The adult human testis transcriptional cell atlas

scRNA-seq and scATAC-seq reveal that Sertoli cell mediates spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia

Non-obstructive azoospermia (NOA) belongs to male infertility due to spermatogenesis failure. However, evidence for cell type-specific abnormalities of spermatogenesis disorders in NOA remains lacking. We performed single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on testicular tissues from patients with obstructive azoospermia (OA) and NOA. HE staining confirmed the structural abnormalities of the seminiferous tubules in NOA patients. We identified 12 germ cell subtypes (spermatogonial stem cell-0 [SSC0], SSC1, SSC2, diffing-spermatogonia [Diffing-SPG], diffed-spermatogonia [Diffed-SPG], pre-leptotene [Pre-Lep], leptotene-zygotene [L-Z], pachytene [Pa], diplotene [Di], spermatids-1 [SPT1], SPT2, and SPT3) and 8 Sertoli cell subtypes (SC1-SC8). Among them, three novel Sertoli cell subtype phenotypes were identified, namely SC4/immature, SC7/mature, and SC8/further mature Sertoli cells. For each germ or Sertoli cell subtype, we identified unique new markers, among which immunofluorescence confirmed co-localization of ST3GAL4, A2M, ASB9, and TEX19 and DDX4 (classical marker of germ cell). PRAP1, BST2, and CCDC62 were co-expressed with SOX9 (classical marker of Sertoli cell) in testes tissues also confirmed by immunofluorescence. The interaction between germ cell subtypes and Sertoli cell subtypes exhibits stage-specific-matching pattern, as evidenced by SC1/2/5/7 involving in SSC0-2 development, SC3 participating in the whole process of spermiogenesis, SC4/6 participating in Diffing and Diffed-SPG development, and SC8 involving in the final stage of SPT3. This pattern of specific interactions between subtypes of germ cell and Sertoli cell was confirmed by immunofluorescence of novel markers in testes tissues. The interaction was mainly regulated by the Notch1/2/3 signaling. Our study profiled the single-cell transcriptome of human spermatogenesis and provided many potential molecular markers for developing testicular puncture-specific marker kits for NOA patients.

Expression profile of Chchd10 gene during testicular development

Chchd10 protein is crucial for sustaining mitochondrial dynamics, physiology and functions, and has been reported to be most abundantly in myocardial cells and skeletal muscle. However, nothing is known for the expression pattern of Chchd10 in gonadal development. Here, we characterized the expression patterns of Chchd10 gene during embryonic gonad development and postnatal testis development in mice, as well as the expression pattern of Chchd10 gene in human puberty testis and young adult testis using publicly available datasets. Besides, we investigated the expression and distribution of Chchd10 in mice testis by RT-qPCR and immunofluorescence and analyzed the possible role and mechanism of Chchd10 in the testis. We noticed that Chchd10 showed abundant expression in embryonic testis compared to ovaries and dynamically expressed during embryonic and postnatal testis development in mice. In addition, Chchd10 was highly abundant within testicular Sertoli cells populations both in embryonic and postnatal mice and mainly located in the mitochondria of Sertoli cells in mice. Furthermore, CHCHD10 was not only enriched in Sertoli cells, but also highly expressed in tMΦ of human puberty testis and adult testis. CHCHD10 may participate in testicular development by regulating multiple biological processes of Sertoli cells. Taken together, our data indicated that Chchd10 appears to be important during testicular development, particularly in the functional modulation of Sertoli cells. Our study revealed the expression profile of Chchd10 gene during testicular development for the first time and will provide new ideas for further studying the function and molecular mechanism of Chchd10.

Identification of leukemia-enriched signature through the development of a comprehensive pediatric single-cell atlas

Single-cell transcriptome profiling enables unparalleled characterization of the heterogeneous microenvironment of pediatric leukemias. To facilitate comparative analyses and generate pediatric leukemia signatures, we collect, process, and annotate single-cell data comprising over 540,000 cells from 159 different pediatric acute leukemia (myeloid, lymphoid, mixed phenotype lineages) and healthy bone marrow (BM) samples, profiled in our lab and curated from publicly available studies. The analysis identifies a leukemia-enriched signature of nine genes with over-expression in leukemic blast compared to healthy BM cells. This signature is also consistently over-expressed in leukemia samples compared to normal BM in bulk RNA-seq datasets (over 2000 samples). Outcome-based analysis on diagnosis samples using measurable residual disease (MRD) status depicts a significant association of oncogene-induced senescence and g-protein activation pathways with MRD positivity. MRD positivity across pediatric leukemias is also correlated with significant depletion of CD8+ and CD4+ naïve T-cells and M1-macrophages at diagnosis. To enable easy access to this comprehensive pediatric leukemia single-cell atlas, we develop the Pediatric Single-cell Cancer Atlas (PedSCAtlas, https://bhasinlab.bmi.emory.edu/PediatricSCAtlas/ ). The atlas allows for quick exploration of single-cell data based on genes, cell type composition, and clinical outcomes to understand the cellular landscape of pediatric leukemias.

Adrenocorticotropic hormone and its receptor as a novel testicular system involves in the development of spermatogenesis

AIMS

To identify functional membrane-associate-specific SSC markers and examine the development of these cells under in vitro conditions.

MATERIALS AND METHODS

Cells were enzymatically isolated from seminiferous tubules (STs) of immature mice. Spermatogonial cells (Thy1, alpha-6-integrin, and C-KIT) were sorted by FACS. RNA was extracted from these cells for RNAseq analysis. The effect of adrenocorticotropic hormone (ACTH) - the ligand of MC2R- on the development of mouse spermatogonial cells was performed in vitro using a methylcellulose culture system (MCS). Immunofluorescence staining was used to localize MC2R-positive cells in the testes of immature and adult humans and mice and testes of busulfan-treated immature mice.

KEY FINDINGS

Our RNAseq analysis revealed a high expression of melanocortin receptor 2 (MC2R) in Thy1-positive sorted cells. MC2R-positive cells were localized in the periphery of the STs of humans (prepubertal and adults) and mice at immature and adult ages (normal and busulfan-treated mice). MC2R was doubled stained with PLZF and CDH1 (SSC markers). ACTH was localized in mouse testicular germ cells (pre-meiotic, meiotic, and post-meiotic cells) and somatic cells (Sertoli, Leydig, and peritubular cells). The addition of ACTH to isolated cells from mouse STs in MCS significantly increased the development of pre-meiotic and meiotic/post-meiotic cells in vitro.

SIGNIFICANCE

We were able to identify, for the first time, a novel membrane-associated and functional SSC marker (MC2R) with relation to ACTH. This marker can be used in future male fertility preservation strategies. Furthermore, we explored a novel testicular system (ACTH system) that regulates the development of spermatogenesis.

RGS14 binds to GNAI3 and regulates the proliferation and apoptosis of human spermatogonial stem cells by affecting PLPP2 expression and MAPK signaling

Background

Non-obstructive azoospermia (NOA) represents a severe form of male infertility, characterized by the absence of sperm in the ejaculate due to impaired spermatogenesis. Spermatogonial stem cells (SSCs), which ensure continuous sperm production, are critical for maintaining male fertility. Despite their importance, the molecular mechanisms governing SSC fate determination and their role in NOA pathogenesis remain incompletely understood. This study investigates the regulatory networks underlying SSC dysfunction in NOA patients.

Results

Using single-cell RNA sequencing, we identified significant downregulation of RGS14 in SSCs of NOA patients compared to normal testes. Immunofluorescence validation confirmed RGS14 localization primarily in SSCs. Functional assays demonstrated that RGS14 knockdown in SSC lines markedly suppressed cell proliferation and induced apoptosis. RNA-sequencing analyses revealed that RGS14 deficiency inhibited PLPP2 expression and MAPK signaling activation. Notably, PLPP2 overexpression rescued the phenotypic defects caused by RGS14 depletion. Protein-protein interaction assays and co-immunoprecipitation experiments further established that RGS14 physically interacts with GNAI3 to coordinately regulate cell proliferation and PLPP2 expression. Expression validation in NOA testes demonstrated concurrent downregulation of GNAI3 and PLPP2 in NOA patients, implicating their dysregulation in spermatogenic failure.

Conclusion

Our findings uncover a novel RGS14-GNAI3-PLPP2 regulatory axis critical for SSC homeostasis. The dysregulation of these molecules contributes to SSC dysfunction and NOA pathogenesis. These data not only elucidate RGS14's role in SSC fate determination but also identify RGS14 and its interactome as promising therapeutic targets for restoring spermatogenesis in male infertility.

CITED2 Binding to EP300 Regulates Human Spermatogonial Stem Cell Proliferation and Survival Through HSPA6

Spermatogonial stem cells (SSCs) are essential for the initiation and continuation of spermatogenesis, a process fundamental to male fertility. Despite extensive studies on mouse SSCs, the mechanisms governing self-renewal and differentiation in human SSCs remain to be elucidated. This study investigated the regulatory mechanisms of SSCs by analyzing single-cell sequencing data from the GEO dataset of human testis. Analysis revealed dominant expression of CITED2 in human SSCs. Reduction of CITED2 levels in hSSC lines significantly inhibited proliferation and increased apoptosis. Protein interaction prediction and immunoprecipitation identified interactions between CITED2 and EP300 in SSC lines. RNA sequencing results indicated that CITED2 knockdown significantly affected the MAPK pathway and the HSPA6 gene. Overexpression of HSPA6 mitigated the proliferative and apoptotic changes provoked by CITED2 downregulation. These findings provide novel insights into the regulatory and functional mechanisms of CITED2-mediated hSSC development.

Applications of spatial transcriptomics in studying spermatogenesis

Spermatogenesis is a complex differentiation process that is facilitated by a series of cellular and molecular events. High-throughput genomics approaches, such as single-cell RNA sequencing, have begun to enable the systematic characterization of these events. However, the loss of tissue context because of tissue disassociations in the single-cell isolation protocols limits our ability to understand the regulation of spermatogenesis and how defects in spermatogenesis lead to infertility. The recent advancement of spatial transcriptomics technologies enables the studying of the molecular signatures of various cell types and their interactions in the native tissue context. In this review, we discuss how spatial transcriptomics has been leveraged to identify spatially variable genes, characterize cellular neighborhood, delineate cell‒cell communications, and detect molecular changes under pathological conditions in the mammalian testis. We believe that spatial transcriptomics, along with other emerging spatially resolved omics assays, can be utilized to further our understanding of the underlying causes of male infertility, and to facilitate the development of new treatment approaches.

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 transcriptomic atlas of the human testis across the reproductive lifespan

Testicular aging is associated with declining reproductive health, but the molecular mechanisms are unclear. Here we generate a dataset of 214,369 single-cell transcriptomes from testicular cells of 35 individuals aged 21-69, offering a resource for studying testicular aging and physiology. Machine learning analysis reveals a stronger aging response in somatic cells compared to germ cells. Two waves of aging-related changes are identified: the first in peritubular cells of donors in their 30s, marked by increased basement membrane thickness, indicating a priming state for aging. In their 50s, testicular cells exhibit functional changes, including altered steroid metabolism in Leydig cells and immune responses in macrophages. Further analyses reveal the impact of body mass index on spermatogenic capacity as age progresses, particularly after age 45. Altogether, our findings illuminate molecular alterations during testis aging and their relationship with body mass index, providing a foundation for future research and offering potential diagnostic markers and therapeutic targets.

SIRT7 links H3K36ac epigenetic regulation with genome maintenance in the aging mouse testis

Reproductive aging is an increasing health concern affecting family planning and overall well-being. While extensively studied in females, the mechanisms driving male reproductive aging remain largely unexamined. Here we found that mammalian Sirtuin 7 (SIRT7) sustains spermatogenesis in an age-dependent manner through the control of histone 3 lysine 36 acetylation (H3K36ac). SIRT7 deficiency in mice resulted in increased levels of H3K36ac in spermatogonia and spermatocytes. In a germ cell line, SIRT7 deficiency disrupted nucleosome stability and increased vulnerability to genotoxic stress. Importantly, undifferentiated spermatogonia, which are required for continuous sperm production, decreased prematurely in Sirt7 -/- mice and showed genome damage accumulation. These changes were concurrent with age-dependent defects in homologous chromosome synapsis and partial meiotic arrest. Taken together, our results indicate that SIRT7 connects H3K36ac epigenetic regulation to long-term genome stability in male germ cells, ensuring steady-state spermatogenesis during the lengthy male reproductive lifespan.

3D Bioprinted Coaxial Testis Model Using Human Induced Pluripotent Stem Cells:A Step Toward Bicompartmental Cytoarchitecture and Functionalization

Fertility preservation following pediatric cancer therapy programs has become a major avenue of infertility research. In vitro spermatogenesis (IVS) aims to generate sperm from banked prepubertal testicular tissues in a lab setting using specialized culture conditions. While successful using rodent tissues, progress with human tissues is limited by the scarcity of human prepubertal testicular tissues for research. This study posits that human induced pluripotent stem cells (hiPSCs) can model human prepubertal testicular tissue to facilitate the development of human IVS conditions. Testicular cells derived from hiPSCs are characterized for phenotype markers and profiled transcriptionally. HiPSC-derived testicular cells are bioprinted into core-shell constructs representative of testis cytoarchitecture and found to capture functional aspects of prepubertal testicular tissues within 7 days under xeno-free conditions. Moreover, hiPSC-derived Sertoli cells illustrate the capacity to mature under pubertal-like conditions. The utility of the model is tested by comparing 2 methods of supplementing retinoic acid (RA), the vitamin responsible for inducing spermatogenesis. The model reveals a significant gain in activity under microsphere-released RA compared to RA medium supplementation, indicating that the fragility of free RA in vitro may be a contributing factor to the molecular dysfunction observed in human IVS studies to date.

Reference-informed evaluation of batch correction for single-cell omics data with overcorrection awareness

Batch effect correction (BEC) is fundamental to integrate multiple single-cell RNA sequencing datasets, and its success is critical to empower in-depth interrogation for biological insights. However, no simple metric is available to evaluate BEC performance with sensitivity to data overcorrection, which erases true biological variations and leads to false biological discoveries. Here, we propose RBET, a reference-informed statistical framework for evaluating the success of BEC. Using extensive simulations and six real data examples including scRNA-seq and scATAC-seq datasets with different numbers of batches, batch effect sizes and numbers of cell types, we demonstrate that RBET evaluates the performance of BEC methods more fairly with biologically meaningful insights from data, while other methods may lead to false results. Moreover, RBET is computationally efficient, sensitive to overcorrection and robust to large batch effect sizes. Thus, RBET provides a robust guideline on selecting case-specific BEC method, and the concept of RBET is extendable to other modalities.

Mechanisms of Hormonal, Genetic, and Temperature Regulation of Germ Cell Proliferation, Differentiation, and Death During Spermatogenesis

Spermatogenesis is a complex and highly regulated process involving the proliferation, differentiation, and apoptosis of germ cells. This process is controlled by various hormonal, genetic, and environmental factors, including temperature. In hormonal regulation, follicle-stimulating hormone (FSH), luteinizing hormone (LH), and testosterone (T) are essential for correct spermatogenesis development from the early stages and spermatogonia proliferation to germ cell maturation. Other hormones, like inhibin and activin, finely participate tuning the process of spermatogenesis. Genetic regulation involves various transcription factors, such as SOX9, SRY, and DMRT1, which are crucial for the development and maintenance of the testis and germ cells. MicroRNAs (miRNAs) play a significant role by regulating gene expression post-transcriptionally. Epigenetic modifications, including DNA methylation, histone modifications, and chromatin remodelling, are also vital. Temperature regulation is another critical aspect, with the testicular temperature maintained around 2-4 °C below body temperature, essential for efficient spermatogenesis. Heat shock proteins (HSPs) protect germ cells from heat-induced damage by acting as molecular chaperones, ensuring proper protein folding and preventing the aggregation of misfolded proteins during thermal stress. Elevated testicular temperature can impair spermatogenesis, increasing germ cell apoptosis and inducing oxidative stress, DNA damage, and the disruption of the blood-testis barrier, leading to germ cell death and impaired differentiation. The cellular mechanisms of germ cell proliferation, differentiation, and death include the mitotic divisions of spermatogonia to maintain the germ cell pool and produce spermatocytes. Spermatocytes undergo meiosis to produce haploid spermatids, which then differentiate into mature spermatozoa. Apoptosis, or programmed cell death, ensures the removal of defective germ cells and regulates the germ cell population. Hormonal imbalance, genetic defects, and environmental stress can trigger apoptosis during spermatogenesis. Understanding these mechanisms is crucial for addressing male infertility and developing therapeutic interventions. Advances in molecular biology and genetics continue to uncover the intricate details of how spermatogenesis is regulated at multiple levels, providing new insights and potential targets for treatment.

Essential Regulation of Spermatogonial Stem Cell Fate Decisions and Male Fertility by APBB1 via Interaction with KAT5 and GDF15 in Humans and Mice

Spermatogonial stem cells (SSCs) are essential for initiating and maintaining normal spermatogenesis, and notably, they have important applications in both reproduction and regenerative medicine. Nevertheless, the molecular mechanisms controlling the fate determinations of human SSCs remain elusive. In this study, we identified a selective expression of APBB1 in dormant human SSCs. We demonstrated for the first time that APBB1 interacted with KAT5, which led to the suppression of GDF15 expression and consequent inhibition of human SSC proliferation. Intriguingly, Apbb1-/- mice assumed the disrupted spermatogenesis and markedly reduced fertility. SSC transplantation assays revealed that Apbb1 silencing enhanced SSC colonization and impeded their differentiation, which resulted in the impaired spermatogenesis. Notably, 4 deleterious APBB1 mutation sites were identified in 2,047 patients with non-obstructive azoospermia (NOA), and patients with the c.1940C>G mutation had a similar testicular phenotype with Apbb1-/- mice. Additionally, we observed lower expression levels of APBB1 in NOA patients with spermatogenic arrest than in obstructive azoospermia patients with normal spermatogenesis. Collectively, our findings highlight an essential role of APBB1/KAT5/GDF15 in governing human SSC fate decisions and maintaining normal spermatogenesis and underscore them as therapeutic targets for treating male infertility.

High resolution tissue and cell type identification via single cell transcriptomic profiling

Tissue identification can be instrumental in reconstructing a crime scene but remains a challenging task in forensic investigations. Conventionally, identifying the presence of certain tissue from tissue mixture by predefined cell type markers in bulk fashion is challenging due to limitations in sensitivity and accuracy. In contrast, single-cell RNA sequencing (scRNA-Seq) is a promising technology that has the potential to enhance or even revolutionize tissue and cell type identification. In this study, we developed a high sensitive general purpose single cell annotation pipeline, scTissueID, to accurately evaluate the single cell profile quality and precisely determine the cell and tissue types based on scRNA profiles. By incorporating a crucial and unique reference cell quality differentiation phase of targeting only high confident cells as reference, scTissueID achieved better and consistent performance in determining cell and tissue types compared to 8 state-of-art single cell annotation pipelines and 6 widely adopted machine learning algorithms, as demonstrated through a large-scale and comprehensive comparison study using both forensic-relevant and Human Cell Atlas (HCA) data. We highlighted the significance of cell quality differentiation, a previously undervalued factor. Thus, this study offers a tool capable of accurately and efficiently identifying cell and tissue types, with broad applicability to forensic investigations and other biomedical research endeavors.

CTCF-anchored chromatin loop dynamics during human meiosis

BACKGROUND

During meiosis, the mammalian genome is organised within chromatin loops, which facilitate synapsis, crossing over and chromosome segregation, setting the stage for recombination events and the generation of genetic diversity. Chromatin looping is thought to play a major role in the establishment of cross overs during prophase I of meiosis, in diploid early primary spermatocytes. However, chromatin conformation dynamics during human meiosis are difficult to study experimentally, due to the transience of each cell division and the difficulty of obtaining stage-resolved cell populations. Here, we employed a machine learning framework trained on single cell ATAC-seq and RNA-seq data to predict CTCF-anchored looping during spermatogenesis, including cell types at different stages of meiosis.

RESULTS

We find dramatic changes in genome-wide looping patterns throughout meiosis: compared to pre-and-post meiotic germline cell types, loops in meiotic early primary spermatocytes are more abundant, more variable between individual cells, and more evenly spread throughout the genome. In preparation for the first meiotic division, loops also include longer stretches of DNA, encompassing more than half of the total genome. These loop structures then influence the rate of recombination initiation and resolution as cross overs. In contrast, in later mature sperm stages, we find evidence of genome compaction, with loops being confined to the telomeric ends of the chromosomes.

CONCLUSION

Overall, we find that chromatin loops do not orchestrate the gene expression dynamics seen during spermatogenesis, but loops do play important roles in recombination, influencing the positions of DNA breakage and cross over events.

Single-cell sequencing in non-obstructive azoospermia: insights from primary and re-analysis studies

Non-obstructive azoospermia (NOA) constitutes one of the most severe forms of male infertility. Recent advancements in single-cell sequencing have significantly contributed to understanding the molecular landscape of NOA in human testicular tissues, elucidating the factors that underpin spermatogenic dysfunction. This technology has improved our understanding of the condition at a cellular level. Concurrently, bioinformatics developments have facilitated the re-analysis of publicly available single-cell datasets, offering novel insights into the disorder. Nevertheless, a comprehensive review integrating primary and re-analysis studies of single-cell sequencing in NOA is lacking. This review systematically evaluates 10 primary studies reporting original single-cell sequencing data of human NOA testicular samples and 22 secondary studies that re-analyzed these published data. We explore single-cell sequencing applications in germ cells, Sertoli cells, and Leydig cells, offering a comprehensive overview of molecular insights into spermatogenic dysfunction. Our review highlights novel findings in secondary studies, including the roles of transcriptional regulators, RNA transcription, endocrine disruptors, and microtubular cytoskeleton, thereby bridging primary studies and re-analysis studies. Additionally, we discussed future research directions and the challenges of translating single-cell research findings into clinical applications. In summary, single-cell sequencing offers a high-resolution, single-cell perspective of NOA testicular tissue, paving the way for innovative therapeutic strategies in male infertility.

Transcriptomic and metabolic profiling reveals the effects of long-term microwave exposure on testicular tissue

The effect of electromagnetic exposure on health is becoming increasingly important as it affects many aspects of human life and health. However, the effects in environmental electromagnetic fields on the male reproductive system were still controversial, and the impacts of long-term microwave exposure on testicular tissue remain poorly defined. This study exposed rats to 30 mW/cm2 of microwave radiation (2.856 GHz) for six weeks and revealed that long-term microwave exposure damaged the testis structures, sperm motility, and morphology, affected hormone levels, energy metabolism, and induced oxidative stress. Assays for bulk RNA, metabonomics, single-cell RNA, and transposase-accessible chromatin with high-throughput sequencing were performed to analyze the transcriptional and metabolic atlas of testicular damage after microwave radiation. Differentially expressed genes were enriched in oxidative stress and energy metabolism pathways. Furthermore, ten subgroups were identified with scRNA-seq, including five developmental phases of germ cells, and radiation-associated changes in cell composition, especially stuck in round spermatids, were observed. Radiation significantly upregulated the expression of Atp6v1e2 in round spermatids and enriched the expression of many transcription factors by disturbing the accessibility profile of chromatin. This study provides effective insights into the long-term impacts of microwave radiation on male reproduction.

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.

The circadian clock orchestrates spermatogonial differentiation and fertilization by regulating retinoic acid signaling in vertebrates

The circadian clock generates and maintains ∼24-hour oscillations in almost all organs. The testis, however, remains mysterious, without a clear understanding of its circadian functions. Our time-series transcriptome analysis reveals more than 1000 rhythmically expressed genes in the zebrafish and mouse testes, respectively. Canonical circadian clock genes are rhythmically expressed in Sertoli cells and regulate retinoic acid (RA) production, which is also evidenced by their co-expression with RA synthesis genes in single Sertoli cells. Genetic and pharmacological manipulations and temporal desynchronization revealed that the circadian clock-regulated RA signaling synchronizes spermatogonial differentiation via zbtb16a and promotes fertilization via izumo1 in zebrafish. Our findings indicate that the testicular circadian clock contributes to reproduction in a cell-specific manner through RA signaling, highlighting circadian roles in male fertility.

Unveiling Leydig cell heterogeneity and its role in male infertility: A single-cell transcriptomic study of human testicular tissue

Male infertility and impaired spermatogenesis are significant concerns in reproductive health, often linked to disruptions in the cellular and molecular processes within the testis. The cellular composition and transcriptional dynamics of human testicular tissue are crucial for understanding these issues. Previous studies have largely relied on bulk tissue analysis, which obscures the distinct roles and interactions of specific cell types. Here, through a comprehensive single-cell transcriptomic analysis of human testes across various developmental stages and pathological conditions, we reveal the intricate cellular heterogeneity and the molecular mechanisms underlying testicular function. Our study identifies significant disruptions in the differentiation trajectories of Germ cells in conditions such as Klinefelter syndrome (KS), AZFa deletion, and Sertoli-cell-only syndrome (SCOS). We further uncover key transcription factors and regulatory networks governing Leydig cell function, particularly those related to steroidogenesis and hormonal regulation. These findings highlight the organized yet complex cellular and molecular landscape of the testis and uncover critical pathways altered in male infertility. Collectively, our data suggest that targeted therapeutic strategies could be developed to address specific disruptions in testicular cell populations and their associated regulatory networks.

Single-cell RNA-seq and pathological phenotype reveal the functional atlas and precise roles of Sox30 in testicular cell development and differentiation

Sox30 has recently been demonstrated to be a key regulator of spermatogenesis. However, the precise roles of Sox30 in the testis remain largely unclear. Here, the specific functions of Sox30 in testicular cells were determined by single-cell sequencing and confirmed via pathological analyses. Sox30 loss appears to damage all testicular cells to different extents. Sox30 chiefly drives the differentiation of primary spermatocytes. Sox30 deficiency causes spermatocyte arrest at the early phase of meiosis I, with nearly no normally developing second spermatocytes and three new spermatocyte -subclusters emerging. In addition, Sox30 seems to play important roles in the mature phenotypes of Sertoli and Leydig cells, and the proliferation and differentiation of spermatogonia. The developmental trajectory of germ cells begins with spermatogonia and splits into two different spermatocyte branches, with Sox30-null spermatocytes and wild-type spermatocytes placed at divergent ends. An opposite developmental trajectory of spermatocyte subclusters is observed, followed by incomplete development of spermatid subclusters in Sox30-null mice. Sox30 deficiency clearly alters the intercellular cross-talk of major testicular cells and dysregulates the transcription factor networks primarily involved in cell proliferation and differentiation. Mechanistically, Sox30 appears to have similar terminal functions that are involved mainly in spermatogenic development and differentiation among major testicular cells, and Sox30 performs these similar crucial roles through preferential regulation of different signalling pathways. Our study describes the exact functions of Sox30 in testicular cell development and differentiation and highlights the primary roles of Sox30 in the early meiotic phase of germ cells.

An integrated transcriptomic analysis unveils the regulatory roles of RNA binding proteins during human spermatogenesis

Background

RNA-binding proteins (RBPs) have emerged as key regulators in testis development and spermatogenesis, yet a comprehensive understanding of their expression dynamics has been lacking.

Methods

This study leverages published single-cell RNA sequencing (scRNA-seq) data to elucidate the complex expression patterns of RBP genes during postnatal testis development and spermatogenesis. Additionally, it uses bulk RNA-seq data to explore the regulatory impact of RBPs on alternative splicing (AS) in non-obstructive azoospermia (NOA).

Results

We have identified cell-specific RNA-binding protein (RBP) genes in various cell types throughout testis development. Notably, distinct RBP gene clusters exhibit significant differential expression, particularly in Sertoli cells as they mature from neonatal to adult stages. Our analysis has revealed temporally-regulated RBP clusters that correlate with the developmental progression of Sertoli cells and the advancement of spermatogenesis. Moreover, we have established links between specific RBPs and the pathogenesis of non-obstructive azoospermia (NOA) through the regulation of alternative splicing (AS) events. Additionally, RPL10, RPL39, and SETX have been identified as potential diagnostic biomarkers for NOA.

Conclusion

This research provided an in-depth look at RBP expression patterns during human testis development and spermatogenesis. It not only deepens our basic comprehension of male fertility and infertility but also indicates promising directions for the creation of innovative diagnostic and treatment methods for NOA.

The use of deidentified organ donor testes for research

Our knowledge of testis development and function mainly comes from research using mammalian model organisms, primarily the mouse. However, there are integral differences between men and other mammalian species regarding cellular composition and expression profiles during fetal and post-natal testis development and in the mature testis. Therefore, to specifically learn more about human testis development and function, there is a need to use human testis tissue for research. Human testicular tissues that have been donated for research have allowed extensive molecular and cytological assessments, as well as single-cell transcriptome and epigenome analyses. These tissues have also been used for the development of cell technologies and in vitro models that aim to improve infertility treatments and diagnostics. Biopsied material taken from patients and designated for research is usually very small in size and is unsuitable for comprehensive studies. On the other hand, research using whole testes obtained from deceased, deidentified donors has become a valuable resource to assess conservation between humans and other organisms and identify human-specific phenomena. This review discusses the acquisition of donated deidentified human testes and their use for basic science research.

Integrated analysis and systematic characterization of the regulatory network for human germline development

Primordial germ cells (PGCs) are the precursors of germline that are specified at the embryonic stage. Recent studies reveal that humans employ different mechanisms for PGC specification compared with model organisms such as mice. Moreover, the specific regulatory machinery remains largely unexplored, mainly due to the inaccessible nature of this complex biological process in humans. Here, we curate and integrate multi-omics data, including 581 RNA-seq, 54 ATAC-seq, 45 ChIP-seq, and 69 single-cell RNA-seq samples from different stages of human PGC development to recapitulate the precisely controlled and stepwise process, presenting an atlas in the human PGC database (hPGCdb). With these uniformly processed data and integrated analyses, we characterize the potential key transcription factors and regulatory networks governing human germ cell fate. We validate the important roles of some of the key factors in germ cell development by CRISPRi knockdown. We also identify the soma-germline interaction network and discover the involvement of SDC2 and LAMA4 for PGC development, as well as soma-derived NOTCH2 signaling for germ cell differentiation. Taken together, we have built a database for human PGCs (http://43.131.248.15:6882) and demonstrate that hPGCdb enables the identification of the missing pieces of mechanisms governing germline development, including both intrinsic and extrinsic regulatory programs.

Dynamic transcriptomic and regulatory networks underpinning the transition from fetal primordial germ cells to spermatogonia in mice

The transition from fetal primordial germ cells (PGCs) to spermatogonia (SPG) is critical for male germ cell development; however, the detailed transcriptomic dynamics and regulation underlying this transition remain poorly understood. Here by interrogating the comprehensive transcriptome atlas dataset of mouse male germ cells and gonadal cells development, we elucidated the regulatory networks underlying this transition. Our single-cell transcriptome analysis revealed that the transition from PGCs to SPG was characterized by global hypertranscription. A total of 315 highly active regulators were identified to be potentially involved in this transition, among which a non-transcription factor (TF) regulator TAGLN2 was validated to be essential for spermatogonial stem cells (SSCs) maintenance and differentiation. Metabolism profiling analysis also revealed dynamic changes in metabolism-related gene expression during PGC to SPG transition. Furthermore, we uncovered that intricate cell-cell communication exerted potential functions in the regulation of hypertranscription in germ cells by collaborating with stage-specific active regulators. Collectively, our work extends the understanding of molecular mechanisms underlying male germ cell development, offering insights into the recapitulation of germ cell generation in vitro.

Cross-species comparative single-cell transcriptomics highlights the molecular evolution and genetic basis of male infertility

In male animals, spermatogonia in testes differentiate into sperm, one of the most diverse cell types across species. Despite the evolutionary retention of key genes essential for spermatogenesis, the extent of their conservation remains unclear. To explore the genetic basis of spermatogenesis under strong selective pressure, we compare single-cell RNA sequencing (scRNA-seq) datasets from the testes of humans, mice, and fruit flies. Our analysis identifies conserved genes involved in key molecular programs, such as post-transcriptional regulation, meiosis, and energy metabolism. We perform gene knockout experiments of 20 candidate genes, three of which, when mutated in fruit flies, result in reduced male fertility, emphasizing the conservation of sperm centriole and steroid lipid processes across mammals and Drosophila. Additionally, deep-learning analysis uncovers potential transcriptional mechanisms driving gene-expression evolution. These findings establish a core genetic foundation for spermatogenesis, offering insights into sperm-phenotype evolution and the underlying mechanisms of male infertility.

Cyclin switch tailors a cell cycle variant to orchestrate multiciliogenesis

Meiosis, endoreplication, and asynthetic fissions are variations of the canonical cell cycle where either replication or mitotic divisions are muted. Here, we identify a cell cycle variantconserved across organs and mammals, where both replication and mitosis are muted, and that orchestrates the differentiation of post-mitotic progenitors into multiciliated cells (MCCs). MCC progenitors reactivate most of the cell cycle transcriptional program but replace the temporal expression of cyclins E2 and A2 with non-canonical cyclins O and A1. In addition, the primary APC/C inhibitor Emi1 is silenced. Re-expressing cyclins E2 and A2 and/or Emi1 can induce partial replication or mitosis. This shows that a cell can co-opt the cell cycle genetic program and regulate only certain elements to qualitatively and quantitatively divert CDK activity toward differentiation rather than division. We propose this cell cycle variant to exploit the existence of a cytoplasmic-or centriolar-CDK threshold lower than the S-phase threshold.

Construction of human pluripotent stem cell-derived testicular organoids and their use as humanized testis models for evaluating the effects of semaglutide

Background: The generation of human testicular organoids from human induced pluripotent stem cells (hiPSCs) presents exciting opportunities for gonadal developmental biology, and reproductive disease modeling. However, creating organoids that closely mimic the tissue structure of testes remains challenging. Methods: In this study, we established a method for generating testicular organoids (TOs) from hiPSCs using a stepwise differentiation approach and a combination of hanging drop and rotational culture systems. The capability of hiPSC-derived precursor testicular cells to self-assemble into organoids was confirmed by detection of morphology, single-cell RNA-sequencing, and protein profiles. The reliability of testicular organoids as a drug evaluation model was assessed by the measurements of transcriptome signatures and functional features, including hormone responsiveness and blood-testis barrier (BTB) formation, and drug sensitivity assessment by recording cell viability and BTB integrity in organoids exposed to reproductive toxicants. Finally, we applied testicular organoids to evaluate the effects of semaglutide, a glucagon-like peptide-1 receptor agonist (GLP-1 RA), on testicular function, thereby underscoring their utility as a model for drug evaluation. Results: These organoids exhibited testicular cord-like structures and BTB function. RNA sequencing and functional assays confirmed that testicular organoids possess gene expression profiles and endocrine functions regulated by gonadotropins, closely resembling those of testicular tissue. Notably, these organoids displayed sensitivity to semaglutide. Treatment with semaglutide resulted in reduced testosterone levels and downregulation of INHBB expression, aligning with previous clinical observations. Conclusions: These findings introduced a method for generating testicular organoids from human pluripotent stem cells, highlighting their potential as valuable models for studying testicular function, drug toxicity, and the effects of compounds like semaglutide on testicular health.

Insights from the single-cell level: lineage trajectory and somatic-germline interactions during spermatogenesis in dwarf surfclam Mulinia lateralis

BACKGROUND

Spermatogenesis is a complex process of cellular differentiation that commences with the division of spermatogonia stem cells, ultimately resulting in the production of functional spermatozoa. However, a substantial gap remains in our understanding of the molecular mechanisms and key driver genes that underpin this process, particularly in invertebrates. The dwarf surfclam (Mulinia lateralis) is considered an optimal bivalve model due to its relatively short generation time and ease of breeding in laboratory settings.

RESULTS

In this study, over 4,600 testicular cells from various samples were employed to identify single-cell heterogeneity on a more comprehensive scale. The four germ cell populations (spermatogonia, primary spermatocytes, secondary spermatocytes, and round spermatids/spermatozoa) and three somatic populations (follicle cell, hemocyte, and nerve cell) were characterized. The four types of germ cells exhibited disparate cell cycle statuses and an uninterrupted developmental trajectory, progressing from spermatogonia to spermatids/spermatozoa. Pseudotime analysis indicates that gene expression, translation, ATP metabolic process, and microtubule-based process are involved in the transition of germ cell types. Weighted gene coexpression network analysis (WGCNA) identified four modules corresponding to the four types of germ cells, as well as key transcription factors (e.g., MYC, SREBF1, SOXH) that may play a critical role in these cell types. Furthermore, our findings revealed that there is extensive bidirectional communication between the somatic cells and the germline cells, including the FGF and TGF-β signaling pathways, as well as other ligand-receptor pairs, such as NTN1-NEO1 and PLG-PLGRKT.

CONCLUSIONS

This study provides a comprehensive single-cell transcriptome landscape of the gonad, which will contribute to the understanding of germ cell fate transition during spermatogenesis, and the development of germ cell manipulation technologies in mollusks.

Classifying cell cycle states and a quiescent-like G0 state using single-cell transcriptomics

Single-cell transcriptomics has unveiled a vast landscape of cellular heterogeneity in which the cell cycle is a significant component. We trained a high-resolution cell cycle classifier (ccAFv2) using single cell RNA-seq (scRNA-seq) characterized human neural stem cells. The ccAFv2 classifies six cell cycle states (G1, Late G1, S, S/G2, G2/M, and M/Early G1) and a quiescent-like G0 state (Neural G0), and it incorporates a tunable parameter to filter out less certain classifications. The ccAFv2 classifier performed better than or equivalent to other state-of-the-art methods even while classifying more cell cycle states, including G0. We demonstrate that the ccAFv2 classifier effectively generalizes the S, S/G2, G2/M, and M/Early G1 states across cell types derived from all three germ layers. While the G0, G1, and Late G1 states perform well in neuroepithelial cell types, their accuracy is lower in other cell types. However, misclassifications are confined to the G0, G1, and Late G1 states. We showcased the versatility of ccAFv2 by successfully applying it to classify cells, nuclei, and spatial transcriptomics data in humans and mice, using various normalization methods and gene identifiers. We provide methods to regress the cell cycle expression patterns out of single cell or nuclei data to uncover underlying biological signals. The classifier can be used either as an R package integrated with Seurat or a PyPI package integrated with SCANPY. We proved that ccAFv2 has enhanced accuracy, flexibility, and adaptability across various experimental conditions, establishing ccAFv2 as a powerful tool for dissecting complex biological systems, unraveling cellular heterogeneity, and deciphering the molecular mechanisms by which proliferation and quiescence affect cellular processes.

Partial rejuvenation of the spermatogonial stem cell niche after gender-affirming hormone therapy in trans women

Although the impact of gender-affirming hormone therapy (GAHT) on spermatogenesis in trans women has already been studied, data on its precise effects on the testicular environment is poor. Therefore, this study aimed to characterize, through histological and transcriptomic analysis, the spermatogonial stem cell niche of 106 trans women who underwent standardized GAHT, comprising estrogens and cyproterone acetate. A partial dedifferentiation of Sertoli cells was observed, marked by the co-expression of androgen receptor and anti-Müllerian hormone which mirrors the situation in peripubertal boys. The Leydig cells also exhibited a distribution analogous to peripubertal tissue, accompanied by a reduced insulin-like factor 3 expression. Although most peritubular myoid cells expressed alpha-smooth muscle actin 2, the expression pattern was disturbed. Besides this, fibrosis was particularly evident in the tubular wall and the lumen was collapsing in most participants. A spermatogenic arrest was also observed in all participants. The transcriptomic profile of transgender tissue confirmed a loss of mature characteristics - a partial rejuvenation - of the spermatogonial stem cell niche and, in addition, detected inflammation processes occurring in the samples. The present study shows that GAHT changes the spermatogonial stem cell niche by partially rejuvenating the somatic cells and inducing fibrotic processes. These findings are important to further understand how estrogens and testosterone suppression affect the testis environment, and in the case of orchidectomized testes as medical waste material, their potential use in research.

Putting Nose into Reproduction: Influence of Nasal and Reproductive Odourant Signaling on Male Reproduction

Odourant receptors (ORs) are not restricted only to the nose, but also occur in many other organs and tissues, including the reproductive system. In fact, ORs are the most heavily expressed in testis than in any other extra-nasal tissue. Accumulating evidence suggests that olfactory and reproductive systems are both structurally and functionally linked and that these interconnections can influence various aspects of reproduction. In this article, we first review our current understanding of these interconnections and then collate accumulated evidence on the presence of ORs in the male reproductive system and sperm cells. We then investigate the potential role of female reproductive tract odourants in sperm chemotaxis and selection. Finally, since the existing evidence especially for sperm odor sensing capability and its physiological function are controversial, we also review potential reasons for the controversy and propose some ways to resolve the debate. Collectively, we conclude that reproductive odourant signaling may play an important, although currently largely unclear role in many key processes directly related to male fertility. However, since we lack holistic understanding of the functional significance of ORs and odor sensing pathways of the male reproductive system, more empirical research is warranted.

scRNA-Seq-Based Transcriptome Profiling and Relevant Bioinformatics Approaches to Uncover Novel Insights in Studying Human Spermatogenesis

This study employs single-cell RNA sequencing (scRNA-seq) to investigate human spermatogenesis across developmental stages and under pathological conditions, including non-obstructive azoospermia (NOA). The analysis highlights the critical role of Sertoli cells in supporting germ cell development by providing structural support, paracrine factors, and essential nutrients. Pathological conditions, such as NOA and Klinefelter syndrome, reveal significant disruptions in Sertoli cell function, including impaired cell signaling, mitochondrial activity, and transcriptional regulation. These changes are closely linked to defects in germ cell progression and spermatogenic failure. Comparative profiling also identifies stage-specific transcriptional changes in both Sertoli and Leydig cells, uncovering their dynamic interactions with germ cells. This work provides new insights into the cellular and molecular mechanisms of spermatogenesis and identifies potential biomarkers and therapeutic targets, particularly emphasizing the pivotal contributions of Sertoli cells in maintaining testicular homeostasis and fertility.

Characterisation and hierarchy of the spermatogonial stem cell compartment in human spermatogenesis by spectral cytometry using a 16-colors panel

About one in six couples experience fertility problems, and male infertility accounts for about half of these cases. Spermatogenesis originates from a small pool of spermatogonial stem cells (SSCs), which are of interest for the treatment of infertility but remain poorly characterised in humans. Using multiparametric spectral flow cytometric analysis with a 16-colours (16-C) panel of cell markers, we identify novel markers of SSCs and provide insights into unravelling and resolving the heterogeneity of the human spermatogonial cells. This 16-C panel of markers allowed the identification of a primitive SSCs state with the β2M-CD51/61-ITGA6+SSEA4+TSPAN33+THY1+CD9medEPCAMmedCD155+CD148+CD47highCD7high phenotype, with a profile close to the most primitive SSCs states 0 and SSC1-B previously defined by sc-RNAseq approach. The hierarchy of events in the spermatogonial stem cell and progenitor compartment of human spermatogenesis can be delineated. This highlights the importance of a multi-parametric and spectral cytometry approach. The in-depth characterisation of testicular cells should help to overcome the lack of stem cell knowledge, that hinders the understanding of the regenerative potential of SSCs, and is a critical parameter for the successful development of new SSCs-based cell therapies.

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.

Epigenetic characterization of adult rhesus monkey spermatogonial stem cells identifies key regulators of stem cell homeostasis

Spermatogonial stem cells (SSCs) play crucial roles in the preservation of male fertility. However, successful ex vivo expansion of authentic human SSCs remains elusive due to the inadequate understanding of SSC homeostasis regulation. Using rhesus monkeys (Macaca mulatta) as a representative model, we characterized SSCs and progenitor subsets through single-cell RNA sequencing using a cell-specific network approach. We also profiled chromatin status and major histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3 and H3K9me3), and subsequently mapped promoters and active enhancers in TSPAN33+ putative SSCs. Comparing the epigenetic changes between fresh TSPAN33+ cells and cultured TSPAN33+ cells (resembling progenitors), we identified the regulatory elements with higher activity in SSCs, and the potential transcription factors and signaling pathways implicated in SSC regulation. Specifically, TGF-β signaling is activated in monkey putative SSCs. We provided evidence supporting its role in promoting self-renewal of monkey SSCs in culture. Overall, this study outlines the epigenetic landscapes of monkey SSCs and provides clues for optimization of the culture condition for primate SSCs expansion.

Male-specific lethal-3 gene is critical for survival and fecundity in rice brown planthopper, Nilaparvata lugens

Male-specific lethal-3 (MSL3) is a component of the dosage compensation complex in Drosophila melanogaster, where its mutation leads to male-specific lethality. However, the function of MSL3 in hemipteran insects remains unclear. This study investigated the role of the MSL3 homolog in a major rice pest, the brown planthopper (Nilaparvata lugens). We cloned and characterized the gene NlMSL3 from N. lugens, which is 1467-bp long and encodes a protein of 488 amino acids. Phylogenetic analysis revealed that MSL3 is conserved across various insect orders, with high conservation in the chromo-barrel domain. Quantitative real-time polymerase chain reaction indicated differential expression levels of NlMSL3 between male and female insects during development, with the highest expression in the testes. RNA interference-mediated knockdown of NlMSL3 in N. lugens resulted in significant mortality in later instar nymphs and adults compared with the control group. In females, NlMSL3 knockdown impaired feeding behavior, leading to decreased body weight, notably reduced honeydew excretion, flat abdomens, decreased vitellogenin expression, and defective ovarian development. When dsNlMSL3-treated males were mated with control females, the number of eggs laid was similar to that laid by the females mated with control males; however, none of the eggs laid by the former hatched into nymphs. These results highlight the crucial role of NlMSL3 in the development and fecundity of N. lugens.

Human-specific epigenomic states in spermatogenesis

Infertility is becoming increasingly common, affecting one in six people globally. Half of these cases can be attributed to male factors, many driven by abnormalities in the process of sperm development. Emerging evidence from genome-wide association studies, genetic screening of patient cohorts, and animal models highlights an important genetic contribution to spermatogenic defects, but comprehensive identification and characterization of the genes critical for male fertility remain lacking. High divergence of gene regulation in spermatogenic cells across species poses challenges for delineating the genetic pathways required for human spermatogenesis using common model organisms. In this study, we leveraged post-translational histone modification and gene transcription data for 15,491 genes in four mammalian species (human, rhesus macaque, mouse, and opossum), to identify human-specific patterns of gene regulation during spermatogenesis. We combined H3K27me3 ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data to define epigenetic states for each gene at two stages of spermatogenesis, pachytene spermatocytes and round spermatids, in each species. We identified 239 genes that are uniquely active, poised, or dynamically regulated in human spermatogenic cells distinct from the other three species. While some of these genes have been implicated in reproductive functions, many more have not yet been associated with human infertility and may be candidates for further molecular and epidemiologic studies. Our analysis offers an example of the opportunities provided by evolutionary and epigenomic data for broadly screening candidate genes implicated in reproduction, which might lead to discoveries of novel genetic targets for diagnosis and management of male infertility and male contraception.

Essential role of germ cell glycerol-3-phosphate phosphatase for sperm health, oxidative stress control and male fertility in mice

OBJECTIVES

Obesity, diabetes and high-calorie diets are associated with defective sperm function and lowered male fertility. Mature spermatozoa primarily use fructose and glucose, and glucose and glycerol metabolism are important for sperm function. We recently discovered a novel mammalian enzyme, glycerol-3-phosphate (Gro3P) phosphatase (G3PP), and showed that it operates the glycerol shunt by hydrolyzing Gro3P to glycerol, and regulates glucose, lipid and energy metabolism in pancreatic β-cells and liver. We now observed that G3PP expression is the highest in the testis and spermatozoa, and investigated its role in male fertility.

METHODS

We examined G3PP expression during spermatogenesis in mouse and assessed male fertility and spermatozoon function in conditional germ cell specific G3PP-KO (cG3PP-KO) mice and tamoxifen-inducible conditional germ cell G3PP-KO (icG3PP-KO) mice. We also determined the structural and metabolic parameters and oxidative stress in the spermatozoa from icG3PP-KO and control mice.

RESULTS

G3PP expression in mouse spermatocytes and spermatids markedly increases during spermatogenesis. Male cG3PP-KO mice, in which germ cell G3PP is deleted from embryonic stage, are infertile due to dysfunctional sperm with reduced motility and capacitation, and elevated spontaneous acrosomal reaction and oxidative stress. However, icG3PP-KO male mice do not have altered fertility, due to the presence of ∼10% normal spermatozoa. icG3PP-KO spermatozoa display significantly reduced functionality and morphological and ultrastructural alterations. The icG3PP-KO spermatozoa show reduced glycerol production, elevated levels of Gro3P and reactive oxygen species (ROS), and oxidative stress that is associated with increased mitochondrial membrane potential.

CONCLUSIONS

Germ cell G3PP deletion leads to the generation of spermatozoa that are functionally and structurally abnormal, likely due to the build-up of Gro3P that increases mitochondrial membrane potential, ROS, and oxidative stress and alters spermatozoa function. Overall, the results indicate that G3PP and the glycerol shunt are essential for normal spermatozoa function and male fertility.

Advances in human In vitro spermatogenesis: A review

Recent advances surrounding in vitro spermatogenesis (IVS) have shown potential in creating a new paradigm of regenerative medicine in the future of fertility treatments for males experiencing non-obstructive azoospermia (NOA). Male infertility is a common condition affecting approximately 15% of couples, with azoospermia being present in 15% of infertile males (Cocuzza et al., 2013; Esteves et al., 2011a). Treatment for patients with NOA has primarily been limited to surgical sperm retrieval combined with in vitro fertilization intracytoplasmic sperm injection (IVF-ICSI); however, sperm retrieval is successful in only half of these patients, and live birth rates typically range between 10 and 25% (Aljubran et al., 2022). Therefore, a significant need exists for regenerative therapies in this patient population. IVS has been considered as a model for further understanding the molecular and cellular processes of spermatogenesis and as a potential regenerative therapeutic approach. While 2D cell cultures using human testicular cells have been attempted in previous research, lack of proper spatial arrangement limits germ cell differentiation and maturation, posing challenges for clinical application. Recent research suggests that 3D technology may have advantages for IVS due to mimicry of the native cytoarchitecture of human testicular tissue along with cell-cell communication directly or indirectly. 3D organotypic cultures, scaffolds, organoids, microfluidics, testis-on-a-chip, and bioprinting techniques have all shown potential to contribute to the technology of regenerative treatment strategies, including in vitro fertilization (IVF). Although promising, further work is needed to develop technology for successful, replicable, and safe IVS for humans. The intersection between tissue engineering, molecular biology, and reproductive medicine in IVS development allows for multidisciplinary involvement, where challenges can be overcome to realize regenerative therapies as a viable option.

Single-cell transcriptomes reveal spermatogonial stem cells and the dynamic heterogeneity of spermatogenesis in a seasonal breeding teleost

Seasonal spermatogenesis in fish is driven by spermatogonial stem cells (SSCs), which undergo a complex cellular process to differentiate into mature sperm. In this study, we characterized spermatogenesis in the large yellow croaker (Larimichthys crocea), a marine fish of significant commercial value, based on a high-resolution single-cell RNA-sequencing atlas of testicular cells from three distinct developmental stages: juvenile, adult differentiating and regressed testes. We detailed a continuous developmental trajectory of spermatogenic cells, from spermatogonia to spermatids, elucidating the molecular events involved in spermatogenesis. We uncovered dynamic heterogeneity in cellular compositions throughout the annual reproductive cycle, accompanied by strong molecular signatures within specific testicular cells. Notably, we identified a distinct population of SSCs and observed a critical metabolic transition from glycolysis to oxidative phosphorylation, enhancing our understanding of the biochemical and molecular characteristics of SSCs. Additionally, we elucidated the interactions between somatic cells and spermatogonia, illuminating the mechanisms that regulate SSC development. Overall, this work enhances our understanding of spermatogenesis in seasonal breeding teleosts and provides essential insights for the further conservation and culture of SSCs.

Germ cell progression through zebrafish spermatogenesis declines with age

Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal, but fertility declines with age. Although morphological studies have informed our understanding of typical spermatogenesis, the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single-cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia, but we observed a progressive decline in spermatogenesis that correlated with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males were transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increased in abundance in testes that could not complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis.

Single-cell transcriptomic and cross-species comparison analyses reveal distinct molecular changes of porcine testes during puberty

The pig is an important model for studying human diseases and is also a significant livestock species, yet its testicular development remains underexplored. Here, we employ single-cell RNA sequencing to characterize the transcriptomic landscapes across multiple developmental stages of Bama pig testes from fetal stage through infancy, puberty to adulthood, and made comparisons with those of humans and mice. We reveal an exceptionally early onset of porcine meiosis shortly after birth, and identify a distinct subtype of porcine spermatogonia resembling transcriptome state 0 spermatogonial stem cells identified in humans, which were previously thought to be primate specific. We also discover the persistent presence of proliferating progenitors for myoid cells in postnatal testes. The regulatory roles of Leydig cell steroidogenesis and estrogen synthesis in supporting cell lineages are also explored, including the potential impact of estrogen on Sertoli cell maturation and spermatogenesis. Overall, this study offers valuable insights into porcine testicular development, paving the way for future research in reproductive biology, advancements in agricultural breeding, and potential applications in translational medicine.

TMEM232 is required for the formation of sperm flagellum and male fertility in mice

Asthenoteratozoospermia is a major cause of male infertility. Thus far, the identified related genes can explain only a small share of asthenoteratozoospermia cases, suggesting the involvement of other genes. The transmembrane protein TMEM232 is highly expressed in mouse testes. In the present study, to determine its function of TMEM232 in testes, we constructed a Tmem232-null mouse model using CRISPR-Cas9 technology. Tmem232 knockout (KO) male mice was completely infertile, and their sperm were immotile, with morphological defects of the flagellum. Electron microscopy revealed an aberrant midpiece-principal junction and the loss of the fourth outer microtubule doublet in the sperm of Tmem232-/- mice. Sperm cells presented an 8 + 2 conformation and an irregular arrangement of the mitochondrial sheath. Proteomic analysis revealed altered expression of proteins related to flagellar motility, sperm capacitation, the integrity and stability of sperm structure, especially an upregulated expression of multiple ribosome components in TMEM232-deficient spermatids. Additionally, TMEM232 was observed to be involved in autophagy by interacting with autophagy-related proteins, such as ATG14, to regulate ribosome homeostasis during spermiogenesis. These results suggest that TMEM232, as a potential scaffold protein involving in the correct assembly, distribution, and stability maintenance of certain functional complexes by recruiting key intracellular proteins, is essential for the formation of a highly structured flagellum and plays an important role in the autophagic elimination of cytosolic ribosomes to provide energy for sperm motility.

Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes

MOTIVATION

Knowledge of the specific cell types affected by genetic alterations in rare diseases is crucial for advancing diagnostics and treatments. Despite significant progress, the cell types involved in the majority of rare disease manifestations remain largely unknown. In this study, we integrated scRNA-seq data from non-diseased samples with known genetic disorder genes and phenotypic information to predict the specific cell types disrupted by pathogenic mutations for 482 disease phenotypes.

RESULTS

We found significant phenotype-cell type associations focusing on differential expression and co-expression mechanisms. Our analysis revealed that 13% of the associations documented in the literature were captured through differential expression, while 42% were elucidated through co-expression analysis, also uncovering potential new associations. These findings underscore the critical role of cellular context in disease manifestation and highlight the potential of single-cell data for the development of cell-aware diagnostics and targeted therapies for rare diseases.

AVAILABILITY AND IMPLEMENTATION

All code generated in this work is available at https://github.com/SergioAlias/sc-coex.

RpL38 modulates germ cell differentiation by controlling Bam expression in Drosophila testis

Switching from mitotic spermatogonia to meiotic spermatocytes is critical to producing haploid sperms during male germ cell differentiation. However, the underlying mechanisms of this switch remain largely unexplored. In Drosophila melanogaster, the gene RpL38 encodes the ribosomal protein L38, one component of the 60S subunit of ribosomes. We found that its depletion in spermatogonia severely diminished the production of mature sperms and thus led to the infertility of male flies. By examining the germ cell differentiation in testes, we found that RpL38-knockdown blocked the transition from spermatogonia to spermatocytes and accumulated spermatogonia in the testis. To understand the intrinsic reason for this blockage, we conducted proteomic analysis for these spermatogonia populations. Differing from the control spermatogonia, the accumulated spermatogonia in RpL38-knockdown testes already expressed many spermatocyte markers but lacked many meiosis-related proteins, suggesting that spermatogonia need to prepare some important proteins for meiosis to complete their switch into spermatocytes. Mechanistically, we found that the expression of bag of marbles (bam), a crucial determinant in the transition from spermatogonia to spermatocytes, was inhibited at both the mRNA and protein levels upon RpL38 depletion. We also confirmed that the bam loss phenocopied RpL38 RNAi in the testis phenotype and transcriptomic profiling. Strikingly, overexpressing bam was able to fully rescue the testis abnormality and infertility of RpL38-knockdown flies, indicating that bam is the key effector downstream of RpL38 to regulate spermatogonia differentiation. Overall, our data suggested that germ cells start to prepare meiosis-related proteins as early as the spermatogonial stage, and RpL38 in spermatogonia is required to regulate their transition toward spermatocytes in a bam-dependent manner, providing new knowledge for our understanding of the transition process from spermatogonia to spermatocytes in Drosophila spermatogenesis.

A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals

PIWI-interacting RNAs (piRNAs) play a crucial role in safeguarding genome integrity by silencing mobile genetic elements. From flies to humans, piRNAs originate from long single-stranded precursors encoded by genomic piRNA clusters. How piRNA clusters form to adapt to genomic invaders and evolve to maintain protection remain key outstanding questions. Here, we generate a roadmap of piRNA clusters across seven species that highlights both similarities and variations. In mammals, we identify transcriptional readthrough as a mechanism to generate piRNAs from transposon insertions (piCs) downstream of genes (DoG). Together with the well-known stress-dependent DoG transcripts, our findings suggest a molecular mechanism for the formation of piRNA clusters in response to retroviral invasion. Finally, we identify a class of dynamic piRNA clusters in humans, underscoring unique features of human germ cell biology. Our results advance the understanding of conserved principles and species-specific variations in piRNA biology and provide tools for future studies.

WDR64, a testis-specific protein, is involved in the manchette and flagellum formation by interacting with ODF1

The WD40 repeat (WDR) domain is present in a wide range of proteins, providing sites for protein‒protein interactions. Recent studies have shown that WDR proteins play indispensable roles in spermatogenesis, such as in spermatocyte division, sperm head formation and flagellar assembly. In this study, we identified a novel testis-specific gene, WDR64, which has the typical characteristics of WD40 proteins with two β-propellers, and is highly conserved in Mammalia. RT-PCR and Western blot results revealed that WDR64 was highly expressed in testis. WDR64 protein was weakly expressed at postnatal Day 7, increased substantially at postnatal Day 28 and maintained at high levels thereafter. Further immunofluorescence demonstrated that WDR64 was localized posterior to the nucleus in steps 8-14 spermatids in line with the dynamic localization of manchette, moved to the flagella in steps 15-16 spermatids, and localized at the midpiece of the flagellum in mature spermatozoa. To explore the function of WDR64, we performed immunoprecipitation‒mass spectrometry (IP‒MS) to screen its interacting proteins and found that WDR64 interacted with ODF1 to form a complex. The WDR64/ODF1 complex is located at the manchette during nucleus shaping and finally at the midpiece of the mature spermatozoa tail, suggesting that it may be involved in the assembly of the manchette and flagella during spermiogenesis. Our findings provide the first understanding of the expression pattern of WDR64 and its potential molecular mechanism in spermiogenesis.

Dissecting the dynamic cellular transcriptional atlas of adult teleost testis development throughout the annual reproductive cycle

Teleost testis development during the annual cycle involves dramatic changes in cellular compositions and molecular events. In this study, the testicular cells derived from adult black rockfish at distinct stages - regressed, regenerating and differentiating - were meticulously dissected via single-cell transcriptome sequencing. A continuous developmental trajectory of spermatogenic cells, from spermatogonia to spermatids, was delineated, elucidating the molecular events involved in spermatogenesis. Subsequently, the dynamic regulation of gene expression associated with spermatogonia proliferation and differentiation was observed across spermatogonia subgroups and developmental stages. A bioenergetic transition from glycolysis to mitochondrial respiration of spermatogonia during the annual developmental cycle was demonstrated, and a deeper level of heterogeneity and molecular characteristics was revealed by re-clustering analysis. Additionally, the developmental trajectory of Sertoli cells was delineated, alongside the divergence of Leydig cells and macrophages. Moreover, the interaction network between testicular micro-environment somatic cells and spermatogenic cells was established. Overall, our study provides detailed information on both germ and somatic cells within teleost testes during the annual reproductive cycle, which lays the foundation for spermatogenesis regulation and germplasm preservation of endangered species.