Gene variants identified by whole-exome sequencing in 33 French women with premature ovarian insufficiency.
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ABSTRACT:
SUBMITTER: Yang X
PROVIDER: S-EPMC6338598 | biostudies-literature | 2019 Jan
REPOSITORIES: biostudies-literature
Publications
Gene variants identified by whole-exome sequencing in 33 French women with premature ovarian insufficiency.
Yang Xiang X Touraine Philippe P Desai Swapna S Humphreys Gregory G Jiang Huaiyang H Yatsenko Alexander A Rajkovic Aleksandar A
Journal of assisted reproduction and genetics 20181107 1
<h4>Purpose</h4>To investigate the potential genetic etiology of premature ovarian insufficiency (POI).<h4>Methods</h4>Whole-exome sequencing (WES) was done on DNA samples from women diagnosed with POI. Mutations identified were analyzed by in silico tools and were annotated according to the guidelines of the American College of Medical Genetics and Genomics. Plausible variants were confirmed by Sanger sequencing.<h4>Results</h4>Four of the 33 individuals (12%) carried pathogenic or likely patho ...[more]
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Project description:PurposeTo investigate the potential etiologies of premature ovarian insufficiency (POI) and diminished ovarian reserve (DOR).MethodsFourteen women with sporadic POI and 6 women with DOR were enrolled. We used whole-exome sequencing (WES) and bioinformatics analysis to identify variants in a subset of 599 selected POI candidate genes. The identified genes were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and protein-protein interaction (PPI) network analyses to uncover key genes and pathways.ResultsAmong the 20 patients, 79 heterozygous variants were detected in 49 genes, which were classified as "likely pathogenic" or "variants of uncertain significance" according to the guidelines of the American College of Medical Genetics and Genomics. Most patients (17/20) carried two or more variants. Monoacylglycerol O-acyltransferase 1 mutations were found in six patients, and cytochrome P450 family 26 subfamily B member 1 and Bardet-Biedl syndrome 9 mutations were each found in four patients. Some variants were shared between DOR and POI. Enrichment analyses showed that the identified genes participate in key ovarian processes, such as follicular development, gonadal development, meiosis, Fanconi anemia, homologous recombination, and transforming growth factor β signaling. A PPI network revealed interactions between these proteins.ConclusionPremature ovarian function decline may be polygenic, and overlap exists between the genetic backgrounds of DOR and POI. WES and in silico analyses may be a useful clinical tool for etiological diagnosis and risk prediction for high-risk women in the future.
| S-EPMC7550486 | biostudies-literature
Project description:BackgroundThe loss of ovarian function in women, referred to as premature ovarian insufficiency (POI), is associated with a series of concomitant diseases. POI is genetically heterogeneous, and in most cases, the etiology is unknown.MethodsWhole-exome sequencing (WES) was performed on DNA samples obtained from patients with POI, and Sanger sequencing was used to validate the detected potentially pathogenic variants. An in silico analysis was carried out to predict the pathogenicity of the variants.ResultsWe recruited 24 patients with POI and identified variants in POI-related genes in 14 patients, including bi-allelic mutations in DNAH6, HFM1, EIF2B2, BNC, and LRPPRC and heterozygous variants in BNC1, EIF2B4, FOXL2, MCM9, FANCA, ATM, EIF2B3, and GHR. No variants in the above genes were detected in the WES data obtained from 29 women in a control group without POI. Determining a clear genetic etiology could significantly increase patient compliance with appropriate intervention strategies.ConclusionsOur study confirmed that POI is a genetically heterogeneous condition and that whole-exome sequencing is a powerful tool for determining its genetic etiology. The results of this study will aid researchers and clinicians in genetic counseling and suggests the potential of WES for the detection of POI and thus early interventions for patients with POI.
| S-EPMC7510158 | biostudies-literature
Project description:BackgroundPremature ovarian failure (POF) is a highly heterogeneous disorder that occurs in 1% of women of reproductive age. Very few causative genes and variants contributing to POF have been detected, and the disease remains incompletely understood. In this study, we used whole exome sequencing (WES) to identify potential causal variants leading to POF.MethodsWES was conducted to identify variants in 34 Korean patients with POF, alongside 10 normal controls. Detected variants were filtered using a range of characterized bioinformatics analyses, and the machine learning tools, CADD and VEST, were used to predict pathogenic variants that could cause disease. VarSome was used for a comprehensive interpretation of the variants. Potential causal variants finally screened by these analyses were confirmed using Sanger sequencing.ResultsWe identified nine potential causative variants in genes previously associated with POF in 8 of 34 (24%) Korean patients by WES variant analysis. These potentially pathogenic variants included mutations in the MCM8, MCM9, and HFM1 genes, which are involved in homologous recombination, DNA repair, and meiosis, and are established as causing POF. Using a combination of CADD and VEST, 72 coding variants were also identified in 72 genes, including ADAMTSL1 and FER1L6, which have plausible functional links to POF.ConclusionsWES is a useful tool to detect genetic variants that cause POF. Accumulation and systematic management of data from a number of WES studies in specialized groups of patients with POF (family data, severe case populations) are needed to better comprehend the genetic landscape underlying POF.
| S-EPMC7590468 | biostudies-literature
Project description:Premature ovarian insufficiency (POI) is a major cause of reduced female fertility and affects approximately 1% women under 40 years of age. Recent advances emphasize the genetic heterogeneity of POI. Fanconi anemia (FA) genes, traditionally known for their essential roles in DNA repair and cytogenetic instability, have been demonstrated to be involved in meiosis and germ cell development. Here, we conducted whole-exome sequencing (WES) in 50 Han Chinese female patients with POI. Rare missense variants were identified in FANCA (Fanconi anemia complementation group A): c.1772G > A (p.R591Q) and c.3887A > G (p.E1296G). Both variants are heterozygous in the patients and very rare in the human population. In vitro functional studies further demonstrated that these two missense variants of FANCA exhibited reduced protein expression levels compared with the wild type, suggesting the partial loss of function. Moreover, mono-ubiquitination levels of FANCD2 upon mitomycin C stimulation were significantly reduced in cells overexpressing FANCA variants. Furthermore, a loss-of-function mutation of Fanca was generated in C57BL/6 mice for in vivo functional assay. Consistently, heterozygous mutated female mice (Fanca+/-) showed reduced fertility and declined numbers of follicles with aging when compared with the wild-type female mice. Collectively, our results suggest that heterozygous pathogenic variants in FANCA are implicated in non-syndromic POI in Han Chinese women, provide new insights into the molecular mechanisms of POI and highlight the contribution of FANCA variants in female subfertility.
| S-EPMC6874525 | biostudies-literature
Project description:Premature ovarian insufficiency (POI) is a severe clinical syndrome defined by ovarian dysfunction in women less than 40 years old who generally manifest with infertility, menstrual disturbance, elevated gonadotrophins, and low estradiol levels. STAG3 is considered a genetic aetiology of POI, which facilitates entry of REC8 into the nucleus of a cell and plays an essential role in gametogenesis. At present, only six truncated variants associated with POI have been reported; there have been no reports of an in-frame variant of STAG3 causing POI. In this study, two novel homozygous in-frame variants (c.877_885del, p.293_295del; c.891_893dupTGA, p.297_298insAsp) in STAG3 were identified in two sisters with POI from a five-generation consanguineous Han Chinese family. To evaluate the effects of these two variants, we performed fluorescence localization and co-immunoprecipitation analyses using in vitro cell model. The two variants were shown to be pathogenic, as neither STAG3 nor REC8 entered nuclei, and interactions between mutant STAG3 and REC8 or SMC1A were absent. To the best of our knowledge, this is the first report on in-frame variants of STAG3 that cause POI. This finding extends the spectrum of variants in STAG3 and sheds new light on the genetic origins of POI.
| S-EPMC6868891 | biostudies-literature
Project description:BackgroundThe genetic causes of the majority of cases of female infertility caused by premature ovarian insufficiency (POI) are unknown.ObjectiveTo identify the genetic causes of POI in 110 patients.MethodsWhole-exome sequencing was performed on 110 patients with POI, and putative disease-causative variants were validated by Sanger sequencing. Bioinformatic and in vitro functional analyses were performed for functional characterisation of the identified candidate disease-causative variants.ResultsWe identified two homozygous variants (NM_001040274: c.150_151del (p.Ser52Profs*7), c.999A>G (p.Ile333Met)) in SYCP2L in two patients, which had co-segregated with POI in these families. Bioinformatic analysis predicted that the two variants are deleterious, and in vitro functional analysis showed that mutant SYCP2L proteins exhibited mislocalisation and loss of function.ConclusionsSYCP2L is a novel gene found to be responsible for human POI. Our findings provide a potential molecular marker for POI and improve the understanding of the genetic basis of female infertility.
| S-EPMC7907585 | biostudies-literature
Project description:PurposeTo identify genetic variation associated to premature ovarian insufficiency (POI).MethodsA total of 74 women with POI (group POI), 45 women with increased FSH levels (group high FSH), and 88 controls (non-POI) were studied. Genotyping of BMP15:c.-9C>G (rs3810682), BMP15:c.328+905A>G (rs3897937), and BMP15:c.852C>T (rs17003221); and GDF9:c.134-694G>A (rs4705974), GDF9:c.-31-951G>A (rs11748063), GDF9:c.-152G>C (rs30177), and GDF9:g.1073C>T (rs803224) was performed by the TaqMan methodology. Chi-square and Fisher's exact tests were performed to evaluate the distribution of genotypes, alleles, odds ratio, and the Hardy-Weinberg equilibrium of each variation. Haplotype analysis was performed for each gene considering the case and control groups. Bonferroni's correction was applied to chi-square and Fisher's exact test data, and p values < 0.007 for genotypes and alleles and < 0.006 for haplotypes were considered significant.ResultsIt was observed a statistically significant difference in genotype distribution of BMP15:c.852C>T between group POI and controls (p < 0.001). TT and TC genotypes were more frequently observed in group POI. Genotype distribution in case group POI, however, was not in the Hardy-Weinberg equilibrium, due to the increased number of heterozygotes in the sample. Concerning GDF9, no association was found among the studied genetic variants and POI or high FSH groups.ConclusionIt is concluded from the present study that the genotypes CT and TT from BMP15:c.852C>T variation may be risk factors for the development of POI.
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Project description:PurposeTo investigate the relationship between vaginal microbial community structure and premature ovarian insufficiency (POI).MethodsTwenty-eight women with POI and 12 healthy women were recruited at Shenzhen Maternity and Child Healthcare Hospital between August and September 2020. Blood samples were collected for glucose tests and detection of sex hormone levels and vaginal secretions were collected for microbial group determination. Vaginal microbial community profiles were analysed by 16S rRNA gene sequencing using the Illumina MiSeq system (Illumina Inc., San Diego, CA, USA).ResultsCompared to the controls, the serum levels of follicle-stimulating hormone, luteinizing hormone, testosterone, and the follicle-stimulating hormone/luteinizing hormone ratio, significantly increased, and oestradiol and anti-Müllerian hormone levels significantly decreased in women with POI. Higher weighted UniFrac values were observed in women with POI than in healthy women. Bacteria in the genera Lactobacillus, Brevundimonas, and Odoribacter were more abundant in the microbiomes of healthy women, while the quantity of bacteria in the genus Streptococcus was significantly increased in the microbiomes of women with POI. Moreover, these differences in microbes in women with POI were closely related to follicle-stimulating hormone, luteinizing hormone, oestradiol, and anti-Müllerian hormone levels and to the follicle-stimulating hormone/luteinizing hormone ratio.ConclusionsWomen with POI had altered vaginal microbial profiles compared to healthy controls. The alterations in their microbiomes were associated with serum hormone levels. These results will improve our understanding of the vaginal microbial community structure in women with POI.Trial registrationCHICTR, ChiCTR2000029576 . Registered 3 August 2020 - Retrospectively registered, https://www.chictr.org.cn/showproj.aspx?proj=48844 .
| S-EPMC8655991 | biostudies-literature
Project description:BackgroundBone morphogenetic protein 15 (BMP15) is expressed in oocytes and plays a crucial role in the reproduction of mono-ovulating species. In humans, BMP15 gene mutations lead to imperfect protein function and premature ovarian insufficiency. Here we investigated the BMP15 gene variants in a population of Iranian women with premature ovarian insufficiency. We conducted predictive bioinformatics analysis to further study the outcomes of BMP15 gene alterations.MethodsTwenty-four well-diagnosed premature ovarian insufficiency cases with normal karyotype participated in this study. The entire coding sequence and exon-intron junctions of the BMP15 gene were analyzed by direct sequencing. In-silico analysis was applied using various pipelines integrated into the Ensembl Variant Effect Predictor online tool. The clinical interpretation was performed based on the approved guidelines.ResultsBy gene screening of BMP15, we discovered p.N103K, p.A180T, and p.M184T heterozygous variants in 3 unrelated patients. The p.N103K and p.M184T were not annotated on gnomAD, 1000 Genome and/or dbSNP. These mutations were not identified in 800 Iranians whole-exome sequencing that is recorded on Iranom database. We identified the p.N103K variant in a patient with secondary amenorrhea at the age of 17, elevated FSH and atrophic ovaries. The p.M184T was detected in a sporadic case with atrophic ovaries and very high FSH who developed secondary amenorrhea at the age of 31.ConclusionsHere we newly identified p.N103K and p.M184T mutation in the BMP15 gene associated with idiopathic premature ovarian insufficiency. Both mutations have occurred in the prodomain region of protein. Despite prodomain cleavage through dimerization, it is actively involved in the mature protein function. Further studies elucidating the roles of prodomain would lead to a better understanding of the disease pathogenesis.
| S-EPMC8886931 | biostudies-literature
Project description:Background and aimpremature ovarian insufficiency (POI) is defined as the menopause before 40 years of age, and its prevalence is reported to be two-fold higher in Iranian women than the average for woman globally. POI is associated with several cardio/cerebrovascular complications as well as an increased overall mortality. Genetic factors, and serum levels of minerals and vitamin D, have been reported to be related to the prevalence of POI. We have investigated the association between some POI -related genotypes with the serum levels of some important micronutrients.MethodsOne hundred and seventeen women with POI and 183 controls without any renal, hepatic, and thyroid abnormalities were recruited as part of the MASHAD study. Demographic and anthropometric features were recorded and blood samples were collected and processed. DNA was extracted from the buffy coat of blood samples from all participants and 8 POI-related single nucleotide polymorphisms (SNPs) were determined using ASO-PCR or Tetra ARMS-PCR. Serum minerals and vitamin D concentrations were measured using routine methods.ResultsIn women with POI, serum copper, phosphate, and calcium were significantly different for those with rs244715, rs16991615, and rs4806660 genotypes, respectively. In our control population, significant differences were also found in serum copper concentrations between different genotypes of rs4806660, rs7246479, rs1046089, and rs2303369. After adjusting for all confounding factors, the women with POI carrying TC genotype (rs4806660) had a lower risk to have serum copper levels < 80 (µg/dL) than those carrying a TT genotype. Furthermore, women with POI carrying GG genotype (rs244715) had a 6-fold higher risk to have serum copper levels > 155 than those carrying AA genotype.ConclusionThe C and G alleles of the rs4806660 and rs244715 polymorphisms respectively are independently associated with serum copper in women with POI. Further studies are necessary to investigate the association of serum copper and other micronutrients in women and other POI -related polymorphisms.
| S-EPMC10840145 | biostudies-literature