Endometrial receptivity revisited: endometrial transcriptome adjusted for tissue cellular heterogeneity

• Published in: Human reproduction (Oxford) 2018-11, Vol.33 (11), p.2074-2086
• Main Authors: Suhorutshenko, Marina, Kukushkina, Viktorija, Velthut-Meikas, Agne, Altmäe, Signe, Peters, Maire, Mägi, Reedik, Krjutškov, Kaarel, Koel, Mariann, Codoñer, Francisco M, Martinez-Blanch, Juan Fco, Vilella, Felipe, Simón, Carlos, Salumets, Andres, Laisk, Triin
• Format: Article
• Language: English
• Subjects: Adult; Biopsy; Embryo Implantation; Endometrium - metabolism; Epithelial Cells - metabolism; Female; Gene Expression Profiling - methods; Humans; Menstrual Cycle - genetics; Menstrual Cycle - metabolism; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; Sequence Analysis, RNA; Stromal Cells - metabolism; Young Adult
• ISSN: 0268-1161; 1460-2350
• DOI: 10.1093/humrep/dey301

Abstract STUDY QUESTION Does cellular composition of the endometrial biopsy affect the gene expression profile of endometrial whole-tissue samples? SUMMARY ANSWER The differences in epithelial and stromal cell proportions in endometrial biopsies modify the whole-tissue gene expression profiles and affect the results of differential expression analyses. WHAT IS ALREADY KNOWN Each cell type has its unique gene expression profile. The proportions of epithelial and stromal cells vary in endometrial tissue during the menstrual cycle, along with individual and technical variation due to the method and tools used to obtain the tissue biopsy. STUDY DESIGN, SIZE, DURATION Using cell-population specific transcriptome data and computational deconvolution approach, we estimated the epithelial and stromal cell proportions in whole-tissue biopsies taken during early secretory and mid-secretory phases. The estimated cellular proportions were used as covariates in whole-tissue differential gene expression analysis. Endometrial transcriptomes before and after deconvolution were compared and analysed in biological context. PARTICIPANTS/MATERIAL, SETTING, METHODS Paired early- and mid-secretory endometrial biopsies were obtained from 35 healthy, regularly cycling, fertile volunteers, aged 23-36 years, and analysed by RNA sequencing. Differential gene expression analysis was performed using two approaches. In one of them, computational deconvolution was applied as an intermediate step to adjust for the proportions of epithelial and stromal cells in the endometrial biopsy. The results were then compared to conventional differential expression analysis. Ten paired endometrial samples were analysed with qPCR to validate the results. MAIN RESULTS AND THE ROLE OF CHANCE The estimated average proportions of stromal and epithelial cells in early secretory phase were 65% and 35%, and during mid-secretory phase, 46% and 54%, respectively, correlating well with the results of histological evaluation (r = 0.88, P = 1.1 × 10−6). Endometrial tissue transcriptomic analysis showed that approximately 26% of transcripts (n = 946) differentially expressed in receptive endometrium in cell-type unadjusted analysis also remain differentially expressed after adjustment for biopsy cellular composition. However, the other 74% (n = 2645) become statistically non-significant after adjustment for biopsy cellular composition, underlining the impact of tissue heterogeneity on differential expression anal