Genetic significance of skewed X-chromosome inactivation in premature ovarian failure

Epigenetic regulation in premature ovarian failure: A literature review

Premature ovarian failure (POF), or premature ovarian insufficiency (POI), is a multifactorial and heterogeneous disease characterized by amenorrhea, decreased estrogen levels and increased female gonadotropin levels. The incidence of POF is increasing annually, and POF has become one of the main causes of infertility in women of childbearing age. The etiology and pathogenesis of POF are complex and have not yet been clearly elucidated. In addition to genetic factors, an increasing number of studies have revealed that epigenetic changes play an important role in the occurrence and development of POF. However, we found that very few papers have summarized epigenetic variations in POF, and a systematic analysis of this topic is therefore necessary. In this article, by reviewing and analyzing the most relevant literature in this research field, we expound on the relationship between DNA methylation, histone modification and non-coding RNA expression and the development of POF. We also analyzed how environmental factors affect POF through epigenetic modulation. Additionally, we discuss potential epigenetic biomarkers and epigenetic treatment targets for POF. We anticipate that our paper may provide new therapeutic clues for improving ovarian function and maintaining fertility in POF patients.

Identification of a Novel Deep Intronic Variant by Whole Genome Sequencing Combined With RNA Sequencing in a Chinese Patient With Menkes Disease

Background: Menkes disease (MD) is a rare X-linked connective tissue disorder of copper metabolism caused by pathogenic variant(s) in ATP7A gene. The aim of the present study is to determine the clinical characteristics and molecular basis of one patient with MD.

Methods: One 10-month-old Chinese boy who met the clinical manifestations of MD was enrolled in this study. Whole genome sequencing (WGS) was performed in the patient in order to identify the variant(s), followed by Sanger sequencing. RNA sequencing (RNA-seq) from whole blood was subsequently applied to assess the effect of variant on transcription levels, and reverse transcriptase-polymerase chain reaction (RT-PCR) was performed for further validation. In addition, X chromosome inactivation (XCI) status of the patient’s mother at the DNA level was measured by capillary electrophoresis.

Results: The patient suffered from intermittent convulsions for more than 6 months, with psychomoto retardation and neurodegenerations. The patient also had curly hair, hypopigmented skin, cutis laxa, decreased muscle strength and hypotonia. MRI showed the intracranial arteries were tortuous with some “spiral” changes. The patient’s serum ceruloplasmin level was low. WGS revealed one novel hemizygous variant, c.2627-501C > T (NM_000,052.7), located in the deep intronic sequence of ATP7A gene. Sanger sequencing confirmed that the variant was inherited from his mother. RNA-seq confirmed the variant itself, and identified a pseudo-exon inserted between exons 12 and 13 in mRNA of ATP7A. The sequencing results of RT-PCR from the patient confirmed this finding, while neither of his parents detected aberrant splicing. The Capillary electrophoresis results showed that the patient’s mother had a skewed XCI.

Conclusion: Our finding of the variant enlarges the variant spectrum in the ATP7A gene. This is a novel deep intronic variant which leads to the activation of a pseudo-exons in the ATP7A gene, and it demonstrates the usefulness of WGS combined with RNA-seq, in terms of revealing disease-causing variants in non-coding regions. Furthermore, the fact that the deep intronic variants cause disease by the activation of pseudo-exon inclusion indicates that in MD this might be an important mechanism.

Skewed X-chromosome inactivation and shorter telomeres associate with idiopathic premature ovarian insufficiency

OBJECTIVE

To analyze whether telomere length, X-chromosome inactivation (XCI), and androgen receptor (AR) GAG polymorphism are related to idiopathic premature ovarian insufficiency (POI).

DESIGN

Case-control study.

SETTING

University hospital.

PATIENT(S)

A total of 121 women, including 46 nonsyndromic POI and 75 controls.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Age, weight, height, body mass index (BMI), systolic and diastolic arterial pressure, E₂, androstenedione, T, and C-reactive protein were assessed. Telomere length was estimated by quantitative real-time polymerase chain reaction, XCI was measured using the Human Androgen Receptor and X-linked retinitis pigmentosa 2 (RP2) methylation assays. AR and FMR1 polymorphism was assessed by quantitative fluorescent polymerase chain reaction and sequencing.

RESULT(S)

Premature ovarian insufficiency women had a higher mean age, weighed less, and exhibited lower C-reactive protein, E₂, and androstenedione levels. The AR polymorphism did not differ between the groups. Four patients had premutation (55-200 CGG repeats), and none displayed a full mutation in the FMR1 gene. However, patients with POI showed shorter telomere length and higher frequency of skewed XCI. Extreme skewing (≥90%) was observed in 15% of women with POI, and shorter telomeres correlated with XCI skewing in both groups.

CONCLUSION(S)

Skewed XCI and shortened telomere length were associated with idiopathic POI, despite no alterations in the AR and FMR1 genes. Additionally, there is a tendency for women with short telomeres to exhibit skewed XCI.

Analysis of C43G mutation in the promoter region of the XIST gene in patients with idiopathic primary ovarian insufficiency

OBJECTIVE

The XIST gene is considered to be an attractive candidate gene for skewed X-chromosome inactivation and a possible cause of primary ovarian insufficiency (POI). The purpose of this study was to investigate whether the XIST gene promoter mutation is associated with idiopathic POI in a sample of the Korean population.

METHODS

Subjects consisted of 102 idiopathic POI patients and 113 healthy controls with normal menstrual cycles. Patients with the following known causes of POI were excluded in advance: cytogenetic abnormalities, prior chemo- or radiotherapy, or prior bilateral oophorectomy. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism analysis.

RESULTS

The mean age of onset of ovarian insufficiency was 28.7±8.5 years and the mean values of serum luteinizing and follicle-stimulating hormones and estradiol in the POI group were 31.4±18.2 mIU/mL, 74.5±41.1 mIU/mL, and 30.5±36.7 pg/mL, respectively. We found no cytosine to guanine (C43G) variation in the XIST gene in both POI patients and controls.

CONCLUSION

The C43G mutation in the promoter region of the XIST gene was not present in the Korean patients with idiopathic POI in our study, in contrast to our expectation, suggesting that the role of XIST in the pathogenesis of POI is not yet clear.

The relationship between skewed X chromosome inactivation and the prognosis of Graves' and Hashimoto's diseases

BACKGROUND

Autoimmune thyroid diseases (AITDs) predominantly develop in females. One of two X chromosomes is randomly inactivated by methylation in each female cell, but it has been reported that skewed X chromosome inactivation (XCI) may be associated with the development of autoimmune diseases. To clarify the significance of skewed XCI in the prognosis and development of AITD, we investigated the proportion of skewed XCI in female patients with AITD.

METHODS

We analyzed the degree of XCI skewing in 120 female patients with AITD (77 patients with Graves' disease [GD] and 43 patients with Hashimoto's disease [HD]) and 49 female controls in DNA from peripheral blood mononuclear cells (PBMC). We performed XCI analysis by digesting inactive DNA with a methylation-sensitive restriction enzyme (HpaII) followed by a polymerase chain reaction (PCR) assay for the polymorphic CAG repeat of the androgen receptor gene and electrophoresis of the PCR products.

RESULTS

The proportion of skewed XCI (≥65% skewing) was not significantly different between AITD patients and control subjects but was higher in patients with intractable GD (66.7%) than those with GD in remission (25.0%, p=0.0033) and control subjects (32.6%, p=0.0038). When the cutoff value for XCI skewing was relaxed, the proportion of skewed XCI (≥60% skewing) was higher in patients with severe HD (76.5%) than in those with mild HD (41.2%, p=0.0342).

CONCLUSIONS

Skewed XCI is related to the prognosis of AITD, particularly the intractability of GD.

The role of genetic and autoimmune factors in premature ovarian failure

PURPOSE

To identify the role of both genetic (number of CGG repeats in the FMR1 gene) and autoimmune factors (anti-ovarian antibodies) in premature ovarian failure (POF).

METHODS

In cross-sectional study, 78 women with POF were divided into 3 groups by the number of CGG repeats (less than 28, 28-36, more than 36) in any of the FMR1 gene alleles. We performed the detection of skewed X-chromosome inactivation, CGG repeats in the FMR1 gene, anti-ovarian antibodies (AOA) and sex hormones tests.

RESULTS

Compared to a higher or lower number of CGG repeats the 28-36 triple CGG counts are strongly associated with the AOA detection (RR = 19.23, 95% CI = 2.63-100.0). The women with autoimmune-driven POF have significantly higher anti-Mullerian hormone levels in comparison to women with non-autoimmune-driven POF.

CONCLUSION

The presence of AOA above 10 IU/mL is associated with the normal number of CGG repeats in regard to ovarian reserve and a better preservation of follicular primordial pool in the women with POF.

Contemporary genetic technologies and female reproduction

BACKGROUND

The Fifth Evian Annual Reproduction (EVAR) Workshop Meeting discussed knowledge regarding contemporary genetics in female reproduction.

METHODS

Specialist reproductive medicine clinicians and geneticists delivered presentations based on published literature and current research. The content of this report is based on the expert presentations and subsequent group discussions that took place during this Workshop.

RESULTS

Numerous ovarian genes with a role in infertility have been identified. Future challenges for genetic screening of patients, such as those with polycystic ovary syndrome, primary ovarian insufficiency or endometriosis, include the identification of high-throughput strategies and how to apply these findings to infertile patients. The identification of high-quality embryos in IVF using objective technologies remains a high priority in order to facilitate single-embryo transfer. Gene expression profiling of cumulus cells surrounding the oocyte, and proteomic and metabolomic approaches in embryo culture media may significantly improve non-invasive embryo quality assessment.

CONCLUSIONS

The way forward in advancing the knowledge of genes involved in reproduction was considered to be through genome-wide association studies involving large numbers of patients. Establishing international collaboration is required to enable the application of such technologies in sufficient numbers of patients.

Role of polymorphism of the androgen receptor gene and non-random X chromosome inactivation in the genesis of androgenic alopecia in women of childbearing potential

The authors describe the results of a study of polymorphism of the androgen receptor gene by the number of CAG repeats in exon 1 of the androgen receptor gene and non-random X chromosome inactivation in 87 women of childbearing potential (at the average age of 29.5 ± 5.4 years) suffering from androgenic alopecia. They revealed an association between the presence of 'short' (≤ 22) CAG repeats in both alleles of the androgen receptor gene (р < 0,05) and a reliable growth of prevalence of non-random X chromosome inactivation in patients with androgenic alopecia as compared to healthy women (50.7% (39/77) and 16.1% (9/56), respectively, р < 0.05). These data demonstrate a pathogenetic role of polymorphism of the androgen receptor gene and non-random X chromosome inactivation in the development of androgenic alopecia in women of childbearing potential as well as urgency of using molecular and genetic studies to study pathogenetic mechanisms of the disease.

Role of polymorphism of the androgen receptor gene andnon-random x chromosome inactivation in the pathogenesisof androgenic alopecia

The article presents data on molecular and genetic studies of mechanisms of development of androgenic alopecia as well as correlation between polymorphism of the androgen receptor gene by the CAG repeat length in exon 1 and androgen-dependent diseases including alopecia.

Skewed X chromosome inactivation may be not associated with premature ovarian failure

BACKGROUND

In view of the controversies about the skewed X chromosome inactivation (XCI) and premature ovarian failure (POF) association, a meta-analysis of the published data was performed to evaluate the relationship between XCI skewing and POF.

METHODS

We searched for all published articles indexed in MEDLINE (1950 approximately 2009) and CNKI (1994 approximately 2009). Any case-control or cohort study that tested the association between skewed XCI and POF was included and data were extracted independently by two reviewers. We performed this meta-analysis involving 325 cases and 403 controls with Review Manager 4.2 software.

RESULTS

Four eligible studies were selected for meta-analysis. It suggested that there was no significant difference between the incidence of skewed XCI (XCI >or=70% skewing) in POF cases comparing to healthy controls, odds ratio (OR) = 1.13 [95% confidence interval (CI): 0.84 approximately 1.53, P = 0.42]. The link between extremely skewed XCI (XCI >or=90% skewing) and POF was also analysed, and no significant difference was found, either, OR = 1.46 (95% CI: 0.79 approximately 2.69, P = 0.22).

CONCLUSIONS

Skewed XCI had no association with POF. However, more case-control and cohort studies are needed in the future.

X chromosome inactivation does not define the development of premature ovarian failure in fragile X premutation carriers

Since only 20% of female fragile X premutation carriers develop premature ovarian failure (POF, i.e., amenorrhea before age of 40 years), and since X chromosome inactivation (XCI) determines the phenotypic severity of full mutation women, we reasoned that the development of POF in fragile X premutation carriers could be due to skewed XCI (XCI ratio >80:20). To determine inactivation ratios and activities of the premutations, inactivation patterns were assessed in peripheral blood samples from 101 fragile X premutation carriers (mean age 47.1 years, range 12-72) through analysis of the AR and FMR1 loci, respectively. In addition, AR inactivation patterns were assessed in peripheral blood samples from 25 women with idiopathic POF (mean age 31.7 years, range 19-48). We addressed the association between age and skewed XCI because older women are prone to XCI skewness. The median XCI ratios were 68% for premutation carriers with POF (N = 37), 67% for premutation carriers without POF (N = 64) and 61% for women with idiopathic POF (N = 25). The incidence of skewing was similar in all groups, that is, 7 of 37 (18.9%) in premutation carriers with POF, 11 of 64 (17.2%) in premutation carriers without POF, and 3 of 25 (12%) in women with idiopathic POF. There was good concordance between inactivation ratios at the two loci tested in 62 premutation carriers (intraclass correlation coefficient = 0.86; P < 0.01). No age-specific skewing was observed. Skewed XCI and activity of the premutation are not associated with POF in fragile X premutation carriers.

Skewed X inactivation and IVF-conceived infants

The objective of this study was to investigate whether skewed X chromosome inactivation (XCI) is associated with IVF. A retrospective cohort study was performed comprising 30 female infants conceived by IVF and 44 naturally conceived control infants matched for gestational age and sex. Cord blood DNA samples were obtained and XCI patterns were analysed using a methylation-sensitive assay. Eight IVF samples and 13 control samples were excluded from the study because they were either homozygous or alleles were too similar for the assay to determine skewing. Mildly skewed XCI (80-90% inactivation of one allele) was present in two of 22 (9.1%) IVF samples and two of 31 (6.5%) control samples. Extremely skewed XCI (>90% inactivation of one allele) was found in two of 22 (9.1%) IVF samples and none of 31 control samples. Neither difference was statistically significant. However, the mean degree of skewed XCI in the IVF group was 72.0% and in the control group was 62.4% (P=0.002). Larger studies are needed to clarify the relationship between IVF and skewed XCI.

Unbalanced translocation in an adult patient with premature ovarian failure and mental retardation detected by spectral karyotyping and array-comparative genomic hybridization

BACKGROUND

There are only three cases of unbalanced translocation (X;1) reported in childhood in the literature, while no such phenotypic information is available in adults.

MATERIALS AND METHODS

To delineate the phenotype-genotype relationship of unbalanced translocation (X;1) in adulthood, we reported here a 20-year-old female with an unbalanced translocation (X;1) which was determined by spectral karyotyping, array-comparative genomic hybridization and subtelomeric fluorescence in situ hybridization (FISH).

RESULTS

The phenotype of partial trisomy 1 and partial monosomy X of the present case was much attenuated, including premature ovarian failure, mental retardation, class I obesity, mild dysmorphism and delayed secondary sexual characteristics. The breakpoints of the unbalanced translocation were accurately located at Xq28 and 1q32.1. The large amplification on Chromosome 1 q arm was found to involve 312 genes and the deletion on Chromosome X q arm also involved 141 genes. Overall, genes associated with physiological process (47 genes), cellular process (33), development (23), response to stimulus (1) and reproduction (1) were observed in the amplification on Chromosome 1 q arm. In addition, genes related to physiological process (23 genes), cellular process (13), development (6) and response to stimulus (2) were observed in the large deletion on chromosome X q arm. Late-replication studies revealed the existence of skewed X inactivation in the derivative X chromosome.

CONCLUSIONS

The phenotype of partial monosomy X and partial trisomy 1q is much attenuated in case of unbalanced translocation (X;1) in adulthood probably owing to skewed X inactivation in derivative X chromosome.

Skewed X chromosome inactivation and trisomic spontaneous abortion: no association

Several studies suggest that highly skewed X chromosome inactivation (HSXI) is associated with recurrent spontaneous abortion. We hypothesized that this association reflects an increased rate of trisomic conceptions due to anomalies on the X chromosome that lead both to HSXI and to a diminished oocyte pool. We compared the distribution of X chromosome inactivation (XCI) skewing percentages (range: 50%-100%) among women with spontaneous abortions in four karyotype groups-trisomy (n = 154), chromosomally normal male (n = 43), chromosomally normal female (n = 38), nontrisomic chromosomally abnormal (n = 61)-to the distribution for age-matched controls with chromosomally normal births (n = 388). In secondary analyses, we subdivided the nontrisomic chromosomally abnormal group, divided trisomies by chromosome, and classified women by reproductive history. Our data support neither an association of HSXI with all trisomies nor an association of HSXI with chromosomally normal male spontaneous abortions. We also find no association between HSXI and recurrent abortion (n = 45).

Skewed X-chromosome inactivation is associated with primary but not secondary ovarian failure

Premature ovarian failure (POF) is the occurrence of menopause before the age of 40, and may present with either primary or secondary amenorrhea. Numerous cases of POF in women with X-chromosome deletions or translocations have been reported; thus, it is possible that smaller rearrangements undetectable by conventional cytogenetics may contribute to POF in some patients. In females with an abnormal X chromosome, cells with inactivation of the normal X may be selected against, causing skewed X-chromosome inactivation (XCI). We therefore assessed XCI by methylation sensitive restriction digestion and PCR amplification at the androgen receptor (AR) locus, in 4 primary and 55 secondary POF patients and 109 control women. In samples heterozygous at AR and therefore informative for the skewing assay, the frequency of skewed XCI among the women with secondary amenorrhea was identical to that in control women, with 4 out of 48 (8.3%) secondary ovarian failure patients and 8 out of 97 (8.2%) control women having > or =90% skewing. Notably, all three primary amenorrhea patients that were informative at AR had skewed XCI > or =90% (P = 0.001 vs. control women; Fisher's exact test). To investigate whether X-chromosome copy number alterations were responsible, DNA from selected patients with skewed XCI was examined by high resolution DNA microarray, however no potential regions of DNA addition or deletion were confirmed by FISH or PCR. X-chromosome abnormalities undetectable by array, or reduced follicular pool due to an early trisomic rescue event, may explain the skewed XCI observed in POF patients presenting with primary amenorrhea.

Extremely skewed X-chromosome inactivation is increased in pre-eclampsia

Pre-eclampsia is a disorder that affects approximately 5% of pregnancies. We tested the hypothesis that skewed X-chromosome inactivation (XCI) could be involved in the pathogenesis of pre-eclampsia. Peripheral blood DNA was obtained from 67 pre-eclampsia patients and 130 control women. Androgen receptor (AR) was analyzed by the HpaII/polymerase chain reaction assay to assess XCI patterns in DNA extracted from peripheral-blood cells. In addition, buccal cells were obtained from seven patients, and the analysis repeated. Extremely skewed XCI was observed in 10 of 46 informative patients (21.74%), and in 2 of 86 informative controls (2.33%, P = 0.0005; chi(2) test). Our findings support a role for the X-chromosome in the pathogenesis of pre-eclampsia in a subgroup of patients.

L and M cone proportions in polymorphic New World monkeys

Platyrrhine monkeys typically have only a single X-chromosome opsin gene. Alleles of this gene code for multiple versions of middle- to long-wavelength cone photopigments. X-chromosome inactivation provides heterozygous females with a retinal mosaic of cones containing either of two types of M and L pigment, thus establishing the photopigment basis for trichromatic color vision. This study examined the proportions of L and M cones created by this process. For that purpose, electroretinogram flicker photometry was used to obtain complete spectral sensitivity functions from 60 heterozygous female monkeys drawn from seven genera of platyrrhine monkeys. To obtain estimates of cone proportions, these functions were subsequently fit with linear combinations of L and M cone fundamentals that were derived from similar recordings made on conspecific animals having only one type of M/L pigment. Consistent with a random X-chromosome inactivation process, the average L:M cone weighting across the sample was close to unity. At the same time, there were significant individual variations in L:M cone proportions. The genesis of this variation and its implications for seeing are discussed.

X-chromosome inactivation and ovarian age during the reproductive years

OBJECTIVE

To explore whether skewed X-chromosome inactivation (XCI) is related to indicators of ovarian age.

DESIGN

The XCI skewing percent and indicators of ovarian age were measured in women with recent pregnancy losses and women with recent livebirths. All analyses adjust for chronologic age and pregnancy outcome.

SETTING

Hospital in eastern central New York.

PATIENT(S)

One hundred thirty-six women with informative XCI assays: 83 with index pregnancy losses and 53 with livebirths.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

The primary indicators of ovarian age were antral follicle count, levels of FSH and inhibin B. A secondary indicator was level of estradiol (E2).

RESULT(S)

The XCI skewing percent, defined either continuously or categorically (> or =90%), was unrelated to the indicators of ovarian age. The sample was large enough to rule out as unlikely a modest decline in antral follicle count or a modest increase in FSH in relation to skewed XCI.

CONCLUSION(S)

X-chromosome anomalies are associated with skewed XCI and with premature ovarian failure. Our data raise the possibility that X-chromosome anomalies may not be an important influence on ovarian aging in menstruating women.

Heterozygosity mapping by quantitative fluorescent PCR reveals an interstitial deletion in Xq26.2-q28 associated with ovarian dysfunction

BACKGROUND

Deletions of Xq chromosome are reported for a number of familial conditions exhibiting premature ovarian failure (POF) and early menopause (EM).

METHODS AND RESULTS

We describe the inheritance of an interstitial deletion of the long arm of the X chromosome associated with either POF or EM in the same family. Cytogenetic studies and heterozygosity mapping by quantitative fluorescent PCR revealed a 46,X,del(X)(q26.2-q28) karyotype in a POF female, in her EM mother, and also in her aborted fetus with severe cardiopathy. Applying a microsatellite approach, we have narrowed the extension of an identical interstitial deletion located between DXS1187 and DXS1073. These data, in line with other mapped deletions, single out the proximal Xq28 as the region most frequently involved in ovarian failure. We also propose that other factors may influence the phenotypic effect of this alteration. Indeed, skewed X inactivation has been ascertained in EM and POF to be associated with different X haplotypes.

CONCLUSION

Our analysis indicates that Xq26.2-q28 deletion is responsible for gonad dysgenesis in a family with EM/POF. The dissimilar deletion penetrance may be due to epigenetic modifications of other X genes that can contribute to human reproduction, highlighting that ovarian failure should be considered as a multifactorial disease.

The association of skewed X chromosome inactivation with aneuploidy in humans

Recently, we reported that skewed X chromosome inactivation (XCI) was more common in women who had experienced a trisomic pregnancy as compared to control women. Rather than an overall shift in the distribution of skewing there appears to only be an excess of extreme (= 95%) skewing. Further analysis of our data reveals that the increase in skewed XCI is dependent on which chromosome is involved in the trisomy and how many trisomies the woman has experienced, although sample sizes in each group are small. In this review we discuss limitations of the commonly used assays of XCI, which use measurements of DNA methylation to infer skewing patterns, and review the data based on current knowledge of the causes of XCI skewing. Gonadal mosaicism, premature aging, loss of methylation at some CpGs, and X-linked mutations can all be considered as potential mechanisms explaining both increased risk of trisomy and skewed XCI. While further research is needed to evaluate the role of each of these, the association of trisomy with apparent skewed XCI in the mother offers new opportunities to clarify the risk factors for and causes of the high incidence of aneuploidy in human females.