Molecular profiling of cumulus cells and their correlation with pregnancy outcome: away from single gene marker and toward pathways analysis [Expression data]

Worldwide the rate of infertility is on rise which put increasing pressure on assisted reproductive technology (ART) programs worldwide. Therefore it is important to increase the efficiency of ART. Toward this aim studies has been performed to find the best predictive biomarkers to choose the best germ cells for fertilization and the best embryo for transfer into uterus. However, across different studies no universal markers were found. In this study we addressed this issue by generating expression and CpG methylation profiles of outer cumulus cells obtained during intra-cytoplasmic sperm injection (ICSI) procedure. Our results highlight the presence of several parameters that affect the results like inter-individual differences, inter-treatment differences and above all treatment protocol specific differences. The signature of FSH hormone treatment was abundant. Therefore stratifying the samples to be compared is a prerequisite for any analysis: comparing the pregnancy outcome for only the long protocol we identified single gene markers (NME6 and ASAP1, FDR<5%), upstream regulators (like: EIF2AK3, FSH, ATF4, MKNK1, TP53) and several disease and bio-function related to cell death/apoptosis, cellular growth and proliferation. The later results were more pronounced by ranking the pairwise Z-scores between all samples: the positive samples resulting in pregnancy were classified, for example according to FSH upstream regulator, in the middle between two negative groups indicating that an overdose of FSH is equally harmful to an under dose. In conclusion, our study highlight the need to stratify the samples and the use of genomic pathway analysis as a more reliable and universal method, rather than the single gene marker in cumulus cell to predict oocyte development potential. Cumulus cells were collected from women undergoing ICSI cycles. As these cells must be removed before performing the ICSI. Upon isolation, the outer cumulus cells were directly stored at -80°C in 70ul buffer RLT Plus from Qiagen (Cat. No.: 1053393, Hilden, Germany) until further used.