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

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.

piRNA-disease association prediction based on multi-channel graph variational autoencoder

Piwi-interacting RNA (piRNA) is a type of non-coding small RNA that is highly expressed in mammalian testis. PiRNA has been implicated in various human diseases, but the experimental validation of piRNA-disease associations is costly and time-consuming. In this article, a novel computational method for predicting piRNA-disease associations using a multi-channel graph variational autoencoder (MC-GVAE) is proposed. This method integrates four types of similarity networks for piRNAs and diseases, which are derived from piRNA sequences, disease semantics, piRNA Gaussian Interaction Profile (GIP) kernel, and disease GIP kernel, respectively. These networks are modeled by a graph VAE framework, which can learn low-dimensional and informative feature representations for piRNAs and diseases. Then, a multi-channel method is used to fuse the feature representations from different networks. Finally, a three-layer neural network classifier is applied to predict the potential associations between piRNAs and diseases. The method was evaluated on a benchmark dataset containing 5,002 experimentally validated associations with 4,350 piRNAs and 21 diseases, constructed from the piRDisease v1.0 database. It achieved state-of-the-art performance, with an average AUC value of 0.9310 and an AUPR value of 0.9247 under five-fold cross-validation. This demonstrates the method's effectiveness and superiority in piRNA-disease association prediction.

Multiple transcriptome analyses reveal mouse testis developmental dynamics

The testes are the organs of gamete production and testosterone synthesis. Up to date, no model system is available for mammalian testicular development, and only few studies have characterized the mouse testis transcriptome from no more than three postnatal ages. To describe the transcriptome landscape of the developing mouse testis and identify the potential molecular mechanisms underlying testis maturation, we examined multiple RNA-seq data of mouse testes from 3-week-old (puberty) to 11-week-old (adult). Sperm cells appeared as expected in 5-week-old mouse testis, suggesting the proper sample collection. The principal components analysis revealed the genes from 3w to 4w clustered away from other timepoints, indicating they may be the important nodes for testicular development. The pairwise comparisons at two adjacent timepoints identified 7,612 differentially expressed genes (DEGs), resulting in 58 unique mRNA expression patterns. Enrichment analysis identified functions in tissue morphogenesis (3-4w), regulation of peptidase activity (4-5w), spermatogenesis (7-8w), and antigen processing (10-11w), suggesting distinct functions in different developmental periods. 50 hub genes and 10 gene cluster modules were identified in the testis maturation process by protein-protein interaction (PPI) network analysis, and the miRNA-lncRNA-mRNA, miRNA-circRNA-mRNA and miRNA-circRNA-lncRNA-mRNA competing endogenous RNA (ceRNA) networks were constructed. The results suggest that testis maturation is a complex developmental process modulated by various molecules, and that some potential RNA-RNA interactions may be involved in specific developmental stages. In summary, this study provides an update on the molecular basis of testis development, which may help to understand the molecular mechanisms of mouse testis development and provide guidance for mouse reproduction.

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.

PIWI-interacting RNAs and human testicular function

Small noncoding RNAs (sncRNAs) are pieces of RNA with a length below 200 bp and represent a diverse group of RNAs having many different biological functions. The best described subtype is the microRNAs which primarily function in posttranscriptional gene regulation and appear essential for most physiological processes. Of particular interest for the germline is the PIWI-interacting RNAs (piRNAs) which are a class of sncRNA of 21-35 bp in length that are almost exclusively found in germ cells. Recently, it has become clear that piRNAs are essential for testicular function, and in this perspective, we outline the current knowledge of piRNAs in humans. Although piRNAs appear unique to germ cells, they have also been described in various somatic cancers and biofluids. Here, we discuss the potential function of piRNAs in somatic tissues and whether detection in biofluids may be used as a biomarker for testicular function. This article is categorized under: Reproductive System Diseases > Genetics/Genomics/Epigenetics Reproductive System Diseases > Molecular and Cellular Physiology.

Liquid Biopsy for Cancer Cachexia: Focus on Muscle-Derived microRNAs

Cancer cachexia displays a complex nature in which systemic inflammation, impaired energy metabolism, loss of muscle and adipose tissues result in unintentional body weight loss. Cachectic patients have a poor prognosis and the presence of cachexia reduces the tolerability of chemo/radio-therapy treatments and it is frequently the primary cause of death in advanced cancer patients. Early detection of this condition could make treatments more effective. However, early diagnostic biomarkers of cachexia are currently lacking. In recent years, although solid biopsy still remains the "gold standard" for diagnosis of cancer, liquid biopsy is gaining increasing interest as a source of easily accessible potential biomarkers. Moreover, the growing interest in circulating microRNAs (miRNAs), has made these molecules attractive for the diagnosis of several diseases, including cancer. Some muscle-derived circulating miRNA might play a pivotal role in the onset/progression of cancer cachexia. This topic is of great interest since circulating miRNAs might be easily detectable by means of liquid biopsies and might allow an early diagnosis of this syndrome. We here summarize the current knowledge on circulating muscular miRNAs involved in muscle atrophy, since they might represent easily accessible and promising biomarkers of cachexia.

Dynamic expression and functional analysis of circular RNA in the gonads of Chinese soft-shelled turtles (Pelodiscus sinensis)

Circular RNA (circRNA) is a noncoding RNA that can regulate a variety of biological processes. CircRNAs can regulate gene expression posttranscriptionally by acting as microRNA sponges. Many turtle species are remarkable organisms due to their reproductive processes. However, information on circRNA in the gonads of turtles is limited. In this study, 6, 121 circRNAs were identified in the testes and ovaries of Chinese soft-shelled turtles (Pelodiscus sinensis) using the Illumina platform, and 710 circRNAs were significantly differentially expressed (DE). The DE circRNAs included 541 upregulated and 169 downregulated circRNAs in the testes. GO and KEGG pathway analysis indicated that the DE circRNAs were enriched in several signaling pathways, including GnRH, Wnt, FoxO, Progesterone mediated oocyte maturation, and mTOR signaling pathways. Five DE circRNAs were randomly selected, and their relative expression levels in ovaries and testes were detected by quantitative real-time PCR. All of these circRNAs were differentially expressed. In addition, 9, 883 interactions between circRNAs and miRNAs were predicted in the turtles. Target genes of the miRNAs include a range of genes regulating gonadal development. Seven ceRNA networks (DE circRNAs-DE miRNAs-DE mRNAs), including 7 DE circRNAs, 11 DE miRNAs and 20 DE mRNAs, were constructed. The networks included Cdc6, the miR-1 family, the miR-203 family, and the miR-302 family. The expression profile of gonadal circRNAs might help to elucidate the roles of nonprotein coding RNAs in turtle gonadal development.

Small RNAs in Seminal Plasma as Novel Biomarkers for Germ Cell Tumors

Simple Summary

Testicular cancer is the most common cancer among young men. It is rarely diagnosed at early stages, being only detected with a highly invasive procedure that presents notable side-effects. Circulating small RNAs have recently been identified as testicular tumor markers, but are unable to diagnose testicular cancer at an early pre-invasive stage. So far, studies have been limited to microRNAs, with other small RNAs remaining unexplored as likely biomarkers. By sequencing all small RNAs in semen samples from men with different stages of testicular cancer and healthy men, we identify signatures predictive of cancer, even at an early stage. Thus, our study provides great potential for non-invasive early diagnosis of testicular cancer. Extensive biological variance in small RNA levels across samples, together with small sample sizes, limit the power to detect single small RNA markers. Hence, larger studies are needed to confirm our findings and deduce their full diagnostic capacity.

Abstract

Circulating miRNAs secreted by testicular germ cell tumors (TGCT) show great potential as novel non-invasive biomarkers for diagnosis of TGCT. Seminal plasma (SP) represents a biofluid closer to the primary site. Here, we investigate whether small RNAs in SP can be used to diagnose men with TGCTs or the precursor lesions, germ cell neoplasia in situ (GCNIS). Small RNAs isolated from SP from men with TGCTs (n = 18), GCNIS-only (n = 5), and controls (n = 25) were sequenced. SP from men with TGCT/GCNIS (n = 37) and controls (n = 22) were used for validation by RT-qPCR. In general, piRNAs were found at lower levels in SP from men with TGCTs. Ten small RNAs were found at significantly (q-value < 0.05) different levels in SP from men with TGCT/GCNIS than controls. Random forests classification identified sets of small RNAs that could detect either TGCT/GCNIS or GCNIS-only with an area under the curve of 0.98 and 1 in ROC analyses, respectively. RT-qPCR validated hsa-miR-6782-5p to be present at 2.3-fold lower levels (p = 0.02) in the SP from men with TGCTs compared with controls. Small RNAs in SP show potential as novel biomarkers for diagnosing men with TGCT/GCNIS but validation in larger cohorts is needed.

The Application of Single-Cell RNA Sequencing in Mammalian Meiosis Studies

Meiosis is a cellular division process that produces gametes for sexual reproduction. Disruption of complex events throughout meiosis, such as synapsis and homologous recombination, can lead to infertility and aneuploidy. To reveal the molecular mechanisms of these events, transcriptome studies of specific substages must be conducted. However, conventional methods, such as bulk RNA-seq and RT-qPCR, are not able to detect the transcriptional variations effectively and precisely, especially for identifying cell types and stages with subtle differences. In recent years, mammalian meiotic transcriptomes have been intensively studied at the single-cell level by using single-cell RNA-seq (scRNA-seq) approaches, especially through two widely used platforms, Smart-seq2 and Drop-seq. The scRNA-seq protocols along with their downstream analysis enable researchers to accurately identify cell heterogeneities and investigate meiotic transcriptomes at a higher resolution. In this review, we compared bulk RNA-seq and scRNA-seq to show the advantages of the scRNA-seq in meiosis studies; meanwhile, we also pointed out the challenges and limitations of the scRNA-seq. We listed recent findings from mammalian meiosis (male and female) studies where scRNA-seq applied. Next, we summarized the scRNA-seq analysis methods and the meiotic marker genes from spermatocytes and oocytes. Specifically, we emphasized the different features of the two scRNA-seq protocols (Smart-seq2 and Drop-seq) in the context of meiosis studies and discussed their strengths and weaknesses in terms of different research purposes. Finally, we discussed the future applications of scRNA-seq in the meiosis field.

Current mechanistic perspectives on male reproductive toxicity induced by heavy metals

Environmental and occupational exposures to heavy metals have led to various deleterious damages to the biological system of which infertility is one of them. Infertility is a global public health concern, affecting 15% of all couples of reproductive age. Out of the 100% cases of reported infertility among couples, 40% of the cases are related to male factors; including decreased semen quality. This review focuses on the recent mechanistic perspectives of heavy metal-induced male reproductive toxicity. The associated toxic metal-mediated mechanisms of male reproductive toxicity include ion mimicry, disruption of cell signaling pathways, oxidative stress, altered gene expression, epigenetic regulation of gene expression, apoptosis, disruption of testis/blood barrier, inflammation and endocrine disruption. The current literature suggests that non-coding RNAs (ncRNAs) mediate paternal intergenerational epigenetic inheritance and thus has a direct functional importance, as well as possess novel biomarker potential, for male reproductive toxicity. To identify the specific ncRNAs with the most profound impacts on heavy metal-induced male reproductive toxicity should be thrust of further research.

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.