Functional characterization of novel NR5A1 variants reveals multiple complex roles in disorders of sex development

Variants in the NR5A1 gene encoding SF1 have been described in a diverse spectrum of disorders of sex development (DSD). Recently, we reported the use of a targeted gene panel for DSD where we identified 15 individuals with a variant in NR5A1, nine of which are novel. Here, we examine the functional effect of these changes in relation to the patient phenotype. All novel variants tested had reduced trans‐activational activity, while several had altered protein level, localization, or conformation. In addition, we found evidence of new roles for SF1 protein domains including a region within the ligand binding domain that appears to contribute to SF1 regulation of Müllerian development. There was little correlation between the severity of the phenotype and the nature of the NR5A1 variant. We report two familial cases of NR5A1 deficiency with evidence of variable expressivity; we also report on individuals with oligogenic inheritance. Finally, we found that the nature of the NR5A1 variant does not inform patient outcomes (including pubertal androgenization and malignancy risk). This study adds nine novel pathogenic NR5A1 variants to the pool of diagnostic variants. It highlights a greater need for understanding the complexity of SF1 function and the additional factors that contribute.

Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

Background

Disorders of sex development (DSD) are congenital conditions in which chromosomal, gonadal, or phenotypic sex is atypical. Clinical management of DSD is often difficult and currently only 13% of patients receive an accurate clinical genetic diagnosis. To address this we have developed a massively parallel sequencing targeted DSD gene panel which allows us to sequence all 64 known diagnostic DSD genes and candidate genes simultaneously.

Results

We analyzed DNA from the largest reported international cohort of patients with DSD (278 patients with 46,XY DSD and 48 with 46,XX DSD). Our targeted gene panel compares favorably with other sequencing platforms. We found a total of 28 diagnostic genes that are implicated in DSD, highlighting the genetic spectrum of this disorder. Sequencing revealed 93 previously unreported DSD gene variants. Overall, we identified a likely genetic diagnosis in 43% of patients with 46,XY DSD. In patients with 46,XY disorders of androgen synthesis and action the genetic diagnosis rate reached 60%. Surprisingly, little difference in diagnostic rate was observed between singletons and trios. In many cases our findings are informative as to the likely cause of the DSD, which will facilitate clinical management.

Conclusions

Our massively parallel sequencing targeted DSD gene panel represents an economical means of improving the genetic diagnostic capability for patients affected by DSD. Implementation of this panel in a large cohort of patients has expanded our understanding of the underlying genetic etiology of DSD. The inclusion of research candidate genes also provides an invaluable resource for future identification of novel genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-016-1105-y) contains supplementary material, which is available to authorized users.

CITED2 mutations potentially cause idiopathic premature ovarian failure

Anomalies in gonadal development in a mouse knockout model of Cited2 have been recently described. In Cited2(-/-) female gonads, an ectopic cell migration was observed and the female program of sex determination was transiently delayed. We hypothesize that, in humans, this temporary inhibition of genes should be sufficient to provoke a developmental impairment of the female gonads, conducive to premature ovarian failure (POF). To establish whether CITED2 mutations are a common cause of the disease, we performed a mutational analysis of this gene in a panel of patients with POF and in a group of control women with normal fertility. We amplified and directly sequenced the complete open reading frame of CITED2 in 139 patients with POF and 290 controls. This study revealed 5 synonymous and 3 nonsynonymous variants. Among these, 7 are novel. The nonsynonymous variant c.604C>A (p.Pro202Thr) was found uniquely in 1 woman from the POF group. In silico analysis of this mutation indicated a potential deleterious effect. We conclude that mutations in CITED2 may be involved in POF pathogenesis.

Copy number variation in patients with disorders of sex development due to 46,XY gonadal dysgenesis

Disorders of sex development (DSD), ranging in severity from mild genital abnormalities to complete sex reversal, represent a major concern for patients and their families. DSD are often due to disruption of the genetic programs that regulate gonad development. Although some genes have been identified in these developmental pathways, the causative mutations have not been identified in more than 50% 46,XY DSD cases. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to analyse copy number variation in 23 individuals with unexplained 46,XY DSD due to gonadal dysgenesis (GD). Here we describe three discrete changes in copy number that are the likely cause of the GD. Firstly, we identified a large duplication on the X chromosome that included DAX1 (NR0B1). Secondly, we identified a rearrangement that appears to affect a novel gonad-specific regulatory region in a known testis gene, SOX9. Surprisingly this patient lacked any signs of campomelic dysplasia, suggesting that the deletion affected expression of SOX9 only in the gonad. Functional analysis of potential SRY binding sites within this deleted region identified five putative enhancers, suggesting that sequences additional to the known SRY-binding TES enhancer influence human testis-specific SOX9 expression. Thirdly, we identified a small deletion immediately downstream of GATA4, supporting a role for GATA4 in gonad development in humans. These CNV analyses give new insights into the pathways involved in human gonad development and dysfunction, and suggest that rearrangements of non-coding sequences disturbing gene regulation may account for significant proportion of DSD cases.

Results from a pediatric surgical centre justify early intervention in disorders of sex development

BACKGROUND

Controversy persists surrounding early management of disorders of sex development. We assessed genital appearance, gender identity, and quality of life in prepubertal children who have had early surgical intervention.

METHODS

Children treated for disorders of sex development who were 5 to 10 years of age were eligible (n = 54). Children were scored (modified Creighton scale) for anatomical and cosmetic outcome, and both patients and parents completed PedsQL quality-of-life and gender identity questionnaires, with ethics approval.

RESULTS

Of 54 patients, 41 presented for review. Treatment began at 13.2 (1.8-250.1) months (median; range) and were reviewed at 7.5 +/- 2.1 (mean +/- SD) years of age. Nineteen were raised as girls and 22 as boys. Girls had good (85%) or satisfactory (15%) anatomical/cosmetic outcome, whereas 52% boys had good, 38% satisfactory, and 10% poor cosmetic outcomes. On gender identity questionnaire, boys scored 3.9 +/- 0.4 (mean +/- SD) and girls 3.6 +/- 0.5; 1 of 19 boys and 3 of 19 girls had lower scores, suggesting risk of gender identity disorder. Quality-of-life scores were 80+ for physical and 65 to 80 for psychosocial scores.

CONCLUSIONS

Early intervention is generally associated with positive outcomes for patients and parents. Girls had better anatomical outcomes than boys, and gender dysphoria risks were low in both sexes.

Effect of Turner's syndrome and X-linked imprinting on cognitive status: analysis based on pedigree data

The effects of a monosomy of either the maternally or paternally derived X chromosome in Turner's syndrome (TS) on general neurocognitive status and some executive abilities were assessed using the maximum likelihood estimators for pedigree data. This method increases the power of analysis by accounting for the effect of background heritable variation on a trait. The sample comprised 42 females with regular non-mosaic X monosomy and their non-affected relatives. Wechsler neurocognitive scores and several executive function tests' scores, including the Behaviour Dyscontrol Scale (BDS-2), the Wisconsin Card Sorting Test (WCST), and the Rey Complex Figure Test (RCFT), were considered in the analysis. Results showed a significant effect of TS on all Wechsler index and subtest scores, with greatest deficits observed in Arithmetic, Block Design, Object Assembly and Picture Arrangement, and on the total BDS, RCFT and WCST scores, regardless of parental origin of the single X-chromosome. Our data also showed a significantly higher effect of a paternally derived X chromosome in diminishing the performance on several Wechsler scores relevant to verbal skills, which might suggest X-linked imprinting loci relevant to these skills. Possible reasons for the inconsistency of the results concerning X-linked imprinting of cognitive loci using TS patients are discussed, and the relevance of pedigree analysis to future studies of this problem is emphasized.

A long-term outcome study of intersex conditions

CONTEXT

Clinical management of intersex conditions is controversial because the available evidence is limited and conflicting, with no long-term population based studies comparing matched controls.

OBJECTIVE

To assess the long-term psychological, sexual and social outcomes of patients with intersex compared with two matched control populations.

DESIGN, SETTING AND PARTICIPANTS

Three different aged-matched (18-32 years) patient groups completed a self-administered questionnaire of established quality of life and well-being inventories measuring physical' health, psychological adjustment and sexuality, following a mail-out to all identified patients. The intersex group (n = 50) and the Hirschsprung disease, a congenital disorder, control group (n = 27), were patients who had attended the Royal Children's Hospital, a tertiary centre, for their clinical care. The insulin dependent diabetes mellitus control group was recruited from an adult tertiary hospital. The study was conducted at the hospital-based Murdoch Childrens Research Institute.

MAIN OUTCOME MEASURES

Psychological, sexual and social outcomes.

RESULTS

The intersex group did not differ from controls on physical or mental health, depression, state anxiety, neuroticism, psychoticism or stressful life events. Intersex participants were satisfied with their overall body appearance, although intersex males were less satisfied than controls with the size (p <0.05) and appearance (p <0.01) of their sex organs. The intersex group was less likely to experience orgasm (p <0.05), tended to experience more pain during intercourse (p = 0.06), had more difficulties with penetration (p <0.01) and were less likely to have sexual activity several times or more a week (p <0.05) than the combined control groups. Intersex participants did not differ from controls in level of sexual desire or enjoyment of sexual activities.

CONCLUSIONS

Most patients with intersex had positive psychosocial and psychosexual outcomes, although some problems were reported with sexual activity. These results overall suggest that a model of care including early genital surgery carried out at a centre of excellence with a multidisciplinary team can minimize long-term complication rates.

Practical management of the intersex infant

Intersex occurs when the appearance of the internal or external genitalia is at variance with normal development for either sex. The first question asked by, and of new parents in relation to their offspring is often "Is it a boy or a girl"? A rational approach, based on knowledge of normal prenatal sexual development, and based on a careful physical examination to guide further investigation, is required to reach a diagnosis. We briefly review prenatal sexual development to provide a background to the assessment of genital ambiguity in the newborn. Aspects of physical examination are discussed in detail, with reference to published normative data where possible. We provide a classification of genital ambiguity and an approach to differential diagnosis. We highlight some of the many syndromes associated with genital ambiguity, with reference to their genetic basis where possible. In 46,XX individuals, the commonest cause of genital ambiguity is congenital adrenal hyperplasia due to 21-hydroxylase deficiency; however, in 46,XY individuals the differential diagnosis is wide, and may remain unexplained, even after extensive investigation. Two algorithms are presented, one of which provides an initial approach based on the presence of a uterus and palpable gonads alone, and a second illustrating a comprehensive differential diagnosis of the undervirilised 46,XY individual. We discuss our approach to sharing information on the diagnosis and management with the parents and highlight the early involvement of an experienced multidisciplinary team. Finally, we consider current controversial issues relating to gender assignment and management of genital ambiguity.

Gonadal dysgenesis with a difference

We report here an exceptional clinical finding of a 46,XY phenotypic female with complete gonadal dysgenesis, but who was found unexpectedly to have absence of the uterus and posterior vagina. Extensive review of current and past literature failed to confirm other reports of this variant form of complete gonadal dysgenesis.

Heterozygous HESX1 mutations associated with isolated congenital pituitary hypoplasia and septo-optic dysplasia

We have previously shown that familial septo-optic dysplasia (SOD), a syndromic form of congenital hypopituitarism involving optic nerve hypoplasia and agenesis of midline brain structures, is associated with homozygosity for an inactivating mutation in the homeobox gene HESX1/Hesx1 in man and mouse. However, as most SOD/congenital hypopituitarism occurs sporadically, the possible contribution of HESX1 mutations to the aetiology of these cases is presently unclear. Interestingly, a small proportion of mice heterozygous for the Hesx1 null allele show a milder SOD phenocopy, implying that heterozygous mutations in human HESX1 could underlie some cases of congenital pituitary hypoplasia with or without midline defects. Accordingly, we have now scanned for HESX1 mutations in 228 patients with a broad spectrum of congenital pituitary defects, ranging in severity from isolated growth hormone deficiency to SOD with panhypopituitarism. Three different heterozygous missense mutations were detected in individuals with relatively mild pituitary hypoplasia or SOD, which display incomplete penetrance and variable phenotype amongst heterozygous family members. Gel shift analysis of the HESX1-S170L mutant protein, which is encoded by the C509T mutated allele, indicated that a significant reduction in relative DNA binding activity results from this mutation. Segregation analysis of a haplotype spanning 6.1 cM, which contains the HESX1 locus, indicated that only one HESX1 mutation was present in the families containing the C509T and A541G mutations. These results demonstrate that some sporadic cases of the more common mild forms of pituitary hypoplasia have a genetic basis, resulting from heterozygous mutation of the HESX1 gene.

Kallmann syndrome gene (KAL-X) is not mutated in schizophrenia

Kallmann syndrome and schizophrenia share several clinical features, including dysfunctional olfactory ability, hypogonadotrophic hypogonadism, an excess of affected males, and psychiatric presentation. Because of this congruence, it has been proposed that up to 70% of male schizophrenics might have mutations affecting the function or expression of the gene mutated in Kallmann syndrome, KAL-X. We identified and studied 9 unrelated males with schizophrenia (as defined by DSM-IIIR criteria) who also have severe anosmia (first percentile of normal range) and low sex drive (seventh percentile of the normal range), and we sequenced the exons and the intron-exon junctions of the KAL-X gene for each. We found no mutations, and conclude that schizophrenia is rarely, if ever, due to a mutation in the coding sequence or splice junctions of KAL-X.

Psychosocial and family functioning in children with insulin-dependent diabetes at diagnosis and one year later

Examined the initial impact and subsequent adjustment to the diagnosis of insulin-dependent diabetes mellitus (IDDM). Children between 1 and 14 years of age and their families were assessed several weeks after diagnosis and again a year later using standardized measures of child behavior, parental mental health, and family functioning. Immediately after diagnosis, the children and both parents exhibited mild symptoms of psychological distress but these had largely resolved at 12-month follow-up. The impact of IDDM diagnosis on family functioning varied with informant, SES, and the age of the child, with an overall tendency for families to become less flexible over the year. Findings suggest that most children and their parents exhibit satisfactory individual adjustment after a period of initial stress but family functioning is affected in complex ways. Serial follow-up of the cohort is planned to establish whether the current findings are predictive of longer term outcome.

Molecular and cytogenetic studies of the Prader-Willi syndrome

Twenty-seven subjects with the Prader-Willi syndrome (PWS) were studied. Sixteen (59%) had a cytogenetic deletion involving chromosome 15q11-13. Nine were non-deletional and two patients had structural rearrangements of chromosome 15: 47,XY, + del(15)(pter----q12), var(15)(p11) and 45,XX,t(14q15q). At the DNA level, a greater proportion of patients (74%) showed loss of one chromosome 15q11-13 allele using a combination of densitometry and RFLP analysis. Deletion sizes were variable with 13 of 20 detectable both cytogenetically and with probe pML34 (D15S9). The remaining seven had microdeletions at the pML34 locus. Heterogeneity was further seen in three subjects who had cytogenetic deletions but normal DNA studies. In one patient there was evidence of a duplication at the pML34 locus. A new molecular rearrangement was identified with probe p3.21 (D15S10) in two patients and their mothers. Fifteen family studies were performed. In all 10 families where there was a molecular deletion, this was shown to have arisen de novo. DNA mapping confirmed that the paternal 15q allele was lost in three patients with PWS.

The effects of benzodiazepines on hormones in women with idiopathic hirsutism

A single blind study was planned to investigate whether benzodiapines would reduce androgens in women with idiopathic hirsutism. Placebo was given for the first month followed by four months of a benzodiazepine (chlorazepate 15 mg nocte or diazepam 10 mg nocte ). Plasma samples were collected during the follicular and luteal phases of each therapy month. Hair growth was assessed monthly. Eighteen women concluded the five months of the trial of whom ten received chlorazepate and eight diazepam. Comparison of follicular plasma samples during the placebo phase and fourth month of benzodiazepine found a significant increase in sex hormone binding globulin and a significant decrease in dehydroepiandrosterone sulphate with benzodiazepine therapy. No significant effects on hair growth were observed. A longer therapy time may be needed to demonstrate effects of benzodiapines on hirsutism. Further studies are needed to determine whether benzodiazepines affect hormonal parameters in normal men and women.