SWS1-complex in premature ovarian insufficiency: SWSAP1 as a new POI gene

ABSTRACT STUDY QUESTION What other zinc finger SWIM domain-containing protein 7 (SWS1/ZSWIM7) partners are involved in premature ovarian insufficiency (POI)? SUMMARY ANSWER This study identifies novel pathogenic variants in zinc finger SWIM domain-containing protein 7 (SWS1/ZSWIM7) and its partner, SWSAP1, which impair interhomolog homologous recombination (IH-HR) and lead to isolated POI. WHAT IS KNOWN ALREADY Knockout mice models of the SWS1-complex (also known as the SWS1–SWSAP1–SPIDR complex or Shu complex) are infertile due to meiotic arrest. Variants of both SWS1/ZSWIM7 and SPIDR are described in POI, but so far, no SWSAP1 variants have been described in female infertility. STUDY DESIGN, SIZE, DURATION Screening for SWS1-complex variants was performed using exome or genome sequencing data from women with POI as ongoing patient care. In silico modelling, IH-HR assays, and western-blot analysis were performed to test the impact of novel variants identified in genes of the SWS1-complex (SWSAP1 and SWS1/ZSWIM7) on homologous recombination, protein expression, and protein interactions. PARTICIPANTS/MATERIALS, SETTING, METHODS Five unrelated patients from France were enrolled based on their exome or genome sequencing result as part of ongoing patient care. All the patients were diagnosed with POI and met the European Society of Human Reproduction and Embryology (ESHRE) diagnostic criteria for POI. Functional validation was performed using mouse embryonic stem cells to study the impact of two novel variants found in two patients. MAIN RESULTS AND THE ROLE OF CHANCE We report five different pathogenic or likely pathogenic variants in five patients. We report the previously described c.231_232del and c.176C>T variants in SWS1/ZSWIM7, as well as two novel variants, c.22del and c.151C>T. Additionally, we report a homozygous frameshift deletion in SWSAP1 (c.353del). All the patients display a similar phenotype of severe isolated POI, associated with primary or early secondary amenorrhea and signs of puberty delay. In silico modelling and IH-HR assays of both SWS1/ZSWIM7 c.176C>T and SWSAP1 c.353del indicated a partial decrease or absence of IH-HR activity in Sws1−/− or Swsap1−/− cells, respectively, and destabilization of the SWSAP1 truncation mutant. LIMITATIONS, REASONS FOR CAUTION Identification of other patients carrying SWSAP1 variants is needed to evaluate in-depth phenotype to genotype correlations. Future studies should evaluate the role of other genes in the SWS1-complex and explore the potential for therapeutic interventions targeting homologous recombination. WIDER IMPLICATIONS OF THE FINDINGS These findings provide direct clinical and functional evidence that all three members of the SWS1-complex are implicated in female fertility and recapitulate the observed mouse phenotypes. IH-HR assays provide a relevant functional approach to validate novel variants in homologous recombination genes for POI patients, given the importance of IH-HR for meiotic progression. STUDY FUNDING/COMPETING INTEREST(S) The French Genomic Medicine Initiative PFMG2025 is supported by grants from the French government, notably by the French National Research Agency under the Programme d’Investissments d’Avenir for the CAD (ANR-21-ESRE0001) and the CRefIX (ANR-10-INBS-09-01). M.J. was supported by R01 HD112624 and R35CA253174 grants. E.J.T. was supported by a Norman Beischer Fellowship and a Centre for Research Excellence for Women’s Health in Reproductive Life (CRE-WHiRL) fellowship from the National Health and Medical Research Council (NHMRC). J.F.M. was supported by a Research Training Program scholarship from the Australian Government. The authors declare no competing interests. TRIAL REGISTRATION NUMBER This manuscript included genomic analysis performed in clinical practice in patients with RD/CGP and cancers in France. Consequently, a clinical trial NCT number was not required as we reported in this manuscript results obtained in clinical practice. In compliance with the French law on bioethics (2004-800, 06/08/2004), patients had signed written informed consent forms for clinical practice and had been informed of the research use of what remained of their samples after establishing the molecular diagnosis.