Systems Biology in Reproductive Medicine最新文献_第4页

Novel bioinformatic analyses of somatic cell contamination in sperm samples. 精子样本中体细胞污染的新型生物信息学分析。

IF 2.1 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2024-12-01 Epub Date: 2024-06-22 DOI: 10.1080/19396368.2024.2368716

Carter Norton, Chad Pollard, Kelaney Stalker, Kenneth Aston, Timothy Jenkins

{"title":"Novel bioinformatic analyses of somatic cell contamination in sperm samples.","authors":"Carter Norton, Chad Pollard, Kelaney Stalker, Kenneth Aston, Timothy Jenkins","doi":"10.1080/19396368.2024.2368716","DOIUrl":"https://doi.org/10.1080/19396368.2024.2368716","url":null,"abstract":"The assessment of epigenetic profiles in sperm is sensitive to somatic cell contamination, which can influence methylation signals at gene promoters. This contamination is particularly problematic in the assessment of DNA methylation in samples with low sperm counts, where fractional amounts of somatic cell DNA can lead to significant shifts in measured methylation state. In this study, a new method of detecting possible somatic cell contamination is proposed through two multi-region bioinformatic models: a traditional differential methylation analysis and a machine learning logistic regression model. These models were trained on publicly available sperm (n = 489) and blood (n = 1029) DNA methylation array data and tested on a contamination set, wherein the sperm of four donors with normal sperm counts were run on a 450k methylation array with four permutations each, including pure blood, half blood and half sperm by DNA concentration, half blood and half sperm by cell count, and pure sperm (n = 16). The DMR and logistic regression model classified the contamination testing set with 100% and 94% accuracy, respectively. These new methods of detecting the effects of somatic cell contamination allow for more accurate differentiation between epigenetic profiles that contain a biological somatic-like shift and those that have somatic-like signatures because of contamination.","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"70 1","pages":"174-182"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141440912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcriptome analyses reveal key features of mouse seminal vesicle during aging. 转录组分析揭示了小鼠精囊衰老过程中的关键特征。

IF 2.1 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2024-12-01 Epub Date: 2024-08-21 DOI: 10.1080/19396368.2024.2388121

Peng Luo, Haibin Guo, Baoning Liu, Zhiqiang Zhang, Yun Xie, Jiahui Yao, Xiangping Li, Jun Bian, Jintao Zhuang, Bin Ouyang, Jinhua Wu

{"title":"Transcriptome analyses reveal key features of mouse seminal vesicle during aging.","authors":"Peng Luo, Haibin Guo, Baoning Liu, Zhiqiang Zhang, Yun Xie, Jiahui Yao, Xiangping Li, Jun Bian, Jintao Zhuang, Bin Ouyang, Jinhua Wu","doi":"10.1080/19396368.2024.2388121","DOIUrl":"https://doi.org/10.1080/19396368.2024.2388121","url":null,"abstract":"Despite the significant morphological changes that occur in the seminal vesicles with aging, the transcriptomic characteristics remain largely unexplored. To address this, we performed bulk RNA sequencing on seminal vesicle samples from mice aged 3, 13, and 21 months to uncover transcriptomic alterations. Our findings reveal that aged seminal vesicles display cystic dilatation, epithelial hypoplasia, disordered muscle layers, fibrosis, and reduced proliferation capability. A comparison between 3-month-old and 21-month-old mice indicated that leukocyte-mediated immunity and leukocyte migration were the most significantly upregulated biological processes among differentially expressed genes (DEGs). Notably, several DEGs associated with \"leukocyte migration,\" such as Vcam1, Cxcl13, and Ccl8, exhibited an increasing trend in transcriptomic and protein expression at three different time points in the seminal vesicles of mice. Additionally, we identified multiple aging-associated DEGs, including P21 and Tnfrsf1b. Two genes (Cd209f and Ccl8) were consistently upregulated across all six regions of the male reproductive glands (testis, epididymis, and seminal vesicle) in the comparison of bulk RNA datasets from 3-month-old and 21-month-old mice. These analyses highlight an enhanced state of immune and inflammatory response in aged seminal vesicles. This study represents the first exploration of the overall transcriptome landscape of seminal vesicles in a murine model of natural aging, offering new insights into the mechanisms underlying aging-related seminal vesicle dysfunction.","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"70 1","pages":"249-260"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142018619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In silico approach uncovers the shared genetic landscape of type 2 diabetes mellitus and asthenozoospermia 硅学方法揭示了 2 型糖尿病和无精子症的共同遗传图谱

IF 2.4 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2024-09-18 DOI: 10.1080/19396368.2024.2395545

Yinwei Chen, Taotao Sun, Chang Liu, Longjie Gu, Penghui Yuan

引用次数: 0

Prediction of deleterious non-synonymous SNPs of human MDC1 gene: an in silico approach 预测人类 MDC1 基因的有害非同义 SNPs：一种硅学方法

IF 2.4 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2024-04-17 DOI: 10.1080/19396368.2024.2325699

Vaishnavee Thote, Susha Dinesh, Sameer Sharma

引用次数: 0

Correlation between standard sperm parameters and sperm DNA fragmentation from 11,339 samples 11 339 份样本中精子标准参数与精子 DNA 碎片之间的相关性

IF 2.4 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2024-04-17 DOI: 10.1080/19396368.2024.2333285

Tingting Yang, Lin Yu, Jinyan Xu, Lijuan Ying, Yelin Jia, Yan Zheng, Bin Zhou, Fuping Li

引用次数: 0

Polyamines modulate mouse sperm motility. 多胺调节小鼠精子运动。

IF 2.4 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2023-12-01 Epub Date: 2023-11-20 DOI: 10.1080/19396368.2023.2262714

Lorena Rodríguez-Páez, Charmina Aguirre-Alvarado, Germán Chamorro-Cevallos, Alcántara-Farfán Veronica, Calderón-Espinosa Sandra Irel, Castillo-Pérez Hugo, Carlos Armando García-Pérez, Guadalupe Elizabeth Jiménez-Gutiérrez, Joaquín Cordero-Martínez

{"title":"Polyamines modulate mouse sperm motility.","authors":"Lorena Rodríguez-Páez, Charmina Aguirre-Alvarado, Germán Chamorro-Cevallos, Alcántara-Farfán Veronica, Calderón-Espinosa Sandra Irel, Castillo-Pérez Hugo, Carlos Armando García-Pérez, Guadalupe Elizabeth Jiménez-Gutiérrez, Joaquín Cordero-Martínez","doi":"10.1080/19396368.2023.2262714","DOIUrl":"10.1080/19396368.2023.2262714","url":null,"abstract":"Polyamines are polycationic molecules which contains two or more amino groups (-NH3+) highly charged at physiological pH, and among them we found spermine, spermidine, putrescine, and cadaverine. They interact with proteins, nucleic acids, modulate Ca2+, K+, and Na+ channels, and protect sperm from oxidative stress. In this work, we evaluate the effect of spermine, spermidine, and putrescine on the total, progressive and kinematic parameters of motility, capacitation, acrosome reaction, also in presence and absence of the dbcAMP, an analogue of the cAMP, and the IBMX, a phosphodiesterase inhibitor. In addition, we evaluated the intracellular concentrations of cAMP [cAMP]i, and performed an in silico analysis between polyamines and the sAC from mouse to predict the possible interaction among them. Our results showed that all polyamines decrease drastically the total, progressive and the kinetic parameters of sperm motility, decrease the capacitation, and only spermidine and putrescine impeded the acquisition of acrosome reaction. Moreover, the effect of polyamines was attenuated but not countered by the addition of db-cAMP and IBMX, suggesting a possible inhibition of the sAC. Also, the presence of polyamines induced a decrease of the [cAMP]i, and the in silico analysis predicted a strong interaction among polyamines and the sAC. Overall, the evidence suggests that probably the polyamines interact and inhibit the activity of the sAC.","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":" ","pages":"435-449"},"PeriodicalIF":2.4,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41183648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of ferroptotic genes and phenotypes in idiopathic nonobstructive azoospermia. 特发性非梗阻性无精子症脱铁基因和表型的鉴定。

IF 2.4 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2023-12-01 Epub Date: 2023-11-20 DOI: 10.1080/19396368.2023.2257352

Chen Liao, Tian-Wen Peng, Xiao-Min Li, Zhi-Cong Chen, Mu-Ye Wang, Xin Ye, Yu Lan, Xin Fu, Geng An

{"title":"Identification of ferroptotic genes and phenotypes in idiopathic nonobstructive azoospermia.","authors":"Chen Liao, Tian-Wen Peng, Xiao-Min Li, Zhi-Cong Chen, Mu-Ye Wang, Xin Ye, Yu Lan, Xin Fu, Geng An","doi":"10.1080/19396368.2023.2257352","DOIUrl":"10.1080/19396368.2023.2257352","url":null,"abstract":"Effective treatments for nonobstructive azoospermia (NOA), which affects 1% of all men globally, are limited by undefined pathogenic mechanisms, especially in idiopathic NOA (iNOA). Here, we tried to identify the functional ferroptosis-related genes and phenotypes involved in iNOA. Differentially expressed ferroptotic genes were identified from iNOA mRNA microarray datasets by bioinformatic analyses, and these ferroptotic genes were subsequently filtered by various algorithms. Then, receiver operating characteristic (ROC) curves were generated to evaluate the diagnostic ability of the abovementioned genes for iNOA. Generally, 11 differentially expressed ferroptotic genes were downregulated, and five genes were upregulated in iNOA samples. Four genes, including DUSP1, GPX4, HSD17B11, and SLC2A8, were technically selected and determined to be potential biomarkers for iNOA. Subsequently, similar expression levels were validated at both the RNA and protein levels in the iNOA specimens. Finally, morphologic and biochemical assays were applied to define the ferroptotic phenotypes in testes. The ferroptotic features, like shrunken mitochondria with electron-dense membranes and a reduction in cristae were observed across various cell types within iNOA patients, accompanied by the overload of ferrous ions and increased lipid peroxidation production. Our findings demonstrated that these ferroptosis genes could be involved in the underlying pathogenesis mechanisms of iNOA by regulating ferroptosis and serve as potential diagnostic biomarkers. Also, the ferroptotic phenotypes were identified in iNOA patients.","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":" ","pages":"410-422"},"PeriodicalIF":2.4,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41153431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Prevalence of human papilloma virus and Chlamydia trachomatis in endometrial and cervical carcinoma: a comparative study in North Indian women. 人乳头状瘤病毒和沙眼衣原体在子宫内膜癌和宫颈癌中的流行:北印度妇女的比较研究。

IF 2.4 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2023-12-01 Epub Date: 2023-09-05 DOI: 10.1080/19396368.2023.2247517

Heena Gautam, Sumita Mehta, Nidhi Nayar, Neha Kumar, Syed Akhtar Husain, Mausumi Bharadwaj

{"title":"Prevalence of human papilloma virus and Chlamydia trachomatis in endometrial and cervical carcinoma: a comparative study in North Indian women.","authors":"Heena Gautam, Sumita Mehta, Nidhi Nayar, Neha Kumar, Syed Akhtar Husain, Mausumi Bharadwaj","doi":"10.1080/19396368.2023.2247517","DOIUrl":"10.1080/19396368.2023.2247517","url":null,"abstract":"Cervical cancer (Cacx) is the second and endometrial cancer (Ec) is the third most common gynecological cancer worldwide. The present study aims to understand the complex and unexplored conditions occurring in cervix and endometrium of the female genital tract caused due to the infection of the human papilloma viruses (HPVs) and Chlamydia trachomatis (CT). A total of 300 tissue biopsy samples of cervix and endometrium were included in the present study and tested for the presence of HPV and CT deoxyribonucleic acid (DNA) by using polymerase chain reaction (PCR) technique. The odds ratios and 95% confidence interval were considered for the calculation of the association of HPV and CT infection with the risk of cervical or Ec. Among endometrial patients, samples were 5% positive for HPV and 5% positive for CT infection. Among endometrial control group, no sample was found positive for either HPV or CT infection. Among cervical patients, 72% samples were positive for only HPV infection and 1% samples were positive for only CT infection. Among control group, 7% of samples were positive for only HPV infection and 3% were positive for only CT infection. The co-infection of CT with HPV in 9% of Cacx cases and in 2% of cervical control samples was also observed. This is the first study in Indian women to detect the prevalence of HPV and CT infections in endometrium cases and control. An updated estimate regarding the HPV and CT prevalence in cervix cases and control samples was also provided.","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":" ","pages":"399-409"},"PeriodicalIF":2.4,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10157277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MEHP activates JNK to inhibit the migration of human foreskin fibroblasts. MEHP激活JNK以抑制人包皮成纤维细胞的迁移。

IF 2.4 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2023-12-01 Epub Date: 2023-11-20 DOI: 10.1080/19396368.2023.2262082

Hu Zhang, Xuan Yi, Wei Hu, Guoqiang Zhu, Xiaowen Fu, Wei Jin, Long Qin, Mingyong Li

{"title":"MEHP activates JNK to inhibit the migration of human foreskin fibroblasts.","authors":"Hu Zhang, Xuan Yi, Wei Hu, Guoqiang Zhu, Xiaowen Fu, Wei Jin, Long Qin, Mingyong Li","doi":"10.1080/19396368.2023.2262082","DOIUrl":"10.1080/19396368.2023.2262082","url":null,"abstract":"This study aimed to investigate the impact of mono(2-ethylhexyl) phthalate (MEHP) on the proliferation, apoptosis, and migration of human foreskin fibroblast cells (HFF-1) and the role of the JNK signaling pathway in cell migration. HFF-1 cells were randomly assigned to the control group with 0 MEHP exposure (M0) or the experimental groups with 25, 50, 100, 200, and 400 μmol/L MEHP exposure (M25, M50, M100, M200, and M400, respectively). After 24 and 48 h of MEHP exposure, the proliferation of HFF-1 cells in any group had no significant change. However, compared with the M0 group, the M200 and M400 groups presented substantially increased apoptosis of HFF-1 cells. Moreover, cell migration ability significantly decreased in all groups (p < 0.05). Additionally, the transcription and phosphorylated protein activation of JNK kinase in HFF-1 cells were substantially upregulated with the increase in MEHP exposure. Subsequently, HFF-1 cells were randomly divided into three groups: the DMSO blank control group, the 100 μM MEHP experimental group (M100), and the 100 μM MEHP plus 10 μM SP600125 (specific JNK inhibitor) experimental group (S10). The activation of JNK protein in HFF-1 cells was substantially downregulated in the S10 group. HFF-1 cells were also divided into the blank control group (M0). They were treated with 100 μM MEHP and varying concentrations of SP600125 (5, 10, and 15 μM for S5, S10, and S15, respectively). As the concentration of the antagonist increased, the migration ability of HFF-1 cells was returned to normal. Finally, the ROS in HFF-1 cells increased under MEHP exposure. This finding indicates that the regulation of cell migration by the JNK signaling pathway may be important in the occurrence of hypospadias.","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":" ","pages":"423-434"},"PeriodicalIF":2.4,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41183647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pharmacological investigation of vitamin E with combined oral contraceptives on INHBA gene against PCOS that intricate through melatonin PKC pathway. 维生素E联合口服避孕药对通过褪黑素PKC通路调控PCOS的INHBA基因的药理学研究。

IF 2.4 4区医学

Systems Biology in Reproductive Medicine Pub Date : 2023-12-01 Epub Date: 2023-11-20 DOI: 10.1080/19396368.2023.2276082

Rukaiah Fatma Begum, Sumithra Mohan

{"title":"Pharmacological investigation of vitamin E with combined oral contraceptives on INHBA gene against PCOS that intricate through melatonin PKC pathway.","authors":"Rukaiah Fatma Begum, Sumithra Mohan","doi":"10.1080/19396368.2023.2276082","DOIUrl":"10.1080/19396368.2023.2276082","url":null,"abstract":"The most prevalent endocrine and metabolic condition in women of reproductive age are polycystic ovary syndrome (PCOS) with significant risk factors such as circadian rhythm and melatonin disruption. The aim of this study is to assess the effect of vitamin E in combination with a combined oral contraceptive (COC) on continuous light-induced PCOS using hormonal measures, oxidative stress (OS) indicators, and the inhibin beta-A (INHBA) gene, which targets the melatonin protein kinase C (PKC) pathway. An in silico technique anticipated INHBA's binding affinity for vitamin E and COC. For the in vivo investigation (IAEC/240/2021), female SD rats were divided into six groups and subjected to a 16-week induction period, followed by a 2-month test drug treatment with drospirenone (DRSP) as a standard. Serum testosterone, FSH, melatonin, and OS were calculated as hormonal markers. The expression of the INHBA gene was studied to see if it could be linked to the circadian rhythm and OS via the melatonin PKC pathway. According to the in silico study, vitamin E and DRSP had higher binding energy for the INHBA (-8.6 kcal/mol and -8.4 kcal/mol, respectively). When compared to the control group, in vivo results showed a substantial decrease in testosterone levels (p = .05), as well as changes in FSH (p = .78) and melatonin (p = .13). IHNBA gene expression has also dramatically increased, stimulating FSH production in the pituitary gland. Vitamin E and COC concomitantly are beneficial against PCOS because it modulates OS, which in turn influences circadian rhythm and the melatonin PKC pathway.","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":" ","pages":"450-464"},"PeriodicalIF":2.4,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92156805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0