Infertility network and hub genes for nonobstructive azoospermia utilizing integrative analysis.
Ontology highlight
ABSTRACT:
SUBMITTER: Han B
PROVIDER: S-EPMC7993690 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Infertility is a problem that affects around 15% of couples. In 40-50% of these couples male infertility is involved. The cause of male infertility is still poorly diagnosed and treated. One of the entities of male infertility is disturbed spermatogenesis, which can lead to nonobstructive azoospermia (NOA), with no sperm cells in the ejaculate. The whole genome sequencing (WGS) allow us to identify novel rare variants in potentially NOA-associated genes. One of them was ESX1 gene. The aim of the study was to activate the ESX1 gene using CRISPRa technology in testicular seminoma cells - TCam2. In this study we achieved the successful activation of ESX1 gene in genetically modified TCam-2 cells using CRISPRa system, in which the expression level of ESX1 gene was significantly higher compared to WT cells and negative control with non-targeted sgRNA (p<0.01). These results were successfully confirmed at protein level by using Western blotting and immunofluorescence. Using RNA-seq analysis we determined the genes that were potentially regulated by ESX1 gene. Such genes associated with proliferation and apoptosis process: CCND1, KDR, WNT11, LGALS3, LINC00662, PDE1C, RPS6KA5, FGF4, NANOG, L1TD1, which were differently expressed in cells with ESX1 gene activation in comparison to the controls (p<0.05).
2023-10-11 | GSE227497 | GEO
Project description:Infertility is a problem that affects approximately 15% of couples, and male infertility is responsible for 40-50% of these cases. The cause of male infertility is still poorly diagnosed and treated. One of the prominent causes of male infertility is disturbed spermatogenesis, which can lead to nonobstructive azoospermia (NOA). Whole-genome sequencing (WGS) allows us to identify novel rare variants in potentially NOA-associated genes, among others, in the ESX1 gene. The aim of this study was to activate the ESX1 gene using CRISPRa technology in human germ cells (testicular seminoma cells-TCam-2). Successful activation of the ESX1 gene in TCam-2 cells using the CRISPRa system was achieved, and the expression level of the ESX1 gene was significantly higher in modified TCam-2 cells than in WT cells or the negative control with nontargeted gRNA (p < 0.01). Using RNA-seq, a network of over 50 genes potentially regulated by the ESX1 gene was determined. Finally, 6 genes, NANOG, CXCR4, RPS6KA5, CCND1, PDE1C, and LINC00662, participating in cell proliferation and differentiation were verified in azoospermic patients with and without a mutation in the ESX1 gene as well as in men with normal spermatogenesis, where inverse correlations in the expression levels of the observed genes were noted.
| S-EPMC10545701 | biostudies-literature
Project description:Processing of pre-mRNA into mRNA is an important regulatory mechanism in eukaryotes that is mediated by the spliceosome, a huge and dynamic ribonucleoprotein complex. Splicing defects are implicated in a spectrum of human disease, but the underlying mechanistic links remain largely unresolved. Using a genome-wide association approach, we have recently identified single nucleotide polymorphisms in humans that associate with nonobstructive azoospermia (NOA), a common cause of male infertility. Here, using genetic manipulation of corresponding candidate loci in Drosophila, we show that the spliceosome component SNRPA1/U2A is essential for male fertility. Loss of U2A in germ cells of the Drosophila testis does not affect germline stem cells, but does result in the accumulation of mitotic spermatogonia that fail to differentiate into spermatocytes and mature sperm. Lack of U2A causes insufficient splicing of mRNAs required for the transition of germ cells from proliferation to differentiation. We show that germ cell-specific disruption of other components of the major spliceosome manifests with the same phenotype, demonstrating that mRNA processing is required for the differentiation of spermatogonia. This requirement is conserved, and expression of human SNRPA1 fully restores spermatogenesis in U2A mutant flies. We further report that several missense mutations in human SNRPA1 that inhibit the assembly of the major spliceosome dominantly disrupt spermatogonial differentiation in Drosophila. Collectively, our findings uncover a conserved and specific requirement for the major spliceosome during the transition from spermatogonial proliferation to differentiation in the male testis, suggesting that spliceosome defects affecting the differentiation of human spermatogonia contribute to NOA.
| S-EPMC4839444 | biostudies-literature
Project description:ObjectiveTo investigate the prevalence and clinical implications of biochemical hypogonadism in infertile men with nonobstructive azoospermia (NOA).DesignCohort study.SettingUniversity-affiliated tertiary center for male reproductive health.Patients767 consecutive normogonadotropic or hypergonadotropic patients with NOA undergoing infertility evaluation from 2014 to 2021.InterventionPatients aged 23-55 years underwent comprehensive clinical, hormonal, genetic, semen analysis, and histopathology evaluations and were classified on the basis of predefined baseline follicle-stimulating hormone (12 IU/L) and total testosterone (350 ng/dL) serum levels cutpoints into four groups: hypergonadotropic hypogonadal, hypergonadotropic eugonadal, normogonadotropic hypogonadal, and normogonadotropic eugonadal. All patients were naïve regarding previous sperm retrieval (SR) or hormonal therapy use.Main outcome measuresThe period prevalence of biochemical hypogonadism, defined as testosterone levels of <350 ng/dL, and the distribution of patients per group were computed. The associations between hypogonadism, clinical factors, and SR success were evaluated using multivariable logistic regression analyses. Adjusted relative risks (aRRs) and 95% confidence intervals (CIs) were estimated to assess the association between SR and patient classification.ResultsThe overall period prevalence of biochemical hypogonadism was 80.8% (95% CI 77.9%-83.4%). The prevalence of patients by group was hypergonadotropic hypogonadal (42.4%, 38.9%-45.9%), normogonadotropic hypogonadal (38.5%; 35.1%-41.9%), hypergonadotropic eugonadal (8.3%; 6.6%-10.5%), and normogonadotropic eugonadal (10.8%; 8.8%-13.2%). Reduced testicular volume and lower estradiol levels were associated with an increased likelihood of hypogonadism. Paternal age was also an independent predictor, with higher age linked to an increased likelihood of hypogonadism. Hypogonadism was less likely in patients with germ cell maturation arrest and more likely in those with Sertoli cell-only. Patients with hypergonadotropic hypogonadism had lower SR success than normogonadotropic eugonadal counterparts (aRR 0.611; 95% CI 0.398-0.855). In the subset of hypogonadal men, hypergonadotropic patients had lower SR success than normogonadotropic participants (aRR 0.632; 0.469-0.811).ConclusionThe prevalence of biochemical hypogonadism among men with NOA is substantial. Hypogonadism is associated with testicular volume, estradiol levels, age, and histopathology patterns. This condition impacts SR success and emphasizes the need for improved care for men with NOA.
| S-EPMC10958705 | biostudies-literature
Project description:BackgroundGenetic causes that lead to spermatogenetic failure in patients with nonobstructive azoospermia (NOA) have not been yet completely established.ObjectiveTo identify low-frequency NOA-associated single nucleotide variants (SNVs) using whole-genome sequencing (WGS).Materials and methodsMen with various types of NOA (n = 39), including samples that had been previously tested with whole-exome sequencing (WES; n = 6) and did not result in diagnostic conclusions. Variants were annotated using the Ensembl Variant Effect Predictor, utilizing frequencies from GnomAD and other databases to provide clinically relevant information (ClinVar), conservation scores (phyloP), and effect predictions (i.e., MutationTaster). Structural protein modeling was also performed.ResultsUsing WGS, we revealed potential NOA-associated SNVs, such as: TKTL1, IGSF1, ZFPM2, VCX3A (novel disease causing variants), ESX1, TEX13A, TEX14, DNAH1, FANCM, QRICH2, FSIP2, USP9Y, PMFBP1, MEI1, PIWIL1, WDR66, ZFX, KCND1, KIAA1210, DHRSX, ZMYM3, FAM47C, FANCB, FAM50B (genes previously known to be associated with infertility) and ALG13, BEND2, BRWD3, DDX53, TAF4, FAM47B, FAM9B, FAM9C, MAGEB6, MAP3K15, RBMXL3, SSX3 and FMR1NB genes, which may be involved in spermatogenesis.Discussion and conclusionIn this study, we identified novel potential candidate NOA-associated genes in 29 individuals out of 39 azoospermic males. Note that in 5 out of 6 patients subjected previously to WES analysis, which did not disclose potentially causative variants, the WGS analysis was successful with NOA-associated gene findings.
| S-EPMC9826517 | biostudies-literature
Project description:ObjectiveTo evaluate the association between promoter DNA methylation and discoidin domain receptor 1 (DDR1) gene expression in men with nonobstructive azoospermia (NOA).DesignComparing fibroblasts cultured from testicular biopsies using a high resolution Infinium 450K methylation array.SettingBasic research laboratory.Patient(s)Men with NOA (n = 16) and with normal spermatogenesis (n = 5).Intervention(s)None.Main outcome measure(s)Bisulfite clonal sequencing for validation and quantification of CpG methylation of DDR1; gene expression analysis of DDR1 with quantitative polymerase chain reaction and immunohistochemistry to validate the array results at mRNA and protein levels.Result(s)We validated promoter methylation, mRNA and protein levels of the CpG sites identified from array results. Differentially methylated CpG sites (∼20K) were identified using an F-test in the NOA samples. We identified 20 genes with >30% difference in DNA methylation within the promoter region of men with NOA and fertile controls. Of the aberrantly methylated genes, 10 were hypomethylated and 10 were hypermethylated genes. From the top 10 hypermethylated genes, six genes (MRI1, DCAF12L1, TMEM95, CECR2, DDR1, and NPHS2) were selected for validation because they were shown to be expressed in the testis. Of the six genes expressed in the fibroblasts cultured from testis, DDR1 showed an abnormal gene expression pattern. Three patients (19%) out of the 16 men with NOA for whom gene expression data were available had lower DDR1 expression levels (1.8x fold decrease) than the fertile men, whereas four (25%) men had higher expression levels (2x fold increase) of DDR1 compared with the levels in fertile men. Quantitative analysis by bisulfite clonal sequencing showed that one of the CpG sites (cg13329862) of DDR1 promoter was hypermethylated in NOA patients compared with fertile controls (53% vs. 15%). Immunohistochemical analysis suggests presence of DDR1 within cytoplasm of germ cells and peritubular connective tissue (in men with hypospermatogenesis) and decreased expression of the protein in men with Sertoli-cell only syndrome.Conclusion(s)Abnormal gene expression of DDR1 is associated with NOA. The functional relevance of aberrant methylation of DDR1 to expression of DDR1 in men with NOA warrants further investigation.
| S-EPMC4184939 | biostudies-literature
Project description:Nonobstructive azoospermia (NOA) refers to the failure of spermatogenesis, which affects approximately 1% of the male population and contributes to 10% of male infertility. NOA has an underlying basis of endocrine imbalances since proper human spermatogenesis relies on complex regulation and cooperation of multiple hormones. A better understanding of subtle hormonal disturbances in NOA would help design and improve hormone therapies with reduced risk in human fertility clinics. The purpose of this review is to summarize the research on the endocrinological aspects of NOA, especially the hormones involved in hypothalamic-pituitary-testis axis (HPTA), including gonadotropin-releasing hormone, follicle-stimulating hormone, luteinizing hormone, prolactin, testosterone, estradiol, sex hormone binding globulin, inhibin B, anti-Müllerian hormone, and leptin. For the NOA men associated with primary testicular failure, the quality of currently available evidence has not been sufficient enough to recommend any general hormone optimization therapy. Some other NOA patients, especially those with hypogonadotropic hypogonadism, could be treated with hormonal replacement. Although these approaches have succeeded in resuming the fertility in many NOA patients, the prudent strategies should be applied in individuals according to specific NOA etiology by balancing fertility benefits and potential risks. This review also discusses how NOA can be induced by immunization against hormones.
| S-EPMC9226686 | biostudies-literature
Project description:This study aimed to identify novel biomarkers associated with cuproptosis in human nonobstructive azoospermia (NOA). We obtained 4 NOA microarray datasets (GSE145467, GSE9210, GSE108886, and GSE45885) from the NCBI Gene Expression Omnibus database and merged them into training set. Another NOA dataset (GSE45887) was used as validation set. Differentially expressed cuproptosis-related genes were identified from training set. Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted. Least absolute shrinkage and selection operator regression and support vector machine-recursive feature elimination were used to identify hub cuproptosis-related genes. We calculated the expression of the hub cuproptosis-related genes in both validation set and patients with NOA. Gene set variation analysis was used to explore their potential biological functions. The risk prediction model was built by logistic regression analysis and was evaluated in the validation set. Finally, we constructed a competing endogenous RNA network. The training set included 29 patents in the control group and 92 in the NOA group, and 10 cuproptosis-related differentially expressed genes were identified. Subsequently, we screened 6 hub cuproptosis-related genes (DBT, GCSH, NFE2L2, NLRP3, PDHA1, and SLC31A1) by least absolute shrinkage and selection operator regression and support vector machine-recursive feature elimination. GCSH, NFE2L2, NLRP3, and SLC31A1 expressed higher in NOA group than in control group (P < .05) in the validation set (4 patients in control and 16 in NOA groups), while the expression levels of GCSH, NFE2L2, NLRP3, PDHA1, and SLC31A1 were higher in NOA group than in control group (P < .05) in our patients (3 patients in control and 4 in NOA groups). The model based on the 6-gene signature showed superior performance with an AUC value of 0.970 in training set, while 1.0 in validation set. Gene set variation analysis revealed a higher enrichment score of "homologous recombination" in the high expression groups of the 6 hub genes. Finally, we constructed a competing endogenous RNA network and found hsa-miR-335-3p and hsa-miR-1-3p were the most frequently related to the 6 hub genes. DBT, GCSH, NFE2L2, NLRP3, PDHA1, and SLC31A1 may serve as predictors of cuproptosis and play important roles in the NOA pathogenesis.
| S-EPMC11296415 | biostudies-literature
Project description:Natural killer (NK)/T-cell lymphoma (NKTCL) is a subtype of non-Hodgkin lymphoma with aggressive progression and poor prognosis. The molecular mechanisms of NKTCL have not been well-studied. Herein, we revealed the lymphoma-associated dysregulated genes and signaling pathways or biological processes in NKTCL. We characterized that the extracellular matrix (ECM) receptor interaction pathway and T-cell receptor signaling pathway were the main dysregulated pathways in NKTCL by Gene Ontology (GO) analysis and pathway enrichment analysis. By using weighted gene co-expression network analysis (WGCNA), the gene co-expression network of NKTCL (SRP049695) was constructed, and hub genes (LMO3, GRB14) were identified. In addition, another Gene Expression Omnibus (GEO) dataset (GSE69406) was used to validate these hub genes. Furthermore, these hub genes were identified and validated by survival analysis (GSE90597). These results provided novel insights into the pathogenesis of NKTCL. Of particular interest, LMO3 and GRB14 might be potential oncoproteins and biomarkers for the diagnosis and treatment of NKTCL.
| S-EPMC7066115 | biostudies-literature
Project description:Nonobstructive azoospermia (NOA) is a severe condition in infertile men, and increasing numbers of causative genes have been identified during the last few decades. Although certain causative genes can explain the presence of NOA in some patients, a proportion of NOA patients remain to be addressed. This study aimed to investigate potential high-risk genes associated with spermatogenesis in idiopathic NOA patients by whole-exome sequencing. Whole-exome sequencing was performed in 46 male patients diagnosed with NOA. First, screening was performed for 119 genes known to be related to male infertility. Next, further screening was performed to determine potential high-risk causative genes for NOA by comparisons with 68 healthy male controls. Finally, risk genes with high/specific expression in the testes were selected and their expression fluctuations during spermatogenesis were graphed. The frequency of cystic fibrosis transmembrane conductance regulator (CFTR) gene pathogenic variant carriers was higher in the NOA patients compared with the healthy controls. Potential risk genes that may be causes of NOA were identified, including seven genes that were highly/specifically expressed in the testes. Four risk genes previously reported to be involved in spermatogenesis (MutS homolog 5 [MSH5], cilia- and flagella-associated protein 54 [CFAP54], MAP7 domain containing 3 [MAP7D3], and coiled-coil domain containing 33 [CCDC33]) and three novel risk genes (coiled-coil domain containing 168 [CCDC168], chromosome 16 open reading frame 96 [C16orf96], and serine protease 48 [PRSS48]) were identified to be highly or specifically expressed in the testes and significantly different in the 46 NOA patients compared with 68 healthy controls. This study on clinical NOA patients provides further evidence for the four previously reported risk genes. The present findings pave the way for further functional investigations and provide candidate risk genes for genetic diagnosis of NOA.
| S-EPMC9933954 | biostudies-literature