High-resolution array-CGH analysis on 46,XX patients affected by early onset primary ovarian insufficiency discloses new genes involved in ovarian function

Abstract

STUDY QUESTION Can high resolution array-CGH analysis on a cohort of women showing a primary ovarian insufficiency (POI) phenotype in young age identify copy number variants (CNVs) with a deleterious effect on ovarian function? SUMMARY ANSWER This approach has proved effective to clarify the role of CNVs in POI pathogenesis and to better unveil both novel candidate genes and pathogenic mechanisms. WHAT IS KNOWN ALREADY POI describes the progression toward the cessation of ovarian function before the age of 40 years. Genetic causes are highly heterogeneous and despite several genes being associated with ovarian failure, most of genetic basis of POI still needs to be elucidated. STUDY DESIGN, SIZE, DURATION The current study included 67 46,XX patients with early onset POI (<19 years) and 134 control females recruited between 2012 and 2016 at the Medical Cytogenetics and Molecular Genetics Lab, IRCCS Istituto Auxologico Italiano. PARTICIPANTS/MATERIALS, SETTING, METHODS High resolution array-CGH analysis was carried out on POI patients’ DNA. Results of patients and female controls were analyzed to search for rare CNVs. All variants were validated and subjected to a gene content analysis and disease gene prioritization based on the present literature to find out new ovary candidate genes. Case-control study with statistical analysis was carried out to validate our approach and evaluate any ovary CNVs/gene enrichment. Characterization of particular CNVs with molecular and functional studies was performed to assess their pathogenic involvement in POI. MAIN RESULTS AND THE ROLE OF CHANCE We identified 37 ovary-related CNVs involving 44 genes with a role in ovary in 32 patients. All except one of the selected CNVs were not observed in the control group. Possible involvement of the CNVs in POI pathogenesis was further corroborated by a case-control analysis that showed a significant enrichment of ovary-related CNVs/genes in patients ( P = 0.0132; P = 0.0126). Disease gene prioritization identified both previously reported POI genes (e.g. BMP15 , DIAPH2 , CPEB1 , BNC1 ) and new candidates supported by transcript and functional studies, such as TP63 with a role in oocyte genomic integrity and VLDLR which is involved in steroidogenesis. LARGE SCALE DATA ClinVar database ( ); accession numbers SCV000787656 to SCV000787743. LIMITATIONS, REASONS FOR CAUTION This is a descriptive analysis for almost all of the CNVs identified. Inheritance studies of CNVs in some non-familial sporadic cases was not performed as the parents’ DNA samples were not available. Addionally, RT-qP...

Novel phenotype of syndromic premature ovarian insufficiency associated with TP63 molecular defect

“…Furthermore, in a family with Rapp Hopkin Syndrome, POI was seen together with other features of early aging . Isolated POI was reported in two teenagers with a paternally inherited intragenic duplication in TP63 , and in two patients with nonsense variants in TP63 exon 14, predicted to cause a truncated protein (Figure ). The phenotypes associated with POI and TP63 variants are thus diverse and include isolated POI as well as syndromic POI of different types: Rapp Hopkin Syndrome, LMS, and a novel LMS‐like phenotype without limb anomalies as seen in our family.…”

“…The overall term POI will be used throughout this paper as recommended in the ESHRE guideline from 2016, and covers POI with primary as well as secondary amenorrhea . There is increasing evidence that TP63 variants play a role in POI …”

p63 sets the threshold for induction of apoptosis using a kinetically encoded ‘doorbell-like’ mechanism

“…Two recent screens have shown, that mutations in TAp63α can lead to POI. In both screens large rearrangements in the domain structure have created activated p63 forms 30,31 . A S592I mutation would have much milder effects but could also contribute to a premature depletion of the primary oocyte reserve.…”

“…Using a relaxation delay of 0.1 s and non-uniform sampling (37.5 % sparse) the total experimental time for each spectrum was 2 min. Phosphorylated Ser/Thr residues were identified on the basis of 3 J CαP couplings using a 31 P-edited intra-HNCA experiment as previously proposed 40 . To enable a direct comparison with the N-CO correlation spectra acquired to monitor the phosphorylation reaction, a carbonyl evolution time (t1) was introduced here, resulting in the 3D [ 15 N, 1 H]-BEST-TROSY-COintraHN(CAP) pulse sequence shown in Supplementary Fig.…”

Familial primary ovarian insufficiency associated with aSYCE1point mutation: Defective meiosis elucidated in humanized mice

“…Regarding CE components of the SC, in the past years mutations potentially associated to clinical conditions have started to be reported. In particular, deletions in human 10q26.3 encompassing SYCE1 gene were found in POI patients [39–41]. Besides, thus far three reports identifying mutations in SYCE1 gene in infertile patients have been made [42–44].…”