Systems Biology in Reproductive Medicine最新文献

{"title":"Unveiling the role of miRNAs in Diminished Ovarian Reserve: an in silico network approach.","authors":"Costanza Cimini, Angela Taraschi, Marina Ramal-Sanchez, Alessia Colosimo, Carlo Di Carlo, Ramses Belda-Perez, Luca Valbonetti, Giulia Capacchietti, Nicola Bernabò, Barbara Barboni","doi":"10.1080/19396368.2024.2434268","DOIUrl":"https://doi.org/10.1080/19396368.2024.2434268","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) have acquired an increased recognition to unravel the complex molecular mechanisms underlying Diminished Ovarian Reserve (DOR), one of the main responsible for infertility. To investigate the impact of miRNA profiles in granulosa cells and follicular fluid, crucial players in follicle development, this study employed a computational network theory approach to reconstruct potential pathways regulated by miRNAs in granulosa cells and follicular fluid of women suffering from DOR. Available data from published research were collected to create the FGC_MiRNome_MC, a representation of miRNA target genes and their interactions. 365 hubs were identified within the network, representing potential key regulators, and 210 nodes that act as both hubs and bottlenecks (H&BN nodes), suggesting that they may control the information flow within the network. GO enrichment analysis of the 210 H&BN nodes revealed their involvement in fundamental cellular processes relevant to ovarian function. In particular, the cluster analysis identified several shared pathways between cluster 1 and cluster 2 involved in the RAS/MAPK pathway, which plays a critical role in cell proliferation, differentiation and survival. These findings suggest that miRNAs play a significant role in DOR and highlight the potential of the RAS/MAPK pathway as a target for further investigation. Additionally, the genes identified as both hubs and bottlenecks revealed interesting connections to reproductive health in KO mice models. This <i>in silico</i> approach provides valuable insights into potential biomarkers and therapeutic targets for age-related reproductive disorders.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"71 1","pages":"2-12"},"PeriodicalIF":2.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143041896","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}

{"title":"An intelligent decision-making system for embryo transfer in reproductive technology: a machine learning-based approach.","authors":"Sanaa Badr, Meryem Tahri, Mohamed Maanan, Jan Kašpar, Noura Yousfi","doi":"10.1080/19396368.2024.2445831","DOIUrl":"https://doi.org/10.1080/19396368.2024.2445831","url":null,"abstract":"<p><p>Infertility has emerged as a significant public health concern, with assisted reproductive technology (ART) is a last-resort treatment option. However, ART's efficacy is limited by significant financial cost and physical discomfort. The aim of this study is to build Machine learning (ML) decision-support models to predict the optimal range of embryo numbers to transfer, using data from infertile couples identified through literature reviews. Binary classification models were developed to classify cases into two groups: those transferring two or fewer embryos and those transferring three or four. Four popular ML algorithms were used, including random forest (RF), logistic regression (LR), support vector machine (SVM), and artificial neural network (ANN), considering seven criteria: the woman's age, sperm origin, the developmental qualities of four potential embryos, infertility duration, assessment of the woman, morphological qualities of the four best embryos on the day of transfer, and number of oocytes extracted. The stratified 3-fold cross-validation results show that the SVM model obtained the highest average accuracy (95.83%) and demonstrated the best overall performance, closely followed by the ANN and LR models with an average accuracy equal to 91.67%. The RF model achieved a slightly lower average accuracy (88.89%), which demonstrated the lowest variability. Testing on a new dataset revealed all models performed well, with ANN and SVM models classified all test set instances correctly, while the RF and LR models achieved 91.68% accuracy. These results highlight the superior generalization and effectiveness of the ANN and SVM models in guiding ART decisions.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"71 1","pages":"13-28"},"PeriodicalIF":2.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053595","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}

{"title":"Navigating the practical challenges and ethical dilemmas of surplus cryopreserved human embryos.","authors":"George Anifandis, Dimitrios Ioannou, Georgia Kokkali, Katerina Chatzimeletiou, Christina Messini, Sevastiani Antonouli, Helen G Tempest","doi":"10.1080/19396368.2025.2449901","DOIUrl":"https://doi.org/10.1080/19396368.2025.2449901","url":null,"abstract":"<p><p>Cryopreservation, the use of very low temperatures to preserve structurally intact living cells and tissues, has seen exponential growth in the field of <i>in vitro</i> fertilization (IVF). In the last decade, cryopreservation of embryos and freeze-all protocols have become an essential aspect and a prerequisite for a successful IVF outcome. Moreover, vitrification, which is a fast and safe cryopreservation method, has proved to be an effective choice for cryopreserving gametes and embryos. The increasing number of cryopreserved embryos worldwide in cryobanks and IVF clinics is an undisputable fact that raises important physiological, ethical, and moral considerations that merit careful examination and discussion. Many couples utilizing assisted reproduction will have a surplus of cryopreserved embryos, in other words they already have completed their family without exhausting all the embryos that were created and cryopreserved during the process. Additionally, the global IVF market has also experienced significant growth due to various factors, including advancements in technology, increased awareness about infertility treatments, and changing societal norms towards delayed parenthood. Thus, for the foreseeable future the number of cryopreserved embryos, and the phenomenon of surplus embryos will likely remain unresolved. In the present review, following a description of the cryopreservation method and the physiological changes during the cryopreservation of embryos, the bioethical issues raised by the surplus cryopreserved embryos will be discussed alongside possible solutions for resolving this phenomenon.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"71 1","pages":"2449901"},"PeriodicalIF":2.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143053622","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}

{"title":"SBiRM: future innovation and practice in Personalized and Precision Reproductive Medicine.","authors":"Stephen A Krawetz, B Charlotte","doi":"10.1080/19396368.2024.2447691","DOIUrl":"https://doi.org/10.1080/19396368.2024.2447691","url":null,"abstract":"","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"71 1","pages":"1"},"PeriodicalIF":2.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143034211","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}

{"title":"Identification of candidate genes for endometrial cancer in multi-omics: a Mendelian randomization analysis.","authors":"Lan-Hui Qin, Chongze Yang, Rui Song, Pei-Yin Chen, Zijian Jiang, Weihui Xu, Guanzhen Zeng, Jin-Yuan Liao, Liling Long","doi":"10.1080/19396368.2024.2411458","DOIUrl":"https://doi.org/10.1080/19396368.2024.2411458","url":null,"abstract":"<p><p>Endometrial cancer is the most common malignant tumor of the uterus, but the underlying genetic mechanisms of EC remain unclear. To identify candidate genes and investigate genetic mechanisms for endometrial cancer, we utilized the summary-data-based Mendelian randomization (SMR) method to investigate causal associations between genetic variants, gene expression, DNA methylation, and endometrial cancer. Three main analyses were conducted utilizing cis-expression and methylation quantitative trait loci (eQTLs and mQTLs) as instrumental variables to examine causal relationships with endometrial cancer, and assessing the causal relationship between DNA methylation and gene expression. Data sources included genetic association data from O'Mara et al. eQTL data from the GTEx database, and mQTL data from McRae et al. Analysis involved the HEIDI test to distinguish pleiotropy, SMR analysis with multiple testing correction, and colocalization analysis to assess associations driven by linkage disequilibrium. Functional enrichment analysis was performed by the Metascape tool. Our study showed that three genes, SNX11, LINC00243, and EVI2A, were identified as causally related to endometrial cancer. SNX11 exhibited a positive causal relationship, while LINC00243 and EVI2A showed negative ones. Furthermore, 24 CpG sites were identified as causally related to endometrial cancer, with cg14424631 (CYP19A1) being the most significant. The study revealed common genes implicated in endometrial cancer, gene expression, and methylation sites, with LINC00243 playing a key role. Colocalization analysis confirmed significant causal relationships between LINC00243, SNX11, and endometrial cancer. Enrichment analysis uncovered pathways like interferon gamma signaling enriched in both endometrial cancer GWAS and e/mQTL. These findings shed light on the molecular mechanisms underlying endometrial cancer development. The study identified candidate genes and DNA methylation loci causally associated with endometrial cancer, which are expected to serve as potential targets for treatment.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"70 1","pages":"299-311"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142475313","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}

{"title":"Classification of idiopathic recurrent spontaneous miscarriage using FTIR and Raman spectroscopic fusion technology.","authors":"Dadoma Sherpa, Chiranjib Bhowmick, Tummala Pavan, Dhruva Abhijit Rajwade, Sumana Halder, Imon Mitra, Sunita Sharma, Pratip Chakraborty, Sanjukta Dasgupta, Koel Chaudhury","doi":"10.1080/19396368.2024.2384386","DOIUrl":"https://doi.org/10.1080/19396368.2024.2384386","url":null,"abstract":"<p><p>Recurrent spontaneous miscarriage refers to the repeated loss of two or more clinically detected pregnancies occurring within 24 weeks of gestation. No identifiable cause has been identified for nearly 50% of these cases. This group is referred to as idiopathic recurrent spontaneous miscarriage (IRSM) or miscarriage of unknown origin. Due to lack of robust scientific evidence, guidelines on the diagnosis and management of IRSM are not well defined and often contradictory. This motivates us to explore the vibrational fingerprints of endometrial tissue in these women. Endometrial tissues were collected from women undergoing IRSM (<i>n</i> = 20) and controls (<i>n</i> = 20) corresponding to the window of implantation. Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectra were obtained within the range of 400-4000 cm^-1 using Agilent Cary 630 FTIR spectrometer. Raman spectra were also generated within the spectral window of 400-4000 cm^-1 using Thermo Fisher Scientific, DXR Raman spectrophotometer. Based on the limited molecular information provided by a single spectroscopic tool, fusion strategy combining Raman and ATR-FTIR spectroscopic data of IRSM is proposed. The significant features were extracted applying principal component analysis (PCA) and wavelet threshold denoising (WTD) and fused spectral data used as input into support vector machine (SVM), adaptive boosting (AdaBoost) and decision tree (DT) models. Altered molecular vibrations associated with proteins, glutamate, and lipid metabolism were observed in IRSM using Raman spectroscopy. FTIR analysis indicated changes in the molecular vibrations of lipids and proteins, collagen dysregulation and impaired glucose metabolism. Combination of both spectroscopic data using mid-level fusion (MLF: 92% using AdaBoost and DT models) and high-level fusion (HLF: 92% using SVM models) methods showed improved IRSM classification accuracy as compared to individual spectral models. Our results indicate that spectral fusion technology hold promise in enhancing diagnostic accuracy of IRSM in clinical settings. Validation of these findings in a larger patient population is underway.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"70 1","pages":"228-239"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141992389","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}

{"title":"Engineered exosome as a biological nanoplatform for drug delivery of Rosmarinic acid to improve implantation in mice with induced endometritis.","authors":"Morteza Taravat, Reza Asadpour, Razi Jafari Jozani, Amir Fattahi, Monireh Khordadmehr, Hamed Hajipour","doi":"10.1080/19396368.2024.2306420","DOIUrl":"10.1080/19396368.2024.2306420","url":null,"abstract":"<p><p>Endometritis is an inflammatory and histopathologic disease in uterine tissues that interferes with the proper decidualization and implantation of the embryo. In this study, rosmarinic acid (RA) is used as an anti-inflammatory agent that encapsulates in exosomes and is used to attenuate lipopolysaccharide (LPS)-induced endometritis and improve implantation. For this purpose, exosomes were loaded with RA and then administrated into the animal groups, including RA, exosome, RA plus exosome (RA + Exo), and RA-loaded exosomes (RALExo) groups. The concentrations of RA or exosomes used in this study were 10 mg/kg, and the compounds were injected into the uterine horn 24 h following the induction of endometritis. Upon the presence of inflammation detected by the histopathological method, the most proper groups were mated with male mice. The effect of the treatment group on the implantation rate, progesterone levels, and gene expressions were assessed by Chicago Blue staining, enzyme-linked immunosorbent assay (ELISA), and Quantitative PCR (qPCR), respectively. Results showed RALExo10 and RA10 + Exo10 groups improved pathological alterations, enhanced progesterone levels, increased implantation rate, as well as heightened expression levels of Leukemia inhibitory factor (LIF) and Mucin-16 (<i>MUC-16</i>) genes. Besides, the expression levels of inflammatory cytokines, including Transforming growth factor-β (TGF-β), Interlukine-10 (IL-10), Interlukine-15 (IL-15), and Interlukine-18 (IL-18), were regulated. Our findings indicated that the expression of LIF, <i>Muc-16</i> genes as well as IL<i>-</i>18, were significantly correlated with serum progesterone concentrations and the implantation rate in the treatment groups. The RALExo10 and RA10 + Exo10 groups showed ameliorated implantation rates in experimental groups.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"70 1","pages":"3-19"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139698365","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}

{"title":"piRNA expression patterns in high vs. low fertility bovine sperm.","authors":"Nicholas Werry, Stewart J Russell, Raamkumaar Sivakumar, Sarah Miller, Katie Hickey, Steven Larmer, Michael Lohuis, Clifford Librach, Jonathan LaMarre","doi":"10.1080/19396368.2024.2364742","DOIUrl":"https://doi.org/10.1080/19396368.2024.2364742","url":null,"abstract":"<p><p>PIWI-interacting RNAs (piRNAs) are 24-32 nucleotide RNA sequences primarily expressed in germ cells and developing embryos that suppress transposable element expression to protect genomic integrity during epigenetic reprogramming events. We characterized the expression of piRNA sequences and their encoding clusters in sperm samples from an idiopathic fertility model of Holstein bulls with high and low Sire Conception Rates. The piRNA populations were determined to be mostly similar between fertility conditions when investigated by principal component and differential expression analysis, suggesting that a high degree of conservation in the piRNA system is likely necessary for the production of viable sperm. Both fertility conditions demonstrated evidence of 'ping-pong' activity - a secondary biogenesis pathway associated with active transposable element targeting and suppression. Most sperm-borne piRNAs were between 29-30 nucleotides in length and originated from 226 clusters across the genome, with the exception of chromosome 20. Mapping analysis revealed abundant targeting of several transposable element families, suggesting a suppressive function of sperm piRNAs consistent with their established roles. Expression of genes targeted by sperm-borne piRNAs is significantly reduced throughout early embryogenesis compared to the mRNA population. Limited transposable element expression is known to be essential for spermatogenesis, thus epigenetic regulation of this pathway is likely to influence sperm quality and fertilizing capacity.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"70 1","pages":"183-194"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141459483","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}

{"title":"In vitro fertilization, intracytoplasmic sperm injection, in vitro maturation, and embryo culture.","authors":"Leah Cooper, Emma Manuel, Min Xu, Samantha B Schon","doi":"10.1080/19396368.2024.2439838","DOIUrl":"https://doi.org/10.1080/19396368.2024.2439838","url":null,"abstract":"<p><p>Infertility is a highly prevalent disease affecting 1 in 6 couples worldwide. While there are numerous treatment options available to treat infertility, <i>in vitro</i> fertilization (IVF) is the most successful therapy available. IVF traditionally involves superovulation of the ovaries followed by ultrasound (US)-guided oocyte retrieval, fertilization of oocytes <i>in vitro,</i> and culture of resultant embryos. Embryo(s) are then either transferred into the uterus or cryopreserved. There have been tremendous advances in each step of this process over the past 40 years, however, much work still remains to be done. This review discusses the history and current techniques involved in oocyte fertilization and embryo culture. Highlighted areas include conventional insemination and intracytoplasmic sperm injection (ICSI), embryo culture, and laboratory assessment. Areas of past and present research including time-lapse imaging and <i>in vitro</i> maturation are also discussed.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"70 1","pages":"312-328"},"PeriodicalIF":2.1,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142898295","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}

{"title":"Preimplantation genetic testing as a preventive strategy for the transmission of mitochondrial DNA disorders.","authors":"Xinpeng Lan, Wu Liji Ao, Ji Li","doi":"10.1080/19396368.2024.2306389","DOIUrl":"10.1080/19396368.2024.2306389","url":null,"abstract":"<p><p>Mitochondrial diseases are distinct types of metabolic and/or neurologic abnormalities that occur as a consequence of dysfunction in oxidative phosphorylation, affecting several systems in the body. There is no effective treatment modality for mitochondrial disorders so far, emphasizing the clinical significance of preventing the inheritance of these disorders. Various reproductive options are available to reduce the probability of inheriting mitochondrial disorders, including <i>in vitro</i> fertilization (IVF) using donated oocytes, preimplantation genetic testing (PGT), and prenatal diagnosis (PND), among which PGT not only makes it possible for families to have genetically-owned children but also PGT has the advantage that couples do not have to decide to terminate the pregnancy if a mutation is detected in the fetus. PGT for mitochondrial diseases originating from nuclear DNA includes analyzing the nuclear genome for the presence or absence of corresponding mutations. However, PGT for mitochondrial disorders arising from mutations in mitochondrial DNA (mtDNA) is more intricate, due to the specific characteristics of mtDNA such as multicopy nature, heteroplasmy phenomenon, and exclusive maternal inheritance. Therefore, the present review aims to discuss the utility and challenges of PGT as a preventive approach to inherited mitochondrial diseases caused by mtDNA mutations.</p>","PeriodicalId":22184,"journal":{"name":"Systems Biology in Reproductive Medicine","volume":"70 1","pages":"38-51"},"PeriodicalIF":2.4,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139698367","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}