Diagnostic utility of high quality RNA in diverse clinical semen and sperm samples
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE52665 | GEO | 2013/11/23
SECONDARY ACCESSION(S): PRJNA229761
REPOSITORIES: GEO
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Project description:We report quantitation of specific mRNAs in two RNA samples isolated from normozoospermic whole semen Examination of 2 different normozoospermic semen samples by RNA-seq Please note that raw data for 'GSM1273824: AY4' is incomplete.
2013-11-23 | E-GEOD-52665 | biostudies-arrayexpress
Project description:RNA-Seq technique was applied to investigate the effects of two semen collection methods (Pelleted vs Liquefied) and two sperm purification methods (SCLB vs PS) to the integrity of isolated RNAs at different perspectives. The same set of semen samples were applied to investigate the qualitative and quantitative effect of semen collection methods and sperm cell purification methods on sperm transcript profiling.
2013-12-09 | E-GEOD-43586 | biostudies-arrayexpress
Project description:To determine if disease can modify aging patterns in an affected tissue without altering the aging patterns of other tissues, blood and semen of individuals with oligozoospermia (n=10) were compared to the blood and semen of individuals with normozoospermia (n=24). The Horvath and Jenkins age calculators were utilized to predict the epigenetic age of blood and sperm through the use of DNA methylation. Using these calculators, it was found that sperm of oligozoospermic men were predicted to be significantly older than the sperm of normozoospermic men; however, there was not a significant epigenetic age difference in blood. These results lead to the conclusion that tissue specific aging is occurring in sperm of oligozoospermic individuals but not in unaffected somatic tissues (in our case, blood).
2023-09-08 | GSE213366 | GEO
Project description:EVs are known to contain important cargo of biologically active and regulatory molecules including ncRNAs. EVs in seminal plasma, play an important role in sperm functions , including motility and fertilization. However, less is known about the comprehensive profile of spEV ncRNAs in clinical cohort and if these profiles differ by semen quality status. We assessed sperm-free spEV ncRNA profiles from semen samples of male partners receiving IVF treatment. Men were classified into having normal (n = 59, Status 0) or poor (n = 32, Status 1) semen quality based on WHO semen parameter guidelines.
2023-04-02 | GSE203494 | GEO
Project description:RNA-Seq technique was applied to investigate the effects of two semen collection methods (Pelleted vs Liquefied) and two sperm purification methods (SCLB vs PS) to the integrity of isolated RNAs at different perspectives.
2013-12-09 | GSE43586 | GEO
Project description:<h4><strong>BACKGROUND: </strong>Semen quality is negatively correlated with male age and is mainly quantified by a routine semen analysis, which is descriptive and inconclusive. Sperm proteins or semen metabolites are used as the intermediate or end-products, reflecting changes in semen quality, and hold much promise as a new biomarker to predict fertility in advanced-aged males.</h4><h4><strong>OBJECTIVES: </strong>In this study, we sought to assess whether the semen metabolome and proteome of aged males can affect semen quality and serve as biomarkers for predicting semen quality.</h4><p><strong>MATERIALS AND METHODS: </strong>We retrospectively analyzed 12825 males that underwent semen routine analysis to understand the age-dependent changes in sperm quality. To identify the difference between aged and young adults, metabolomics (n=60) analyses of semen and proteomics (n=12) analyses of sperm were conducted. Finally, integrated machine learning of metabolomics was conducted to screen biomarkers to identify aging semen.</p><p><strong>RESULTS:</strong> We discovered that male age was positively correlated with sperm concentration as well as DNA fragmentation index(DFI), and negatively with progressive motile sperm count, total sperm count, sperm volume and progressive sperm motility. The differential metabolites were significantly enriched in various metabolic pathways, and four of these differential metabolites (Pipamperone, 2,2-Bis(hydroxymethyl)-2,2',2''-nitrilotriethanol, Arg-Pro and Triethyl phosphate) were utilized to establish a biomarker panel to identify aging semen. Proteomic analysis showed that differential proteins were significantly enriched in protein digestion and absorption and some energy-related pathways. An integrated analysis of the metabolome and proteome identified differential energy metabolism and oxidative stress-related proteins, which could explain the decreased motility and the increased DFI of aging sperm.</p><p><strong>DISCUSSION AND CONCLUSION:</strong> We provide compelling evidence that the changes in semen metabolome and sperm proteome are related to the decline of semen quality in aged males. Moreover, a biomarker panel based on four metabolites was established to identify aging semen.</p>
2024-01-16 | MTBLS5289 | MetaboLights
Project description:human semen metagenome Targeted Locus (Loci)
| PRJNA319051 | ENA
Project description:PurposeMale infertility is a complex health condition. To our knowledge there are no molecular biomarkers of male infertility. Sperm RNA is a potential biomarker for detecting sperm abnormalities and viability at infertility clinics. However, RNA use is hindered by its inconsistent quantity, quality, multiple cell types in semen and condensed sperm structure.Materials and methodsWe tested the usefulness of high quality RNA isolated from mature sperm and whole semen by our protocol, which reduces RNA degradation by maintaining semen and protocol components at 37 C and decreasing processing time. We isolated RNA from 83 whole semen samples, 18 samples of motile sperm prepared by the swim-up protocol and 18 of sperm prepared by the standard Percoll gradient method.ResultsElectrophoretic and spectral analysis of RNA revealed high quality 18S and 28S rRNAs in 71 of 83 whole semen samples (86%) and 15 of 18 mature sperm swim-up samples (83%). However, high quality RNA was isolated from only 7 of 18 Percoll gradient sperm samples (39%). Interestingly quantitative reverse transcriptase-polymerase chain reaction analysis of 4 somatic and 10 germ cell markers showed that whole semen and swim-up samples had similar RNA profiles. RNA sequencing revealed that most encoded proteins were involved in mature sperm function, regulation of DNA replication, transcription, translation, cell cycle and embryo development.ConclusionsWe believe that semen and sperm specific RNAs are highly informative biomarkers for germ cell stages and somatic cell contribution. Therefore, these RNAs could be valuable diagnostic indicators of sperm survival, fertilization and early embryogenesis, and could serve as a predictor of the in vitro fertilization prognosis.
| S-EPMC4382362 | biostudies-literature
Project description:We present a pilot study based on a multi-level molecular profiling of semen from 33 healthy young subjects residing in a high (n=18) and low (n=15) polluted area in Italy. Samples were analyzed for spermiogram parameters, protamine/histone ratio, Sperm Nuclear Basic Proteins (SNBP) and DNA interaction, oxidative DNA damage, trace metals in semen, and spermatocyte small-noncoding RNA expression. Although comparable mobility and concentration of sperm cells were observed between samples from the two areas, a higher immature/immune cell concentration characterized the semen of subjects from the high-polluted area. These subjects also showed a lower ratio of protamine to histone and a reduced ability of SNBP to bind and protect DNA from oxidative damage. Trace metal analysis showed an altered ratio of copper to zinc in their semen. In spermatocytes from the high-polluted area, altered levels of 32 microRNAs involved in intraflagellar transport, response to oxidative species, nuclear envelope organization, and lipid metabolism were observed. These miRNA profiles resemble those of spermatocytes undergoing differentiation, including a decrease of miR-23b-3p and let-7f-5p and an increase of miR-34b-3p levels. MicroRNAs expression profiles were coherently related to the sperm concentration in both study groups. In addition, a significant decrease of piRNA levels was also observed. These results support a model that provides new insights into the environmental impact on male germ cells.
2023-12-18 | GSE237651 | GEO