Systems Biology in Reproductive Medicine最新文献

The differential expression and direct targeting of mRNA by miRNA are two main logics of the traditional approach to constructing the miRNA-mRNA network. This approach, could be led to the loss of considerable information and some challenges of direct targeting. To avoid these problems, we analyzed the rewiring network and constructed two miRNA-mRNA expression bipartite networks for both normal and primary prostate cancer tissue obtained from PRAD-TCGA. We then calculated beta-coefficient of the regression-model when miR was dependent and mRNA independent for each miR and mRNA and separately in both networks. We defined the rewired edges as a significant change in the regression coefficient between normal and cancer states. The rewired nodes through multinomial distribution were defined and network from rewired edges and nodes was analyzed and enriched. Of the 306 rewired edges, 112(37%) were new, 123(40%) were lost, 44(14%) were strengthened, and 27(9%) weakened connections were discovered. The highest centrality of 106 rewired mRNAs belonged to PGM5, BOD1L1, C1S, SEPG, TMEFF2, and CSNK2A1. The highest centrality of 68 rewired miRs belonged to miR-181d, miR-4677, miR-4662a, miR-9.3, and miR-1301. SMAD and beta-catenin binding were enriched as molecular functions. The regulation was a frequently repeated concept in the biological process. Our rewiring analysis highlighted the impact of β-catenin and SMAD signaling as also some transcript factors like TGFB1I1 in prostate cancer progression. Altogether, we developed a miRNA-mRNA co-expression bipartite network to identify the hidden aspects of the prostate cancer mechanism, which traditional analysis -like differential expression- was not detect it.

Infertility is clinically defined as the inability to achieve pregnancy within 12 months of regular unprotected sexual intercourse and affects 15% of couples worldwide. Therefore, the identification of novel biomarkers that can accurately predict male reproductive health and couples' reproductive success is of major public health significance. The objective of this pilot study is to test whether untargeted metabolomics is capable of discriminating reproductive outcomes and understand associations between the internal exposome of seminal plasma and the reproductive outcomes of semen quality and live birth among ten participants undergoing assisted reproductive technology (ART) in Springfield, MA. We hypothesize that seminal plasma offers a novel biological matrix by which untargeted metabolomics is able to discern male reproductive status and predict reproductive success. The internal exposome data was acquired using UHPLC-HR-MS on randomized seminal plasma samples at UNC at Chapel Hill. Unsupervised and supervised multivariate analyses were used to visualize the differentiation of phenotypic groups classified by men with normal or low semen quality based on World Health Organization guidelines as well as by successful ART: live birth or no live birth. Over 100 exogenous metabolites, including environmentally relevant metabolites, ingested food components, drugs and medications, and metabolites relevant to microbiome-xenobiotic interaction, were identified and annotated from the seminal plasma samples, through matching against the NC HHEAR hub in-house experimental standard library. Pathway enrichment analysis indicated that fatty acid biosynthesis and metabolism, vitamin A metabolism, and histidine metabolism were associated sperm quality; while pathways involving vitamin A metabolism, C21-steroid hormone biosynthesis and metabolism, arachidonic acid metabolism, and Omega-3 fatty acid metabolism distinguished live birth groups. Taken together, these pilot results suggest that seminal plasma is a novel matrix to study the influence of the internal exposome on reproductive health outcomes. Future research aims to increase the sample size to validate these findings.

There is a correlation between teratozoospermia and production of reactive oxygen species leading to poor assisted reproductive techniques outcomes. This study aimed to examine the effect of plasma-rich in growth factors (PRGF) on teratozoospermic samples. Twenty-five teratozoospermic samples were included in this study. After sperm preparation, it was divided into four groups, including 0 (control), 1, 5, and 10% PRGF. Sperm motility, viability (eosin-nigrosin staining), morphology (Papanicolaou staining), DNA fragmentation (sperm chromatin dispersion test), mitochondrial membrane potential (JC-1 staining by flow cytometry), and lipid peroxidation (measurement of malondialdehyde, MDA) were evaluated before and after 1 h of incubation with or without PRGF. Our results showed that after 1 h of incubation, the addition of 1% PRGF improved sperm progressive motility (47.72 ± 13.76%) compared to the control group (17.36 ± 8.50%) (p < 0.001). Also, 1% PRGF preserved the sperm's total motility (77.50 ± 13.28% vs. 65.63 ± 19.03%, for 1% PRGF and control, respectively) and viability after incubation. The rate of normal sperm morphology was the same between different groups. Higher mitochondrial membrane potential and lower DNA fragmentation were also observed in sperm treated with different concentrations of PRGF compared to the control group, but the differences were non-significant. The MDA levels were significantly decreased in PRGF-treated groups compared to the control group (0.99 ± 0.62, 0.95 ± 0.33, 0.95 ± 0.79, and 1.49 ± 0.27 for 1% PRGF, 5% PRGF, 10% PRGF and control, respectively). Based on our results, it seems that PRGF incubation can improve sperm parameters and especially decrease the level of malondialdehyde as an indicator of oxidative stress, which is one of the main problems of teratozoospermic samples.

For decades, the endometrium was considered to be a sterile environment. However, now this concept is disputed, and there is growing evidence that microbiota composition might affect endometrial receptivity. Routine clinical management of infertility is still limited to a microbiological assessment of the lower reproductive tract. The purpose of this study was to compare the abundance of various bacterial, fungal, and viral species, qualitatively and quantitatively, in vaginal, cervical, and endometrial biomaterial of infertile patients. A total of 300 samples from 100 infertile patients of a private assisted reproduction clinic were analyzed. A broad real-time polymerase chain reaction panel was used to identify 28 relevant microbial taxa as well as three members of the Herpesviridae family. All patients underwent endometrial biopsy for further histopathological evaluation. Analysis of the microbial diversity (within the boundaries of the detection panel) revealed that Shannon indexes in the cervix and vagina were similar (1.4 × 10^-2 (1.6 × 10^-3 - 6.5 × 10^-1) vs 1.9 × 10^-2 (2.3 × 10^-3 - 5.3 × 10^-1), respectively, p = 0.502), whereas endometrial indexes differed significantly from both regions (0 (0 - 1.4 × 10^-1), p < 0.0001). Surprisingly, 17 microbial and viral taxa were detected in at least one sample. Endometrium exhibited a quite distinct microbiological profile, being different at the detection rates of 14 taxa (p < 0.05). Remarkably, 4% and 2% of endometrial samples were positive for Cytomegalovirus and Candida spp., respectively, while these were undetectable in corresponding cervical and vaginal samples. Prevalence of the Gardnerella vaginalis + Prevotella bivia + Porphyromonas spp. group in endometrium was associated with a low abundance of Lactobacillus spp. (p = 0.039). No noteworthy associations were identified between various microbiota characteristics and clinical parameters, such as chronic endometritis, uterine polyps and adhesions, endometriosis, and a history of sexually transmitted infections. These findings indicate that the microbiological profile of the endometrium is unique, and the analysis of the lower reproductive tract should supplement, rather than be a substitute for it.

Vertebrate sex determination and differentiation are coordinated by the activations and maintenance of reproductive transcriptional-regulatory networks (TRNs). There is considerable interest in studying the conserved design principles and functions of reproductive TRNs given that their intricate regulation is susceptible to disruption by gene mutations or exposures to exogenous endocrine disrupting chemicals (or EDCs). In this manuscript, the Boolean rules describing reproductive TRNs in humans, mice, and zebrafish, were represented as a pseudo-stoichiometric matrix model. This model mathematically described the interactions of 35 transcription factors with 21 sex determination and differentiation genes across the three species. The in silico approach of Extreme Pathway (ExPa) analysis was used to predict the extent of TRN gene activations subject to the species-specific transcriptomics data, from across various developmental life-stages. A goal of this work was to identify conserved and functional reproductive TRNs across the three species. ExPa analyses predicted the sex differentiation genes, DHH, DMRT1, and AR, to be highly active in male humans, mice, and zebrafish. Whereas FOXL2 was the most active gene in female humans and mice; and CYP19A1A in female zebrafish. These results agree with the expectation that regardless of a lack of sex determination genes in zebrafish, the TRNs responsible for canalizing male vs. female sexual differentiation are conserved with mammalian taxa. ExPa analysis therefore provides a framework with which to study the TRNs that influence the development of sexual phenotypes. And the in silico predicted conservation of sex differentiation TRNs between mammals and zebrafish identifies the piscine species as an effective in vivo model to study mammalian reproductive systems under normal or perturbed pathologies.

Long non-coding RNA PSMG3-AS1 is known to play critical roles in several types of cancer, while its role in prostate carcinoma (PC) is unknown. This study aimed to explore the involvement of PSMG3-AS1 in PC. In this study, RT-qPCR analysis showed that PSMG3-AS1 was upregulated, while miR-106b was downregulated in PC. PSMG3-AS1 and miR-106b were inversely and significantly correlated across PC tissue samples. In addition, in PC cells, overexpression of PSMG3-AS1 increased the DNA methylation of miR-106b and decreased the expression levels of miR-106b. In contrast, no significant alteration in the expression of PSMG3-AS1 was observed in cells transfected with miR-106b mimic. Cell proliferation analysis showed that PSMG3-AS1 reduced the inhibitory effects of miR-106b overexpression on cell proliferation. Taken together, our data suggested that PSMG3-AS1 could downregulate miR-106b through DNA methylation to suppress PC cell proliferation.

It is well known that various human papillomavirus (HPV) genotypes are present in semen specimens. Also, it has been demonstrated that sperm parameters are negatively affected when HPV infection is present in the sperm sample. Besides all these, the effect of cryopreservation on HPV sensitivity and resistance is not known. The aim of the present study is to evaluate first the prevalence of HPV and secondly to elucidate whether cryopreservation of sperm HPV-positive samples has any effect on the viability of HPV. For this purpose, a cohort of 78 sperm specimens was used from a respective number of patients. After giving informed consent, semen analysis was performed. Each sperm sample was divided into four equal aliquots. The first one (fresh) was evaluated for the prevalence of HPV, while the other three aliquots were cryopreserved by adding an equal quantity of cryoprotectant and plunged into the LN. Each of the three aliquots was thawed 3, 6, and 12 months later, respectively, so as to evaluate whether there is a time-resistance period of HPV prevalence. HPV infection was found to be in eleven sperm samples, demonstrating a 14.1% (11/78) HPV prevalence. Among the HPV-positive samples, six of them were high-risk and the remaining were low-risk genotypes. Moreover, the high-risk fresh samples demonstrated higher motility values than the low-risk samples (60% ± 2.7 vs 45.6% ± 3.7, p < .05), while semen volume in the high-risk samples was significantly lower than the respective volume in the low-risk samples (2.26 ± 0.2ml vs 3.5 ± 0.6ml, p < .05). Interestingly, cryopreservation of the HPV-positive samples resulted in the sustainability and time-resistance of HPV in all high-risk HPV-positive samples, something that was not the case with the low-risk HPV-positive samples. Conclusively, sperm samples infected with high-risk HPV, demonstrate lower sperm parameters and time-resistance activity during cryopreservation.

The purpose of this study is to provide novel information through Next Generation Sequencing (NGS) for the characterization of viral and bacterial RNA cargo of human sperm cells from healthy fertile donors. For this, RNA-seq raw data of poly(A) RNA from 12 sperm samples from fertile donors were aligned to microbiome databases using the GAIA software. Species of viruses and bacteria were quantified in Operational Taxonomic Units (OTU) and filtered by minimal expression level (>1% OTU in at least one sample). Mean expression values (and their standard deviation) of each species were estimated. A Hierarchical Cluster Analysis (HCA) and a Principal Component Analysis (PCA) were performed to detect common microbiome patterns among samples. Sixteen microbiome species, families, domains, and orders surpassed the established expression threshold. Of the 16 categories, nine corresponded to viruses (23.07% OTU) and seven to bacteria (2.77% OTU), among which the Herperviriales order and Escherichia coli were the most abundant, respectively. HCA and PCA displayed four clusters of samples with a differentiated microbiome fingerprint. This work represents a pilot study into the viruses and bacteria that make up the human sperm microbiome. Despite the high variability observed, some patterns of similarity among individuals were identified. Further NGS studies under standardized methodological procedures are necessary to achieve a deep knowledge of the semen microbiome and its implications in male fertility.

This retrospective study assessed the biological intra-individual variability of the percentage of sperm with DNA damage (SDF) observed in subsequent ejaculates of the same individual. Variation in SDF was analyzed using the Mean Signed Difference (MSD) statistic based on 131 individuals, comprising 333 ejaculates. Either two, three or four ejaculates were collected from each individual. With this cohort of individuals two main questions were addressed; (1) does the number of ejaculates analyzed influence the variability in the level of SDF associated with each individual? and (2) is the variability observed in SDF similar when individuals are ranked according to their level of SDF? Results showed that the variation observed in mean SDF was not different when 2, 3 or 4 ejaculates were analyzed; consequently, we suggest that the assessment of SDF based on two ejaculates is likely to be representative of the mean SDF expected for the individual. In parallel, it was determined that the variation in SDF increased as SDF increased; in individuals presenting with an SDF value of lower than 30% (potentially fertile), only 5% possessed levels of MSD that could be considered as variable as that presented by individuals presenting with a recurrent high SDF. Finally, we showed that a single assessment of SDF in individuals with medium SDF (20-30%) was less likely to be predictive of the SDF value in the next ejaculate, and therefore, less informative of the patient's SDF status.

There is a need to understand the molecular basis of testes under Non-Obstructive Azoospermia (NOA), a state of failed spermatogenesis. There has been a lack of attention to the transcriptome at the level of alternatively spliced mRNAs (iso-mRNAs) and the mechanism of gene expression regulation. Hence, we aimed to establish a reliable iso-mRNA profile of NOA-testes, and explore molecular mechanisms - especially those related to gene expression regulation. We sequenced mRNAs from testicular samples of donors with complete spermatogenesis (control samples) and a failure of spermatogenesis (NOA samples). We identified differentially expressed genes and their iso-mRNAs via standard NGS data analyses. We then listed these iso-mRNAs hierarchically based on the extent of consistency of differential quantities across samples and groups, and validated the lists via RT-qPCRs (for 80 iso-mRNAs). In addition, we performed extensive bioinformatic analysis of the splicing features, domains, interactions, and functions of differentially expressed genes and iso-mRNAs. Many top-ranking down-regulated genes and iso-mRNAs, i.e., those down-regulated more consistently across the NOA samples, are associated with mitosis, replication, meiosis, cilium, RNA regulation, and post-translational modifications such as ubiquitination and phosphorylation. Most down-regulated iso-mRNAs correspond to full-length proteins that include all expected domains. The predominance of alternative promoters and termination sites in these iso-mRNAs indicate their gene expression regulation via promoters and UTRs. We compiled a new, comprehensive list of human transcription factors (TFs) and used it to identify TF-'TF gene' interactions with potential significance in down-regulating genes under the NOA condition. The results indicate that RAD51 suppression by HSF4 prevents SP1-activation, and SP1, in turn, could regulate multiple TF genes. This potential regulatory axis and other TF interactions identified in this study could explain the down-regulation of multiple genes in NOA-testes. Such molecular interactions may also have key regulatory roles during normal human spermatogenesis.