the presence of five distinct germ cell types and eight somatic cell types in cattle testes. Gene expression profiling and enrichment analysis were utilized to uncover the varied functional roles of different cell types involved in cattle spermatogenesis. Additionally, unique gene markers specific to each testicular cell type were identified. Moreover, differentially expressed genes in spermatogonia exhibited notable enrichment in GO terms and KEGG pathway linked to alternative splicing. Notably, our study has shown that the activity of the YY1 regulation displays distinct expression patterns in spermatogonia, specifically targeting spliceosome proteins including RBM39, HNRNPA2B1, HNRNPH3, CPSF1, PCBP1, SRRM1, and SRRM2, which play essential roles in mRNA splicing. These results emphasize the importance of mRNA processing in spermatogonia within cattle testes, providing a basis for further investigation into their involvement in spermatogonial development.

Innovative Insights into Single-Cell Technologies and Multi-Omics Integration in Livestock and Poultry

In recent years, single-cell RNA sequencing (scRNA-seq) has marked significant strides in livestock and poultry research, especially when integrated with multi-omics approaches. These advancements provide a nuanced view into complex regulatory networks and cellular dynamics. This review outlines the application of scRNA-seq in key species, including poultry, swine, and ruminants, with a focus on outcomes related to cellular heterogeneity, developmental biology, and reproductive mechanisms. We emphasize the synergistic power of combining scRNA-seq with epigenomic, proteomic, and spatial transcriptomic data, enhancing molecular breeding precision, optimizing health management strategies, and refining production traits in livestock and poultry. The integration of these technologies offers a multidimensional approach that not only broadens the scope of data analysis but also provides actionable insights for improving animal health and productivity.

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.

Advances in single-cell transcriptomics in animal research

Understanding biological mechanisms is fundamental for improving animal production and health to meet the growing demand for high-quality protein. As an emerging biotechnology, single-cell transcriptomics has been gradually applied in diverse aspects of animal research, offering an effective method to study the gene expression of high-throughput single cells of different tissues/organs in animals. In an unprecedented manner, researchers have identified cell types/subtypes and their marker genes, inferred cellular fate trajectories, and revealed cell‒cell interactions in animals using single-cell transcriptomics. In this paper, we introduce the development of single-cell technology and review the processes, advancements, and applications of single-cell transcriptomics in animal research. We summarize recent efforts using single-cell transcriptomics to obtain a more profound understanding of animal nutrition and health, reproductive performance, genetics, and disease models in different livestock species. Moreover, the practical experience accumulated based on a large number of cases is highlighted to provide a reference for determining key factors (e.g., sample size, cell clustering, and cell type annotation) in single-cell transcriptomics analysis. We also discuss the limitations and outlook of single-cell transcriptomics in the current stage. This paper describes the comprehensive progress of single-cell transcriptomics in animal research, offering novel insights and sustainable advancements in agricultural productivity and animal health.

Single-Nucleus RNA-Seq Reveals Spermatogonial Stem Cell Developmental Pattern in Shaziling Pigs

Normal testicular development ensures the process of spermatogenesis, which is a complex biological process. The sustained high productivity of spermatogenesis throughout life is predominantly attributable to the constant proliferation and differentiation of spermatogonial stem cells (SSCs). The self-renewal and differentiation processes of SSCs are strictly regulated by the SSC niche. Therefore, understanding the developmental pattern of SSCs is crucial for spermatogenesis. The Shaziling pig is a medium-sized indigenous pig breed originating from central China. It is renowned for its superior meat quality and early male sexual maturity. The spermatogenic ability of the boars is of great economic importance to the pig industry. To investigate testicular development, particularly the pattern of SSC development in Shaziling pigs, we used single-cell transcriptomics to identify gene expression patterns in 82,027 individual cells from nine Shaziling pig testes at three key postnatal developmental stages. We generated an unbiased cell developmental atlas of Shaziling pig testicular tissues. We elucidated the complex processes involved in the development of SSCs within their niche in the Shaziling pig. Specifically, we identified potential marker genes and cellular signaling pathways that regulate SSC self-renewal and maintenance. Additionally, we proposed potential novel marker genes for SSCs that could be used for SSC isolation and sorting in Shaziling pigs. Furthermore, by immunofluorescence staining of testicular tissues of different developmental ages using marker proteins (UCHL1 and KIT), the developmental pattern of the spermatogonia of Shaziling pigs was intensively studied. Our research enhances the comprehension of the development of SSCs and provides a valuable reference for breeding Shaziling pigs.

CFAP58 is involved in the sperm head shaping and flagellogenesis of cattle and mice

CFAP58 is a testis-enriched gene that plays an important role in the sperm flagellogenesis of humans and mice. However, the effect of CFAP58 on bull semen quality and the underlying molecular mechanisms involved in spermatogenesis remain unknown. Here, we identified two single-nucleotide polymorphisms (rs110610797, A>G and rs133760846, G>T) and one indel (g.-1811_ g.-1810 ins147bp) in the promoter of CFAP58 that were significantly associated with semen quality of bulls, including sperm deformity rate and ejaculate volume. Moreover, by generating gene knockout mice, we found for the first time that the loss of Cfap58 not only causes severe defects in the sperm tail, but also affects the manchette structure, resulting in abnormal sperm head shaping. Cfap58 deficiency causes an increase in spermatozoa apoptosis. Further experiments confirmed that CFAP58 interacts with IFT88 and CCDC42. Moreover, it may be a transported cargo protein that plays a role in stabilizing other cargo proteins, such as CCDC42, in the intra-manchette transport/intra-flagellar transport pathway. Collectively, our findings reveal that CFAP58 is required for spermatogenesis and provide genetic markers for evaluating semen quality in cattle.

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.

Integrated single cell transcriptome sequencing analysis reveals species-specific genes and molecular pathways for pig spermiogenesis

Mammalian spermatogenesis is a highly complicated and intricately organized process involving spermatogonia propagation (mitosis) and meiotic differentiation into mature sperm cells (spermiogenesis). In pigs, spermatogonia development and the role of somatic cells in spermatogenesis were previously investigated in detail. However, the characterization of key molecules fundamental to pig spermiogenesis remains less explored. Here we compared spermatogenesis between humans and pigs, focusing on spermiogenesis, by integrative testicular single-cell RNA sequencing (scRNA-seq) analysis. Human and pig testicular cells were clustered into 26 different groups, with cell-type-specific markers and signalling pathways. For spermiogenesis, pseudo-time analysis classified the lineage differentiation routes for round, elongated spermatids and spermatozoa. Moreover, markers and molecular pathways specific to each type of spermatids were examined for humans and pigs, respectively. Furthermore, high-dimensional weighted gene co-expression network analysis (hdWGCNA) identified gene modules specific for each type of human and pig spermatids. Hub genes (pig: SNRPD2.1 related to alternative splicing; human: CATSPERZ, Ca[2+] ion channel) potentially involved in spermiogenesis were also revealed. Taken together, our integrative analysis found that human and pig spermiogeneses involve specific genes and molecular pathways and provided resources and insights for further functional investigation on spermatid maturation and male reproductive ability.