Meiotic gene variants contribute to recurrent blastulation failure

STUDY QUESTION What is the genetic etiology of recurrent blastulation failure, particularly in morphologically good-quality cleavage-stage embryos? SUMMARY ANSWER Variants in meiotic genes may contribute to gamete-derived complex aneuploidy and impaired embryonic genome activation, which are strongly associated with recurrent blastulation failure in good-quality cleavage-stage embryos (R-GQBF). WHAT IS KNOWN ALREADY Successful blastocyst formation is critical for implantation. Embryonic development undergoes a major transition around the 8‑cell stage, shifting from reliance on maternal transcripts to embryonic genome activation. While pathogenic variants in maternal-effect genes have been linked to developmental arrest before the 8-cell stage, the genetic basis of failure occurring between the 8-cell stage and blastulation remains unclear. STUDY DESIGN, SIZE, DURATION From 2018 to 2023, 707 couples who met the R-GQBF criteria were recruited. After rigorous exclusion, 204 couples remained, of whom 97 were ultimately included for genetic etiology analysis. PARTICIPANTS/MATERIALS, SETTING, METHODS A total of 109 individuals from 97 selected couples (93 females and 16 males, including 13 couples with both partners) underwent whole-exome sequencing (WES). Genetic variants were compared with those from 1,000 fertile controls (500 females and 500 males). The chromosomal constitutions of 103 blastulation-failure embryos from 50 R-GQBF couples were analyzed via WES. Copy number variation (CNV) parental origin analysis was performed on 13 aneuploid embryos. Paternally derived chromosomal anomalies were further investigated using single-sperm chromosome analysis. Additionally, single-cell RNA sequencing was carried out on 15 arrested embryos. MAIN RESULTS AND THE ROLE OF CHANCE Twenty-five variants in 10 meiotic genes were identified in 20 patients (18.3%). Female carriers predominantly harbored prophase I variants (SPO11, MEI1, REC114, ANKRD31, DMC1, CNTD1, MLH3, SYCE1 and SYCP2), while three male patients carried MEIKIN variants. Female carriers generally had preserved ovarian reserve, whereas male carriers showed severe oligoasthenoteratozoospermia. Chromosomal analysis revealed a high prevalence of complex aneuploidy in blastulation-failure embryos (63.1%). CNV tracing confirmed the parental origin of abnormalities from the meiotic variant carrier in analyzed case, and sperm from all MEIKIN carriers also exhibited severe chromosomal abnormalities. Single-cell transcriptomics revealed defective embryonic genome activation, impaired lineage-specification, and activation of stress pathways. These consistent findings minimize the likelihood of chance associations. LARGE SCALE DATA： N/A. LIMITATIONS, REASONS FOR CAUTION Direct evaluation of oocyte chromosomal integrity was not feasible. Larger cohorts may reveal additional genes, and functional studies in animal models are required to validate genotype–phenotype relationships. WIDER IMPLICATIONS OF THE FINDINGS This study identifies biparental meiotic variants as an underrecognized cause of R-GQBF. Clinically, beyond routine extended embryo culture, chromosomal analysis should be recommended for etiological investigation. For couples experiencing recurrent complex aneuploidy in good-quality cleavage-stage embryos, genetic screening for meiotic variants may aid in diagnosis, counseling, and personalized treatment planning. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the National Natural Science Foundation of China (32270911, 82371672, 82471697, 62588301), the Natural Science Foundation of Hunan Province (2024JJ2083, 2023JJ30714, 2023JJ10084), the Science and Technology Innovation Program of Hunan Province (2023RC3233), the Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China (JYB2025XDXM117), the National Key R&D Program of China (2023YFC2705504), and the project of the Reproductive and Genetic Hospital of CITIC-XIANGYA (YNXM-202221, YNXM-202402 and YNXM-202505). The authors declare no competing interests.