Epigenetic disruption of the PIWI pathway in human spermatogenic disorders

Epigenetics of nonobstructive azoospermia

Nonobstructive azoospermia (NOA) is a severe and heterogeneous form of male factor infertility caused by dysfunction of spermatogenesis. Although various factors are well defined in the disruption of spermatogenesis, not all aspects due to the heterogeneity of the disorder have been determined yet. In this review, we focus on the recent findings and summarize the current data on epigenetic mechanisms such as DNA methylation and different metabolites produced during methylation and demethylation and various types of small noncoding RNAs involved in the pathogenesis of different groups of NOA.

The functions and mechanisms of piRNAs in mediating mammalian spermatogenesis and their applications in reproductive medicine

As the most abundant small RNAs, piwi-interacting RNAs (piRNAs) have been identified as a new class of non-coding RNAs with 24-32 nucleotides in length, and they are expressed at high levels in male germ cells. PiRNAs have been implicated in the regulation of several biological processes, including cell differentiation, development, and male reproduction. In this review, we focused on the functions and molecular mechanisms of piRNAs in controlling spermatogenesis, including genome stability, regulation of gene expression, and male germ cell development. The piRNA pathways include two major pathways, namely the pre-pachytene piRNA pathway and the pachytene piRNA pathway. In the pre-pachytene stage, piRNAs are involved in chromosome remodeling and gene expression regulation to maintain genome stability by inhibiting transposon activity. In the pachytene stage, piRNAs mediate the development of male germ cells via regulating gene expression by binding to mRNA and RNA cleavage. We further discussed the correlations between the abnormalities of piRNAs and male infertility and the prospective of piRNAs' applications in reproductive medicine and future studies. This review provides novel insights into mechanisms underlying mammalian spermatogenesis and offers new targets for diagnosing and treating male infertility.

Genome-wide DNA methylation changes in human spermatogenesis

Sperm production and function require the correct establishment of DNA methylation patterns in the germline. Here, we examined the genome-wide DNA methylation changes during human spermatogenesis and its alterations in disturbed spermatogenesis. We found that spermatogenesis is associated with remodeling of the methylome, comprising a global decline in DNA methylation in primary spermatocytes followed by selective remethylation, resulting in a spermatids/sperm-specific methylome. Hypomethylated regions in spermatids/sperm were enriched in specific transcription factor binding sites for DMRT and SOX family members and spermatid-specific genes. Intriguingly, while SINEs displayed differential methylation throughout spermatogenesis, LINEs appeared to be protected from changes in DNA methylation. In disturbed spermatogenesis, germ cells exhibited considerable DNA methylation changes, which were significantly enriched at transposable elements and genes involved in spermatogenesis. We detected hypomethylation in SVA and L1HS in disturbed spermatogenesis, suggesting an association between the abnormal programming of these regions and failure of germ cells progressing beyond meiosis.

DNA Methylation Mediates Sperm Quality via piwil1 and piwil2 Regulation in Japanese Flounder (Paralichthys olivaceus)

DNA methylation is an important way to regulate gene expression in eukaryotes. In order to reveal the role of DNA methylation in the regulation of germ cell-specific piwi gene expression during spermatogenesis of Japanese flounder (Paralichthys olivaceus), the expression profiles of piwil1 (piwi-like 1) and piwil2 (piwi-like 2) genes in the gonads of female, male, and sex-reversed pseudo-male P. olivaceus were analyzed, and the dynamic of DNA methylation was investigated. As a result, piwil1 and piwil2 genes were highly expressed in the testis of both male and pseudo-male P. olivaceus, with significant variation among male individuals. The DNA methylation levels in the promoter regions of both piwil1 and piwil2 were negatively correlated with their expression levels, which may contribute to the transcriptional regulation of piwi genes during spermatogenesis. There was also sperm quality variation among male P. olivaceus, and the sperm curvilinear velocity was positively correlated with the expression of both piwil1 and piwil2 genes. These results indicated that the DNA methylation in piwil1 and piwil2 promoter regions may affect the initiation of piwi gene transcription, thereby regulating gene expression and further affecting the spermatogenesis process and gamete quality in P. olivaceus.

Molecular mechanisms of cellular dysfunction in testes from men with non-obstructive azoospermia

Male factor infertility affects 50% of infertile couples worldwide; the most severe form, non-obstructive azoospermia (NOA), affects 10-15% of infertile males. Treatment for individuals with NOA is limited to microsurgical sperm extraction paired with in vitro fertilization intracytoplasmic sperm injection. Unfortunately, spermatozoa are only retrieved in ~50% of patients, resulting in live birth rates of 21-46%. Regenerative therapies could provide a solution; however, understanding the cell-type-specific mechanisms of cellular dysfunction is a fundamental necessity to develop precision medicine strategies that could overcome these abnormalities and promote regeneration of spermatogenesis. A number of mechanisms of cellular dysfunction have been elucidated in NOA testicular cells. These mechanisms include abnormalities in both somatic cells and germ cells in NOA testes, such as somatic cell immaturity, aberrant growth factor signalling, increased inflammation, increased apoptosis and abnormal extracellular matrix regulation. Future cell-type-specific investigations in identifying modulators of cellular transcription and translation will be key to understanding upstream dysregulation, and these studies will require development of in vitro models to functionally interrogate spermatogenic niche dysfunction in both somatic and germ cells.

Small RNAs, spermatogenesis, and male infertility: a decade of retrospect

Small non-coding RNAs (sncRNAs), being the top regulators of gene expression, have been thoroughly studied in various biological systems, including the testis. Research over the last decade has generated significant evidence in support of the crucial roles of sncRNAs in male reproduction, particularly in the maintenance of primordial germ cells, meiosis, spermiogenesis, sperm fertility, and early post-fertilization development. The most commonly studied small RNAs in spermatogenesis are microRNAs (miRNAs), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), and transfer RNA-derived small RNAs (ts-RNAs). Small non-coding RNAs are crucial in regulating the dynamic, spatial, and temporal gene expression profiles in developing germ cells. A number of small RNAs, particularly miRNAs and tsRNAs, are loaded on spermatozoa during their epididymal maturation. With regard to their roles in fertility, miRNAs have been studied most often, followed by piRNAs and tsRNAs. Dysregulation of more than 100 miRNAs has been shown to correlate with infertility. piRNA and tsRNA dysregulations in infertility have been studied in only 3-5 studies. Sperm-borne small RNAs hold great potential to act as biomarkers of sperm quality and fertility. In this article, we review the role of small RNAs in spermatogenesis, their association with infertility, and their potential as biomarkers of sperm quality and fertility.

H3K4me2 cooperates with Wnt/TCF7L2 to regulate TDRD1 and promote chicken spermatogonia stem cell formation

Spermatogonia Stem Cells (SSCs) are the basis of spermatogenesis. In the poultry industry, asthenospermia and azoospermia in roosters seriously reduce economic benefits. In this study, we explored SSCs formation mechanisms in detail. TDRD1, which is a downstream target gene of TCF7L2 and is modified by histone methylation, was screened through multiomics analysis. Functionally, RT-qPCR, flow cytometry, immunohistochemistry, and indirect immunofluorescence results showed that H3K4me2 regulated TDRD1 to promote SSCs formation both in vivo and in vitro. Furthermore, ChIP-qPCR and dual luciferase assays showed that H3K4me2 was enriched in the -800 to 0 bp region of the TDRD1 promoter and positively regulated TDRD1 transcription to promote SSCs formation. Interestingly, in mechanistic terms, dual luciferase assays showed that TDRD1 transcription levels were significantly decreased after co-transfection with dCas9-LSD1-P1/P2/P3 and OETCF7L2, while TDRD1 transcript levels were not significantly altered after transfecting dCas9-LSD1-P4 and OETCF7L2. These results suggested that H3K4me2 enrichment in P1, P2, and P3 of the TDRD1 promoter promotes TDRD1 transcription by reducing enrichment of TCF7L2. This study explored the specific regulatory mechanisms involving the Wnt signaling pathway, H3K4me2, and TDRD1, enriched the regulatory network regulating the formation of SSCs, and laid a theoretical foundation for the specific application of SSCs.

PIWI-interacting RNAs in human diseases: databases and computational models

PIWI-interacting RNAs (piRNAs) are short 21-35 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.

The regulatory function of piRNA/PIWI complex in cancer and other human diseases: The role of DNA methylation

Piwi-interacting RNAs (piRNAs) are a class of short chain noncoding RNAs that are constituted by 26-30 nucleotides (nt) and can couple with PIWI protein family. piRNAs were initially described in germline cells and are believed to be critical regulators of the maintenance of reproductive line. Increasing evidence has extended our perspectives on the biological significance of piRNAs and indicated that they could still affect somatic gene expression through DNA methylation, chromatin modification and transposon silencing, etc. Many studies have revealed that the dysregulation of piRNAs might contribute to diverse diseases through epigenetic changes represented by DNA methylation and chromatin modification. In this review, we summarized piRNA/PIWI protein-mediated DNA methylation regulation mechanisms and methylation changes caused by piRNA/PIWI proteins in different diseases, especially cancers. Since DNA methylation and inhibitory chromatin marks represented by histone H3 lysine 9 (H3K9) methylation frequently cooperate to silence genomic regions, we also included methylation in chromatin modification within this discussion. Furthermore, we discussed the potential clinical applications of piRNAs as a new type promising biomarkers for cancer diagnosis, as well as the significance of piRNA/PIWI protein-associated methylation changes in treatment, providing disparate insights into the potential applications of them.

Predicting male fertility from the sperm methylome: application to 120 bulls with hundreds of artificial insemination records

BACKGROUND

Conflicting results regarding alterations to sperm DNA methylation in cases of spermatogenesis defects, male infertility and poor developmental outcomes have been reported in humans. Bulls used for artificial insemination represent a relevant model in this field, as the broad dissemination of bull semen considerably alleviates confounding factors and enables the precise assessment of male fertility. This study was therefore designed to assess the potential for sperm DNA methylation to predict bull fertility.

RESULTS

A unique collection of 100 sperm samples was constituted by pooling 2-5 ejaculates per bull from 100 Montbéliarde bulls of comparable ages, assessed as fertile (n = 57) or subfertile (n = 43) based on non-return rates 56 days after insemination. The DNA methylation profiles of these samples were obtained using reduced representation bisulfite sequencing. After excluding putative sequence polymorphisms, 490 fertility-related differentially methylated cytosines (DMCs) were identified, most of which were hypermethylated in subfertile bulls. Interestingly, 46 genes targeted by DMCs are involved in embryonic and fetal development, sperm function and maturation, or have been related to fertility in genome-wide association studies; five of these were further analyzed by pyrosequencing. In order to evaluate the prognostic value of fertility-related DMCs, the sperm samples were split between training (n = 67) and testing (n = 33) sets. Using a Random Forest approach, a predictive model was built from the methylation values obtained on the training set. The predictive accuracy of this model was 72% on the testing set and 72% on individual ejaculates collected from an independent cohort of 20 bulls.

CONCLUSION

This study, conducted on the largest set of bull sperm samples so far examined in epigenetic analyses, demonstrated that the sperm methylome is a valuable source of male fertility biomarkers. The next challenge is to combine these results with other data on the same sperm samples in order to improve the quality of the model and better understand the interplay between DNA methylation and other molecular features in the regulation of fertility. This research may have potential applications in human medicine, where infertility affects the interaction between a male and a female, thus making it difficult to isolate the male factor.

Seminal plasma piRNA array analysis and identification of possible biomarker piRNAs for the diagnosis of asthenozoospermia

Asthenozoospermia (AZS) is characterized by reduced sperm motility and its pathogenesis remains poorly understood. Piwi-interacting RNAs (piRNAs) have been indicated to serve important roles in spermatogenesis. However, little is known about the correlation of piRNA expression with AZS. In the present study, small RNA sequencing (small RNA-seq) was performed on sperm samples from AZS patients and fertile controls. Reverse transcription-quantitative (RT-q) PCR was used to validate the small RNA-seq results. Bioinformatics analyses were performed to predict the functions of differentially expressed piRNAs (DEpiRNAs). Logistic regression models were constructed and receiver operating characteristic curve (ROC) analysis was used to evaluate their diagnostic performance. A total of 114 upregulated and 169 downregulated piRNAs were detected in AZS patients. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that the DEpiRNAs were mainly associated with transcription, signal transduction, cell differentiation, metal ion binding and focal adhesion. These results were verified by RT-qPCR analysis of eight selected piRNAs. The PCR results were consistent with the sequencing results in patients with AZS compared with controls in the first cohort. The expression of piR-hsa-32694, piR-hsa-26591, piR-hsa-18725 and piR-hsa-18586 was significantly upregulated in patients with AZS. The diagnostic power of the four piRNAs was further analyzed using ROC analysis; piR-hsa-26591 exhibited an area under the ROC curve (AUC) of 0.913 (95% CI: 0.795-0.994). Logistic regression modelling and subsequent ROC analysis indicated that the combination of the 4 piRNAs achieved good diagnostic efficacy (AUC: 0.935).

Transcriptional states of retroelement-inserted regions and specific KRAB zinc finger protein association are correlated with DNA methylation of retroelements in human male germ cells

DNA methylation, repressive histone modifications, and PIWI-interacting RNAs are essential for controlling retroelement silencing in mammalian germ lines. Dysregulation of retroelement silencing is associated with male sterility. Although retroelement silencing mechanisms have been extensively studied in mouse germ cells, little progress has been made in humans. Here, we show that the Krüppel-associated box domain zinc finger proteins are associated with DNA methylation of retroelements in human primordial germ cells. Further, we show that the hominoid-specific retroelement SINE-VNTR-Alus (SVA) is subjected to transcription-directed de novo DNA methylation during human spermatogenesis. The degree of de novo DNA methylation in SVAs varies among human individuals, which confers significant inter-individual epigenetic variation in sperm. Collectively, our results highlight potential molecular mechanisms for the regulation of retroelements in human male germ cells.

Epigenetic regulation of human non-coding RNA gene transcription

Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states and of mRNA translation and stability. However, despite its centrality, the epigenetic regulation of ncRNA genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncRNA gene transcription by the three human nuclear RNA polymerases. Emerging common features, like the heterogeneity of chromatin states within ncRNA multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.

Microenvironment for spermatogenesis and sperm maturation

The male reproductive system consists of testes, a series of ducts connecting the testes to the external urethral orifice, accessory sex glands, and the penis. Spermatogonial stem cells differentiate and mature in testes and epididymides, and spermatozoa are ejaculated with exocrine fluids secreted by accessory sex glands. Many studies have clarified the detailed structure and function of the male reproductive system, and have shown that various biologic controls, including genomics, epigenetics, and the neuroendocrine-immune system regulate proliferation, differentiation, and maturation of germ cells. In other words (1) genetic deletion or abnormalities, (2) aberration of DNA methylation and histone modifications, as well as small RNA dysfunction, and (3) neuroendocrine-immune disorders are involved in functional failure of the male reproductive system. In this article, we review these three factors for germ cell microcircumstance, especially focused on the immunoendocrine environment. In particular, the relation between factors protecting germ cells with strong auto-immunogenicity and opposite factors compromising this protection are discussed. Reductions in sperm count, concentration, and semen quality are serious problems in developed countries, although the causes are complex and remain unclear. The accumulation of basic knowledge regarding the structure, function, and regulation of the male reproductive system under various experimental conditions will be important to resolve these problems.

Functional role of piRNAs in animal models and its prospects in aquaculture

The recent advances in the field of aquaculture over the last decade has helped the cultured‐fish industry production sector to identify problems and choose the best approaches to achieve high‐volume production. Understanding the emerging roles of non‐coding RNA (ncRNA) in the regulation of fish physiology and health will assist in gaining knowledge on the possible applications of ncRNAs for the advancement of aquaculture. There is information available on the practical considerations of epigenetic mechanisms like DNA methylation, histone modification and ncRNAs, such as microRNA in aquaculture, for both fish and shellfish. Among the non‐coding RNAs, PIWI‐interacting RNA (piRNA) is 24–31 bp long transcripts, which is primarily involved in silencing the germline transposons. Besides, the burgeoning reports and studies establish piRNAs' role in various aspects of biology. Till date, there are no reviews that summarize the recent findings available on piRNAs in animal models, especially on piRNAs biogenesis and biological action. To gain a better understanding and get an overview on the process of piRNA genesis among the different animals, this work reviews the literature available on the processes of piRNA biogenesis in animal models with special reference to aquatic animal model zebrafish. This review also presents a short discussion and prospects of piRNA’s application in relevance to the aquaculture industry.

Non-Coding RNAs and Splicing Activity in Testicular Germ Cell Tumors

Testicular germ cell tumors (TGCTs) are the most common tumors in adolescent and young men. Recently, genome-wide studies have made it possible to progress in understanding the molecular mechanisms underlying the development of tumors. It is becoming increasingly clear that aberrant regulation of RNA metabolism can drive tumorigenesis and influence chemotherapeutic response. Notably, the expression of non-coding RNAs as well as specific splice variants is deeply deregulated in human cancers. Since these cancer-related RNA species are considered promising diagnostic, prognostic and therapeutic targets, understanding their function in cancer development is becoming a major challenge. Here, we summarize how the different expression of RNA species repertoire, including non-coding RNAs and protein-coding splicing variants, impacts on TGCTs’ onset and progression and sustains therapeutic resistance. Finally, the role of transcription-associated R-loop misregulation in the maintenance of genomic stability in TGCTs is also discussed.

Epigenetics of Male Infertility: The Role of DNA Methylation

In recent years, a number of studies focused on the role of epigenetics, including DNA methylation, in spermatogenesis and male infertility. We aimed to provide an overview of the knowledge concerning the gene and genome methylation and its regulation during spermatogenesis, specifically in the context of male infertility etiopathogenesis. Overall, the findings support the hypothesis that sperm DNA methylation is associated with sperm alterations and infertility. Several genes have been found to be differentially methylated in relation to impaired spermatogenesis and/or reproductive dysfunction. Particularly, DNA methylation defects of MEST and H19 within imprinted genes and MTHFR within non-imprinted genes have been repeatedly linked with male infertility. A deep knowledge of sperm DNA methylation status in association with reduced reproductive potential could improve the development of novel diagnostic tools for this disease. Further studies are needed to better elucidate the mechanisms affecting methylation in sperm and their impact on male infertility.

Personalized Medicine for the Infertile Male

Personalized medicine uses a patient's genotype, environment, and lifestyle choices to create a tailored diagnosis and therapy plan, with the goal of minimizing side effects, avoiding lost time with ineffective treatments, and guiding preventative strategies. Although most precision medicine strategies are still within the laboratory phase of development, this article reviews the promising technologies with the greatest potential to improve the diagnosis and treatment options for male infertility, including sperm cell transplantation, genomic editing, and new biomarker assays, based on the latest proteomic and epigenomic studies.

The Biogenesis and Functions of piRNAs in Human Diseases

Piwi-interacting RNAs (piRNAs) are a novel type of small noncoding RNAs, which are 26-30 nt in length and bind to Piwi proteins. These short RNAs were originally discovered in germline cells and are considered as key regulators for germline maintenance. A growing body of evidence has now extended our views into piRNA biological significance showing that they can also regulate gene expression in somatic cells through transposon silencing, epigenetic programming, DNA rearrangements, mRNA turnover, and translational control. Mounting studies have revealed that the dysregulation of piRNAs may cause epigenetic changes and contribute to diverse diseases. This review illustrates piRNA biogenesis, mechanisms behind piRNA-mediated gene regulation, and changes of piRNAs in different diseases, especially in cancers.

The Clinical Significance of PIWIL3 and PIWIL4 Expression in Pancreatic Cancer

P-element-induced wimpy testis (PIWI) proteins have been described in several cancers. PIWIL1 and PIWIL2 have been recently evaluated in pancreatic cancer, and elevated expression of PIWIL2 conferred longer survival to patients. However, PIWIL3's and PIWIL4's role in carcinogenesis is rather controversial, and their clinical implication in pancreatic cancer has not yet been investigated. In the present study, we evaluated PIWIL1, PIWIL2, PIWIL3 and PIWIL4 expression in pancreatic cancer-derived cell lines and in one non-tumor cell line as healthy control. Here, we show a differential expression in tumor and non-tumor cell lines of PIWIL3 and PIWIL4. Subsequently, functional experiments with PIWIL3 and/or PIWIL4 knockdown revealed a decrease in the motility ratio of tumor and non-tumor cell lines through downregulation of mesenchymal factors in pro of epithelial factors. We also observed that PIWIL3 and/or PIWIL4 silencing impaired undifferentiated phenotype and enhanced drug toxicity in both tumor- and non-tumor-derived cell lines. Finally, PIWIL3 and PIWIL4 evaluation in human pancreatic cancer samples showed that patients with low levels of PIWIL4 protein expression presented poor prognosis. Therefore, PIWIL3 and PIWIL4 proteins may play crucial roles to keep pancreatic cell homeostasis not only in tumors but also in healthy tissues.

Promoter hypermethylation of PIWI/piRNA pathway genes associated with diminished pachytene piRNA production in bovine hybrid male sterility

Hybrid male sterility (HMS) is a postzygotic reproductive isolation mechanism that enforces speciation. A bovine example of HMS is the yattle (also called dzo), an interspecies hybrid of taurine cattle (Bos taurus) and yak (Bos grunniens). The molecular mechanisms underlying HMS of yattle are not well understood. Epigenetic modifications of DNA methylation and P-element induced wimpy testis (PIWI)-interacting RNA (piRNAs) are important regulators in spermatogenesis. In this study, we investigated DNA methylation patterns and piRNA expression in adult testes in hybrid infertile yattle bulls and fertile cattle and yak bulls using whole genome bisulphite-seq and small RNA-seq. Promoter hypermethylation in yattle were associated with DNA methylation involved in gamete generation, piRNA metabolic processes, spermatogenesis, and spermatid development (P < 2.6 × 10^-5). Male infertility in yattle was associated with the promoter hypermethylation-associated silencing of PIWI/piRNA pathway genes including PIWIL1, DDX4, PLD6, MAEL, FKBP6, TDRD1 and TDRD5. The downstream effects of silencing these genes were diminished production of 29- to 31- nucleotide pachytene piRNAs in yattle testes. Hypermethylation events at transposable element loci (LINEs, SINEs, and LTRs) were found in yattle. LINE-derived prepachytene piRNAs increased and SINE-derived prepachytene piRNAs were reduced in yattle testes. Our data suggests that DNA methylation affects the PIWI/piRNA pathway and is involved in gene expression and pachytene piRNA production during spermatogenesis in bovine HMS. DNA hypermethylation and disruption of piRNA production contributed to unsuccessful germ cell development that may drive bovine HMS.

The Importance of Small Non-Coding RNAs in Human Reproduction: A Review Article

Background

MicroRNAs (miRNA) play a key role in the regulation of gene expression through the translational suppression and control of post-transcriptional modifications.

Aim

Previous studies demonstrated that miRNAs conduct the pathways involved in human reproduction including maintenance of primordial germ cells (PGCs), spermatogenesis, oocyte maturation, folliculogenesis and corpus luteum function. The association of miRNA expression with infertility, polycystic ovary syndrome (PCOS), premature ovarian failure (POF), and repeated implantation failure (RIF) was previously revealed. Furthermore, there are evidences of the importance of miRNAs in embryonic development and implantation. Piwi-interacting RNAs (piRNAs) and miRNAs play an important role in the post-transcriptional regulatory processes of germ cells. Indeed, the investigation of small RNAs including miRNAs and piRNAs increase our understanding of the mechanisms involved in fertility. In this review, the current knowledge of microRNAs in embryogenesis and fertility is discussed.

Conclusion

Further research is necessary to provide new insights into the application of small RNAs in the diagnosis and therapeutic approaches to infertility.

Semen miRNAs Contained in Exosomes as Non-Invasive Biomarkers for Prostate Cancer Diagnosis

Although it is specific for prostatic tissue, serum prostate-specific antigen (PSA) screening has resulted in an over-diagnosis of prostate cancer (PCa) and many unnecessary biopsies of benign disease due to a well-documented low cancer specificity, thus improvement is required. We profiled the expression level of miRNAs contained in semen exosomes from men with moderately increased PSA levels to assess their usefulness, either alone or in addition to PSA marker, as non-invasive biomarkers, for the early efficient diagnosis and prognosis of PCa. An altered miRNA expression pattern was found by a high throughput profiling analysis in PCa when compared with healthy individuals (HCt) exosomal semen samples. The presence of vasectomy was taken into account for the interpretation of results. Fourteen miRNAs were selected for miRNA validation as PCa biomarkers in a subsequent set of semen samples. In this explorative study, we describe miRNA-based models, which included miRNA expression values together with PSA levels, that increased the classification function of the PSA screening test with diagnostic and/or prognostic potential: [PSA + miR-142-3p + miR-142-5p + miR-223-3p] model (AUC:0,821) to discriminate PCa from BPH (Sn:91,7% Sp:42,9% vs Sn:100% Sp:14,3%); and [PSA + miR-342-3p + miR-374b-5p] model (AUC: 0,891) to discriminate between GS ≥ 7 tumours and men presenting PSA ≥ 4 ng/ml with no cancer or GS6 tumours (Sn:81,8% Sp:95% vs Sn:54,5% Sp:90%). The pathway analysis of predicted miRNA target genes supports a role for these miRNAs in PCa aetiology and/or progression. Our study shows semen exosome miRNA-based models as molecular biomarkers with the potential to improve PCa diagnosis/prognosis efficiency. As the next step, further prospective studies on larger cohorts of patients are required to validate the diagnostic and/or prognostic role of the miRNA panel before it could be adopted into clinical practice.

Promoter DNA methylation and expression analysis of PIWIL1 gene in purebred and crossbred cattle bulls

Major credit for India being the largest producer of milk in the world, goes to crossbred cows produced by inseminating low-producing indigenous cattle with semen from high producing exotic bulls. However, over the years, the policy of crossbreeding has been confronted with a major problem of subfertility in crossbred male progenies, culminating into disposal of a major fraction of mature bulls. Many studies have demonstrated relationship between epigenetic alterations and male fertility across different species. PIWIL1 is an important candidate gene for spermatogenesis and germ line development. Negative correlation between DNA methylation and expression of this gene has been highlighted in inter species hybrids of cattle and yaks. The present study envisaged elucidating promoter methylation status and expression profile of PIWIL1 gene in exotic Holstein Friesian cattle, indigenous Sahiwal cattle and their crossbreds with varying semen motility parameters. Semen samples were collected from bulls for isolation of DNA and RNA from spermatozoa. Bisulfite converted DNA was used to amplify promoter of PIWIL1 gene using methylation specific primers. The amplified products were sequenced after cloning in pTZ57R/ T vector. The degree of methylation of the PIWIL1 promoter region was significantly higher in poor motility crossbred bulls (7.17%) as compared to good motility crossbreds (1.02%), Sahiwal (1.02%) and Holstein Friesian bulls (0.77%). PIWIL1 expression was 1.75, 1.71 and 1.59 folds higher in HF, Sahiwal and good motility crossbreds, respectively as compared to poor motility crossbreds.

Identification of circulating small non-coding RNAs in relation to male subfertility and reproductive hormones

Male subfertility is often associated with sub-optimal health status and traditional semen and hormone analysis reveal only limited information about the reduced fertility potential. Circulating small non-coding RNAs (sncRNAs) are paracrine and endocrine messengers, with prognostic potential. Here, we utilised small RNA-Seq to identify novel cell-free circulating sncRNAs that could act as potential biomarkers of male subfertility. We analysed sera from twelve subfertile men and four controls. The subfertile men were further sub-divided into the three groups based on reproductive hormone levels: group 1 (n = 4): hormone levels similar to the controls, group 2 (n = 4) showing elevated FSH levels, and group 3 (n = 4) with low total testosterone (TT). Total RNA was extracted from serum and sequenced to identify miRNAs and piRNAs. Selected sncRNAs were qPCR validated in a larger and independent cohort of subfertile men (n = 57) and normozoospermic controls (n = 19). RNA-Seq resulted in the identification of 1123 and 330 circulating miRNAs and piRNAs, respectively. Several miRNAs and piRNAs were differentially (p = 0.05) present between controls and subfertile men. Subfertile men with low TT appeared to have a distinct sncRNA profile, compared to group 1 and 2. Validation of two miRNAs (hsa-miR-542-5p and hsa-let-7i-3p) and one piRNA (hsa-piR-26399) in an independent cohort confirmed a significant difference in circulating levels between subfertile and control men. Enrichment analysis of the putative miRNA targets showed association with steroid biosynthesis pathway highlighting a potential regulatory role of these miRNAs. We propose that circulating sncRNAs may represent new important functional biomarkers in male reproductive endocrinology.

Decreased expression of DNA methyltransferases in the testes of patients with non-obstructive azoospermia leads to changes in global DNA methylation levels

DNA methylation plays key roles in epigenetic regulation during mammalian spermatogenesis. DNA methyltransferases (DNMTs) function in de novo and maintenance methylation processes by adding a methyl group to the fifth carbon atom of the cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinucleotide sites. Azoospermia is one of the main causes of male infertility, and is classified as obstructive (OA) or non-obstructive (NOA) azoospermia based on histopathological characteristics. The molecular background of NOA is still largely unknown. DNA methylation performed by DNMTs is implicated in the transcriptional regulation of spermatogenesis-related genes. The aim of the present study was to evaluate the cellular localisation and expression levels of the DNMT1, DNMT3A and DNMT3B proteins, as well as global DNA methylation profiles in testicular biopsy samples obtained from men with various types of NOA, including hypospermatogenesis (hyposperm), round spermatid (RS) arrest, spermatocyte (SC) arrest and Sertoli cell-only (SCO) syndrome. In the testicular biopsy samples, DNMT1 expression and global DNA methylation levels decreased gradually from the hyposperm to SCO groups (P P P <0.05). Although both DNMT1 and DNMT3A were localised in the cytoplasm and nucleus of the spermatogenic cells, staining for DNMT3B was more intensive in the nucleus of spermatogenic cells. In conclusion, the findings suggest that significant changes in DNMT expression and global DNA methylation levels in spermatogenic cells may contribute to development of male infertility in the NOA groups. Further studies are needed to determine the molecular biological effects of the altered DNMT expression and DNA methylation levels on development of male infertility.

Altered PIWI-LIKE 1 and PIWI-LIKE 2 mRNA expression in ejaculated spermatozoa of men with impaired sperm characteristics

In about half the cases of involuntary childlessness, a male infertility factor is involved. The PIWI-LIKE genes, a subclade of the Argonaute protein family, are involved in RNA silencing and transposon control in the germline. Knockout of murine Piwi-like 1 and 2 homologs results in complete infertility in males. The aim of this study was to analyze whether the mRNA expression of human PIWI-LIKE 1-4 genes is altered in ejaculated spermatozoa of men with impaired sperm characteristics. Ninety male participants were included in the study, among which 47 were with normozoospermia, 36 with impaired semen characteristics according to the World Health Organization (WHO) manual, 5^th edition, and 7 with azoospermia serving as negative control for the PIWI-LIKE 1-4 mRNA expression in somatic cells in the ejaculate. PIWI-LIKE 1-4 mRNA expression in the ejaculated spermatozoa of the participants was measured by quantitative real-time PCR. In nonazoospermic men, PIWI-LIKE 1-4 mRNA was measurable in ejaculated spermatozoa in different proportions. PIWI-LIKE 1 (100.0%) and PIWI-LIKE 2 (49.4%) were more frequently expressed than PIWI-LIKE 3 (9.6%) and PIWI-LIKE 4 (15.7%). Furthermore, a decreased PIWI-LIKE 2 mRNA expression showed a significant correlation with a decreased sperm count (P = 0.022) and an increased PIWI-LIKE 1 mRNA expression with a decreased progressive motility (P = 0.048). PIWI-LIKE 1 and PIWI-LIKE 2 mRNA expression exhibited a significant association with impaired sperm characteristics and may be a useful candidate for the evaluation of the impact of PIWI-LIKE 1-4 mRNA expression on male infertility.

Non-coding RNAs, epigenetics, and cancer: tying it all together

While only a small part of the human genome encodes for proteins, biological functions for the so-called junk genome are increasingly being recognized through high-throughput technologies and mechanistic experimental studies. Indeed, novel mechanisms of gene regulation are being discovered that require coordinated interaction between DNA, RNA, and proteins. Therefore, interdisciplinary efforts are still needed to decipher these complex transcriptional networks. In this review, we discuss how non-coding RNAs (ncRNAs) are epigenetically regulated in cancer and metastases and consequently how ncRNAs participate in the sculpting of the epigenetic profile of a cancer cell, thus modulating the expression of other RNA molecules. In the latter case, ncRNAs not only affect the DNA methylation status of certain genomic loci but also interact with histone-modifying complexes, changing the structure of the chromatin itself. We present several examples of epigenetic changes causing aberrant expression of ncRNAs in the context of tumor progression. Interestingly, there are also important epigenetic changes and transcriptional regulatory effects derived from their aberrant expression. As ncRNAs can also be used as biomarkers for diagnosis and prognosis or explored as potential targets, we present insights into the use of ncRNAs for targeted cancer therapy.

Exosomal microRNAs in seminal plasma are markers of the origin of azoospermia and can predict the presence of sperm in testicular tissue

STUDY QUESTION

Are exosomal microRNAs (miRNAs) in seminal plasma (SP) useful as markers of the origin of azoospermia and the presence of sperm in the testis?

SUMMARY ANSWER

Our study demonstrated the potential of several miRNAs contained in small extracellular vesicles (sEVs) of seminal fluid as sensitive and specific biomarkers for selecting those azoospermic individuals with real chances of obtaining spermatozoa from the testicular biopsy.

WHAT IS KNOWN ALREADY

There are no precise non-invasive diagnostic methods for classifying the origin of the sperm defects in semen and the spermatogenic reserve of the testis in those infertile men with a total absence of sperm in the ejaculate (azoospermia). The diagnosis of such individuals is often based on the practice of biopsies. In this context it is reasonable to study the presence of organ-specific markers in human semen that contains fluid from the testis and the male reproductive glands, which could help in the diagnosis and prognosis of male infertility. Additionally, seminal fluid contains high concentrations of sEVs that are morphologically and molecularly consistent with exosomes, which originate from multiple cellular sources in the male reproductive tract.

STUDY DESIGN, SIZE, DURATION

A case and control prospective study was performed. This study compares the miRNA content of exosomes in semen samples obtained from nine normozoospermic fertile individuals (control group), 14 infertile men diagnosed with azoospermia due to spermatogenic failure, and 13 individuals with obstructive azoospermia and conserved spermatogenesis. Additionally, three severe oligozoospermic individuals (<5 × 10⁶ sperm/ml) were included in the study.

PARTICIPANTS/MATERIALS, SETTING, METHODS

A differential high-throughput miRNA profiling analysis using miRNA quantitative PCR panels was performed in SP exosomes from azoospermic patients and fertile individuals.

MAIN RESULTS AND THE ROLE OF CHANCE

A total of 623 miRNAs were included in the miRNA profiling stage of the study. A total of 397 miRNAs (63.7%) were consistently detected in samples from all groups and statistically analysed, which revealed altered patterns of miRNA expression in infertile patients. We focused on the miRNAs that were differentially expressed between azoospermia as a result of an obstruction in the genital tract (i.e. having conserved spermatogenesis) and azoospermia caused by spermatogenic failure, and described, in a miRNA validation stage of the study, the expression values of one miRNA (miR-31-5p) in exosomes from semen as a predictive biomarker test for the origin of azoospermia with high sensitivity and specificity (>90%). The efficacy of the predictive test was even better when the blood FSH values were included in the analysis. Furthermore a model that included miR-539-5p and miR-941 expression values is also described as being useful for predicting the presence of residual spermatogenesis in individuals with severe spermatogenic disorders with diagnostic accuracy.

LIMITATIONS, REASONS FOR CAUTION

Further studies, with an independent second population involving a larger number of samples, are needed to confirm our findings.

WIDER IMPLICATIONS OF THE FINDINGS

Our findings contribute to the search for the most valuable genetic markers that are potentially useful as tools for predicting the presence of testicular sperm in azoospermic individuals.

STUDY FUNDING/COMPETING INTEREST(S)

This work was financially supported by grants from the Fondo de Investigaciones Sanitarias/Fondo Europeo de Desarrollo Regional “Una manera de hacer Europa” (FIS/FEDER) [Grant number PI15/00153], the Generalitat de Catalunya [Grant number 2014SGR5412]. S.L. is sponsored by the Researchers Stabilization Program (ISCIII/Generalitat de Catalunya) from the Spanish National Health System [CES09/020].

Human-specific subcellular compartmentalization of P-element induced wimpy testis-like (PIWIL) granules during germ cell development and spermatogenesis

STUDY QUESTION

What is the dynamics of expression of P-element induced wimpy testis-like (PIWIL) proteins in the germline during human fetal development and spermatogenesis?

SUMMARY ANSWER

PIWIL1, PIWIL2, PIWIL3 and PIWIL4 were expressed in a sex-specific fashion in human germ cells (GC) during development and adulthood. PIWILs showed a mutually exclusive pattern of subcellular localization. PIWILs were present in the intermitochondrial cement and a single large granule in meiotic GC and their expression was different from that observed in mice, highlighting species-differences.

WHAT IS KNOWN ALREADY

In mice, PIWIL proteins play prominent roles in male infertility. PIWIL mouse mutants show either post-meiotic arrest at the round spermatid stage (PIWIL1) or arrest at the zygotene-pachytene stage of meiosis I (PIWIL2 and PIWIL4) in males, while females remain fertile. Recent studies have reported a robust piRNA pool in human fetal ovary.

STUDY DESIGN, SIZE, DURATION

This is a qualitative analysis of PIWILs expression in paraffin-embedded fetal human male (N = 8), female gonads (N = 6) and adult testes (N = 5), and bioinformatics analysis of online available single-cell transcriptomics data of human fetal germ cells (n = 242).

PARTICIPANTS/MATERIALS, SETTING, METHODS

Human fetal gonads from elective abortion without medical indication and adult testes biopsies were donated for research with informed consent. Samples were fixed, paraffin-embedded and analyzed by immunofluorescence to study the temporal and cellular localization of PIWIL1, PIWIL2, PIWIL3 and PIWIL4.

MAIN RESULTS AND THE ROLE OF CHANCE

PIWIL1, PIWIL2 and PIWIL4 showed a mutually exclusive pattern of subcellular localization, particularly in female oocytes. To our surprise, PIWIL1 immunostaining revealed the presence of a single dense paranuclear body, resembling the chromatoid body of haploid spermatocytes, in meiotic oocytes. Moreover, in contrast to mice, PIWIL4, but not PIWIL2, localized to the intermitochondrial cement. PIWIL3 was not expressed in GC during development. The upregulation of PIWIL transcripts correlated with the transcription of markers associated with piRNAs biogenesis like the TDRDs and HENMT1 in fetal GC.

LARGE SCALE DATA

Non-applicable.

LIMITATIONS, REASONS FOR CAUTION

This study is limited by the restricted number of samples and consequently stages analyzed.

WIDER IMPLICATIONS OF THE FINDINGS

In the germline, PIWILs ensure the integrity of the human genome protecting it from ‘parasitic sequences’. This study offers novel insights on the expression dynamics of PIWILs during the window of epigenetic remodeling and meiosis, and highlights important differences between humans and mice, which may prove particularly important to understand causes of infertility and improve both diagnosis and treatment in humans.

STUDY FUNDING/COMPETING INTEREST(S)

M.G.F. was funded by Fundação para a Ciência e Tecnologia (FCT) [SFRH/BD/78689/2011]; N.H. by China Scholarship Council (CSC) [No. 201307040026] and F.W. by Medical Personnel Training Abroad Project of Henan Province [No. 2015022] and S.M.C.d.S.L. by the Netherlands Organization of Scientific Research (NWO) [ASPASIA 015.007.037] and the Interuniversity Attraction Poles-Phase VII [IUAP/PAI P7/14]. The authors have no conflicts of interest to declare.

Genome-wide methylation study of whole blood cells DNA in men with congenital hypopituitarism disease

Congenital hypopituitarism (CH) is a relatively rare disease that is characterized by the deficiency of one or more hormones secreted by the pituitary gland, which leads to metabolic disorders, amenorrhea and infertility. However, the underlying molecular mechanisms of CH have not yet been fully elucidated. The present study evaluated the genome-wide methylation level of whole blood DNA in 12 patients with CH and 12 age-matched controls using Illumina Human Methylation 450 array, in order to determine the roles of epigenetic regulation in the pathogenesis of CH. The results demonstrated that the methylation levels of 51 CpG sites were significantly different between the patients with CH and the controls. Functional enrichment analysis identified that the aberrant methylated genes were enriched in gene sets associated with metabolic or cellular process, immune system process and reproduction. In addition, two CpG sites on genes LIM domain kinase 2 (LIMK2) and piwi-like RNA-mediated gene silencing 2 (PIWIL2), which are involved in spermatogenesis and/or testicular development, were identified to be hypermethylated in male patients with CH. The hypermethylation of these sites was further validated in another 40 patients with CH and 40 matched controls with a quantitative bisulfite pyrosequencing method, and the methylation levels of these two loci demonstrated promising diagnostic capacities for CH. The present results suggested that aberrant methylation of genes may be involved in the pathogenesis of CH, and hypermethylation of LIMK2 and PIWIL2 may contribute to the infertility of male patients with CH. Further studies are required to elucidate the underlying mechanisms of the epigenetic regulation of these genes.

Differential Regulation of PIWI-LIKE 2 Expression in Primordial Germ Cell Tumor Cell Lines by Promoter Methylation

PIWI-LIKE 2, a member of the ARGONAUTE protein family, is exclusively expressed in pre-pachytene and pachytene stages of spermatogenesis. PIWI-LIKE 2 acts in the germ cell development and the silencing of retrotransponsons to maintain the genomic integrity and stem cell character. In the present study we investigated DNA methylation as potential mechanism for the regulation of human PIWI-LIKE 2 expression in cell lines related to spermatozoa precursor cells. We detected a high methylation of the PIWI-LIKE 2 promoter in TCam-2 cells, while in NT2/D1 cells the promoter was hypomethylated. Concordantly, PIWI-LIKE 2 expression is higher in NT2/D1 cells than in TCam-2 cells. By demethylation of the promoter with 5'-Aza-2'-deoxycytidine, PIWI-LIKE 2 expression in TCam-2 was increased, while in NT2/D1 no alterations in PIWI-LIKE 2 expression could be detected. In conclusion, we analyzed the DNA methylation driving PIWI-LIKE 2 expression in undifferentiated germ cell tumors and demonstrated an epigenetic basis for PIWI-LIKE 2 expression in this cell type.

The status of global DNA methylation in the spermatozoa of smokers and non-smokers

RESEARCH QUESTION

Does regular smoking affect semen quality and the levels of DNA methylation in mature human spermatozoa?

DESIGN

Spermatozoa from 109 men were evaluated (55 smokers and 54 non-smokers). DNA was extracted from purified spermatozoa, and DNA methylation was quantified by enzyme-linked immunosorbent assay (ELISA).

RESULTS

Global DNA methylation of non-smokers is significantly lower (P < 0.001) than that of smokers (4.85 ± 2.72 and 7.08 ± 1.77 ng/μl, respectively). Moreover, the mean global DNA methylation levels were significantly correlated (r = 0.22;P = 0.02) with non-condensed chromatin in the spermatozoa. Levels of non-condensed chromatin were significantly higher (P < 0.001) in smokers (29.75 ± 9.38%) compared with non-smokers (20.96 ± 11.31%). Furthermore, global sperm DNA methylation was negatively correlated with high significance (P < 0.010) with sperm: count (r = -0.27), motility (r = -0.30) and vitality (r = -0.26).

CONCLUSION

Smoking interferes with DNA methylation. Also, DNA methylation is significantly correlated with sperm parameters and sperm non-condensed chromatin. These data emphasize another detrimental effect of smoking on male fertility. DNA methylation may, therefore, be considered as a fertility marker in men.

A multi-scale analysis of bull sperm methylome revealed both species peculiarities and conserved tissue-specific features

BACKGROUND

Spermatozoa have a remarkable epigenome in line with their degree of specialization, their unique nature and different requirements for successful fertilization. Accordingly, perturbations in the establishment of DNA methylation patterns during male germ cell differentiation have been associated with infertility in several species. While bull semen is widely used in artificial insemination, the literature describing DNA methylation in bull spermatozoa is still scarce. The purpose of this study was therefore to characterize the bull sperm methylome relative to both bovine somatic cells and the sperm of other mammals through a multiscale analysis.

RESULTS

The quantification of DNA methylation at CCGG sites using luminometric methylation assay (LUMA) highlighted the undermethylation of bull sperm compared to the sperm of rams, stallions, mice, goats and men. Total blood cells displayed a similarly high level of methylation in bulls and rams, suggesting that undermethylation of the bovine genome was specific to sperm. Annotation of CCGG sites in different species revealed no striking bias in the distribution of genome features targeted by LUMA that could explain undermethylation of bull sperm. To map DNA methylation at a genome-wide scale, bull sperm was compared with bovine liver, fibroblasts and monocytes using reduced representation bisulfite sequencing (RRBS) and immunoprecipitation of methylated DNA followed by microarray hybridization (MeDIP-chip). These two methods exhibited differences in terms of genome coverage, and consistently, two independent sets of sequences differentially methylated in sperm and somatic cells were identified for RRBS and MeDIP-chip. Remarkably, in the two sets most of the differentially methylated sequences were hypomethylated in sperm. In agreement with previous studies in other species, the sequences that were specifically hypomethylated in bull sperm targeted processes relevant to the germline differentiation program (piRNA metabolism, meiosis, spermatogenesis) and sperm functions (cell adhesion, fertilization), as well as satellites and rDNA repeats.

CONCLUSIONS

These results highlight the undermethylation of bull spermatozoa when compared with both bovine somatic cells and the sperm of other mammals, and raise questions regarding the dynamics of DNA methylation in bovine male germline. Whether sperm undermethylation has potential interactions with structural variation in the cattle genome may deserve further attention.

An unusual intragenic promoter of PIWIL2 contributes to aberrant activation of oncogenic PL2L60

PIWIL2-like (PL2L) protein 60 (PL2L60), a product of aberrantly activated PIWIL2 gene, is widely expressed in various types of tumors and may promote tumorigenesis. However, the mechanisms underlying the activation of expression of PL2L60 remain unknown. In this study, an intragenic promoter responsible for the activation of PL2L60 within the human PIWIL2 gene has been identified, cloned and characterized. The promoter of PL2L60 is located in the intron 10 of the host gene PIWIL2. Bioinformatic and mutagenic analysis reveals that this intragenic promoter within the sequence of 50 nucleotides contains two closely arranged cis-acting elements specific for the hepatic leukemia factor (HLF) in the positive strand and signal transducer and activator of transcription 3 (STAT3) in the negative strand. Chromatin immunoprecipitation analysis demonstrates that both the HLF and polymerase II (Pol II), a hallmark of active promoters, directly bind to the sequence, although STAT3 does not. Knockdown of HLF and STAT3 alone or both by RNA interference significantly reduced both promoter activity and the PL2L60 protein expression, although there is no additive effect. The expression of PL2L60 proteins was enhanced when host gene Piwil2 was genetically disrupted in a murine cell model. Taken together, we have identified a PL2L60-specific intragenic promoter in the host gene of PIWIL2, which is interdependently activated by HLF and STAT3 through steric interaction. This activation is dependent on cellular milieu rather than the integrity of host gene PIWIL2, highlighting a novel, important mechanism for a cancer-causing gene to be activated during tumorigenesis.

Investigation of piwi-interacting RNA pathway genes role in idiopathic non-obstructive azoospermia

Genes involved in piwi-interacting RNAs (piRNAs) pathway have an essential role in spermatogenesis. HIWI and TDRD proteins are critical for piRNA biogenesis and function. Therefore, Mutations and polymorphisms in HIWI and TDRD genes may play role in male infertility. The aim of the present study was to investigate the role of HIWI2 rs508485 (T>C) and HIWI3 rs11703684 (C>T) polymorphisms and mutational analysis of TDRD5 gene in idiopathic non-obstructive azoospermia in a case-control study including 226 non-obstructive azoospermia patients and 200 fertile males. Genotyping for both polymorphisms was performed using Tetra-Primer ARMS PCR. Mutation analysis of TDRD5 gene was done using multi-temperature single strand conformation polymorphism technique (MSSCP). The frequency of rs508485TC genotype was significantly different in the studied groups (P = 0.0032; OR = 2.12; 95% CI, 1.29-3.48). In addition, the genotype frequencies showed a significant difference under dominant model (P = 0.005; OR = 2.79; 95% CI, 1.22-3.13). No mutation was detected in the Tudor domain of the TDRD5 in the studied patients. In conclusion, we provide evidence for association between genetic variation in the HIWI2 gene and idiopathic non-obstructive azoospermia in Iranian patients. Therefore, piRNA pathway genes variants can be considered as risk factors for male infertility.

Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery

Reproductive isolation defines species divergence and is linked to adaptive evolution of hybrid incompatibility genes. Hybrids between Drosophila melanogaster and Drosophila simulans are sterile, and phenocopy mutations in the PIWI interacting RNA (piRNA) pathway, which silences transposons and shows pervasive adaptive evolution, and Drosophila rhino and deadlock encode rapidly evolving components of a complex that binds to piRNA clusters. We show that Rhino and Deadlock interact and co-localize in simulans and melanogaster, but simulans Rhino does not bind melanogaster Deadlock, due to substitutions in the rapidly evolving Shadow domain. Significantly, a chimera expressing the simulans Shadow domain in a melanogaster Rhino backbone fails to support piRNA production, disrupts binding to piRNA clusters, and leads to ectopic localization to bulk heterochromatin. Fusing melanogaster Deadlock to simulans Rhino, by contrast, restores localization to clusters. Deadlock binding thus directs Rhino to piRNA clusters, and Rhino-Deadlock co-evolution has produced cross-species incompatibilities, which may contribute to reproductive isolation.

Expression patterns of HENMT1 and PIWIL1 in human testis: implications for transposon expression

This study aimed to define the expression patterns of HENMT1 and PIWI proteins in human testis and investigate their association with transposon expression, infertility sub-type or development of testicular germ cell tumours (TGCTs). Testis biopsies showing normal spermatogenesis were used to identify normal localisation patterns of HENMT1 and PIWIL1 by immunolocalisation and RT-PCR after laser microdissection. 222 testis biopsies representing normal spermatogenesis, hypospermatogenesis, spermatogenic arrests, Sertoli cell-only (SCO) tumours and TGCTs were analysed by RT-qPCR for expression of HENMT1/PIWIL1/PIWIL2/PIWIL3/PIWIL4 and LINE-1 Additionally, HENMT1-overexpressing TCam2 seminoma cell lines were analysed for the same parameters by RT-qPCR. We found that HENMT1 and PIWIL1 are coexpressed in pachytene spermatocytes and spermatids. Expression of HENMT1, PIWIL1 and PIWIL2 was mainly dependent on germ cell content but low levels of expression were also detected in some SCO samples. Levels of HENMT1, PIWIL1 and PIWIL2 expression were low in TGCT. Samples with HENMT1, PIWIL2 and PIWIL4 expression showed significantly (P < 0.05) lower transposon expression compared to samples without expression in the same histological group. HENMT1-overexpressing TCam2 cells showed lower LINE-1 expression than empty vector-transfected control lines. Our findings support that the transposon-regulating function of the piRNA pathway found in the mouse is conserved in adult human testis. HENMT1 and PIWI proteins are expressed in a germ-cell-specific manner and required for transposon control.

Intact piRNA pathway prevents L1 mobilization in male meiosis

The PIWI-interacting RNA (piRNA) pathway is essential for retrotransposon silencing. In piRNA-deficient mice, L1-overexpressing male germ cells exhibit excessive DNA damage and meiotic defects. It remains unknown whether L1 expression simply highlights piRNA deficiency or actually drives the germ-cell demise. Specifically, the sheer abundance of genomic L1 copies prevents reliable quantification of new insertions. Here, we developed a codon-optimized L1 transgene that is controlled by an endogenous mouse L1 promoter. Importantly, DNA methylation dynamics of a single-copy transgene were indistinguishable from those of endogenous L1s. Analysis of Mov10l1^-/- testes established that de novo methylation of the L1 transgene required the intact piRNA pathway. Consistent with loss of DNA methylation and programmed reduction of H3K9me2 at meiotic onset, the transgene showed 1,400-fold increase in RNA expression and consequently 70-fold increase in retrotransposition in postnatal day 14 Mov10l1^-/- germ cells compared with the wild-type. Analysis of adult Mov10l1^-/- germ-cell fractions indicated a stage-specific increase of retrotransposition in the early meiotic prophase. However, extrapolation of the transgene data to endogenous L1s suggests that it is unlikely insertional mutagenesis alone accounts for the Mov10l1^-/- phenotype. Indeed, pharmacological inhibition of reverse transcription did not rescue the meiotic defect. Cumulatively, these results establish the occurrence of productive L1 mobilization in the absence of an intact piRNA pathway but leave open the possibility of processes preceding L1 integration in triggering meiotic checkpoints and germ-cell death. Additionally, our data suggest that many heritable L1 insertions originate from individuals with partially compromised piRNA defense.

Genome-Scale Assessment of Age-Related DNA Methylation Changes in Mouse Spermatozoa

DNA methylation plays important roles in the production and functioning of spermatozoa. Recent studies have suggested that DNA methylation patterns in spermatozoa can change with age, but the regions susceptible to age-related methylation changes remain to be fully elucidated. In this study, we conducted genome-scale DNA methylation profiling of spermatozoa obtained from C57BL/6N mice at 8 weeks (8w), 18 weeks (18w) and 17 months of age (17m). There was no substantial difference in the global DNA methylation patterns between 18w and 17m samples except for a slight increase of methylation levels in long interspersed nuclear elements in the 17m samples. We found that maternally methylated imprinting control regions (mICRs) and spermatogenesis-related gene promoters had 5–10% higher methylation levels in 8w samples than in 18w or 17m samples. Analysis of individual sequence reads suggested that these regions were fully methylated (80–100%) in a subset of 8w spermatozoa. These regions are also known to be highly methylated in a subset of postnatal spermatogonia, which might be the source of the increased DNA methylation in 8w spermatozoa. Another possible source was contamination by somatic cells. Although we carefully purified the spermatozoa, it was difficult to completely exclude the possibility of somatic cell contamination. Further studies are needed to clarify the source of the small increase in DNA methylation in the 8w samples. Overall, our findings suggest that DNA methylation patterns in mouse spermatozoa are relatively stable throughout reproductive life.

Progress towards human primordial germ cell specification in vitro

Primordial germ cells (PGCs) have long been considered the link between one generation and the next. PGC specification begins in the early embryo as a result of a highly orchestrated combination of transcriptional and epigenetic mechanisms. Understanding the molecular events that lead to proper PGC development will facilitate the development of new treatments for human infertility as well as species conservation. This article describes the latest, most relevant findings about the mechanisms of PGC formation, emphasizing human PGC. It also discusses our own laboratory's progress in using transdifferentiation protocols to derive human PGCs (hPGCs). Our preliminary results arose from our pursuit of a sequential hPGC induction strategy that starts with the repression of lineage-specific factors in the somatic cell, followed by the reactivation of germ cell-related genes using specific master regulators, which can indeed reactivate germ cell-specific genes in somatic cells. While it is still premature to assume that fully functional human gametes can be obtained in a dish, our results, together with those recently published by others, provide strong evidence that generating their precursors, PGCs, is within reach.

Reproductive/Developmental Abnormalities Induced by Epigenetic Aberrations and Possible Environmental Causes

Foetal environmental factors, including maternal nutrition, hormonal disturbance, and chemical exposure, affect foetal growth and can cause birth defects. Recent studies have shown the link of poor foetal growth with increased risks of coronary heart disease, type II diabetes, kidney disease, and brain disorders in adulthood. Epigenetic modifications, such as DNA methylation and histone modifications, are involved in tissue- and developmental stage-specific gene expression and silencing, and they can be transmitted stably through mitotic cell division, thereby inducing long-term changes in gene regulation. Developmental programming during the foetal period, therefore, could affect adult health through epigenetic mechanisms. In fact, many studies using animal models have demonstrated that nutrient manipulation during pregnancy induces epigenetic alterations at specific loci or globally in the offspring. In this review, we summarize our findings that elucidate the effects of in utero environments on the human placental epigenome.

Small non-coding RNAs and their associated proteins in spermatogenesis

The importance of the gene regulation roles of small non-coding RNAs and their protein partners is of increasing focus. In this paper, we reviewed three main small RNA species which appear to affect spermatogenesis. MicroRNAs (miRNAs) are single stand RNAs derived from transcripts containing stem-loops and hairpins which target corresponding mRNAs and affect their stability or translation. Many miRNA species have been found to be related to normal male germ cell development. The biogenesis of piRNAs is still largely unknown but several models have been proposed. Some piRNAs and PIWIs target transposable elements and it is these that may be active in regulating translation or stem cell maintenance. endo-siRNAs may also participate in sperm development. Some possible interactions between different kinds of small RNAs have even been suggested. We also show that male germ granules are seen to have a close relationship with a considerable number of mRNAs and small RNAs. Those special structures may also participate in sperm development.

Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner

Di-(2-ethylhexyl)phtalate (DEHP) is a plasticizer with endocrine disrupting properties found ubiquitously in the environment and altering reproduction in rodents. Here we investigated the impact of prenatal exposure to DEHP on spermatogenesis and DNA sperm methylation in two distinct, selected, and sequenced mice strains. FVB/N and C57BL/6J mice were orally exposed to 300 mg/kg/day of DEHP from gestation day 9 to 19. Prenatal DEHP exposure significantly decreased spermatogenesis in C57BL/6J (fold-change = 0.6, p-value = 8.7*10^-4), but not in FVB/N (fold-change = 1, p-value = 0.9). The number of differentially methylated regions (DMRs) by DEHP-exposure across the entire genome showed increased hyper- and decreased hypo-methylation in C57BL/6J compared to FVB/N. At the promoter level, three important subsets of genes were massively affected. Promoters of vomeronasal and olfactory receptors coding genes globally followed the same trend, more pronounced in the C57BL/6J strain, of being hyper-methylated in DEHP related conditions. In contrast, a large set of micro-RNAs were hypo-methylated, with a trend more pronounced in the FVB/N strain. We additionally analyze both the presence of functional genetic variations within genes that were associated with the detected DMRs and that could be involved in spermatogenesis, and DMRs related with the DEHP exposure that affected both strains in an opposite manner. The major finding in this study indicates that prenatal exposure to DEHP can decrease spermatogenesis in a strain-dependent manner and affects sperm DNA methylation in promoters of large sets of genes putatively involved in both sperm chemotaxis and post-transcriptional regulatory mechanisms.