Next-Generation Sequencing of Matched Ectopic and Eutopic Endometrium Identifies Novel Endometriosis-Related Genes

Here, we determined basic differentially expressed genes in endometrial lesions compared to eutopic endometrium of the patients with endometriosis (EM). Endometrial biopsy and tissue sampling were performed in ten women with pelvic EM and nine controls at their mid-secretory phase. NGS of mRNA combined with bioinformatic analysis and complemented by RT-qPCR analysis were used for analysis. A list of differentially expressed genes of ectopic compared to eutopic endometrium during mid-secretary phase has been composed. Functional annotation has found profound gene expression perturbations in numerous EM pathways including extracellular matrix, complement and coagulation, as well as cell cycle-related gene family. The genes of alcohol dehydrogenase 1B (ADH1B) and fatty binding protein 4 (FABP4) were determined as the most dramatically up-regulated genes in ectopic endometrial lesions. Both genes were not reported before to be associated with EM. Several other genes including PLA2G2A were also up-regulated in ectopic EM lesions. Notably, FABP4 and ADH1B are key genes in basic metabolism and known for their function in adipose tissue. The results provide intriguing new avenue for endometriosis studies. Similar content being viewed by others

Endometriosis: Science and Practice, Giudice, L.C., Evers, J.L.H., and Healy, D.L., Eds., New York: Blackwell, 2012. Eisenberg, V.H., Weil, C., Chodick, G., and Shalev, V., Epidemiology of endometriosis: a large population-based database study in a 2-million-member health care provider, BJOG, 2018, vol. 125, no. 1, pp. 55-62. doi 10.1111/1471-0528.14711 Simoens, S., Dunselman, G., Dirksen, C, et al., The burden of endometriosis: costs and quality of life of women with endometriosis and treated in referral centres, Hum. Reprod., 2012, vol. 27, no. 5, pp. 1292-1299. doi 10.1093/humrep/des073 Baranov, V.S., Ivaschenko, T.E., and Yarmolinskaya, M.I., Systems genetics view of endometriosis: a common complex disorder, Eur. J. Obstet. Gynecol. Reprod. Biol., 2015, vol. 185, pp. 59-65. doi 10.1016/j.ejogrb. 2014.11.036 May, K.E., Villar, J., Kirtley, S., et al., Endometrial alterations in endometriosis: a systematic review of putative biomarkers, Hum. Reprod. Update, 2011, vol. 17, pp. 637-653. doi 10.1093/humupd/dmr013 Bulun, S.E., Monsivais, D., Kakinuma T., et al., Molecular biology of endometriosis: from aromatase to genomic abnormalities, Semin. Reprod. Med., 2015, vol. 33, pp. 220-224. doi 10.1055/s-0035-1554053 Králíčková, M. and Vetvicka, V., Immunological aspects of endometriosis: a review, Ann. Transl. Med., 2015, vol. 3, p. 153. doi 10.3978/j.issn.2305-5839.2015.06.08 Aznaurova, Y.B., Zhumataev, M.B., Roberts, T.K., et al., Molecular aspects of development and regulation of endometriosis, Reprod. Biol. Endocrinol., 2014, vol. 12, p. 50. doi 10.1186/1477-7827-12-50 Rahmioglu, N., Nyholt, D.R., Morris, A.P., et al., Genetic variants underlying risk of endometriosis: insights from meta-analysis of eight genome-wide association and replication datasets, Hum. Reprod. Update, 2014, vol. 20, pp. 702-716. doi 10.1093/humupd/ dmu015 Rogers, P.A., Adamson, G.D., Al-Jefout, M., et al., Research priorities for endometriosis, Reprod. Sci., 2017, vol. 24, pp. 202-226. doi 10.1177/1933719116654991 Zhao, L., Gu, C., Ye, M., et al., Identification of global transcriptome abnormalities and potential biomarkers in eutopic endometria of women with endometriosis: a preliminary study, Biomed. Rep., 2017, vol. 6, no. 6, pp. 654-662. doi 10.3892/br.2017.902 Saare, M., Rekker, K., Laisk-Podlar, T., et al., Challenges in endometriosis miRNA studies—from tissue heterogeneity to disease specific miRNAs, Biochim. Biophys. Acta, 2017, vol. 1863, no. 9, pp. 2282-2292. doi 10.1016/j.bbadis.2017.06.018 Baranov, V.S., Ivaschenko, T.E., and Yarmolinskaya, M.I., Comparative systems genetics view of endometriosis and uterine leiomyoma: two sides of the same coin?, Syst. Biol. Reprod. Med., 2016, vol. 62, no. 2, pp. 93-105. doi 10.3109/19396368.2015.1123325 Wang, Z., Gerstein, M., and Snyder, M., RNA-Seq: a revolutionary tool for transcriptomics, Nat. Rev. Genet., 2009, vol. 10, pp. 57-63. doi 10.1038/nrg2484 Zhang, Y.H., Huang, T., Chen L., et al., Identifying and analyzing different cancer subtypes using RNA-seq data of blood platelets, Oncotarget, 2017, vol. 8, pp. 87494-87511. doi 10.18632/oncotarget.20903 Vashukova, E.S., Glotov, A.S., Fedotov, P.V., et al., Placental microRNA expression in pregnancies complicated by superimposed pre eclampsia on chronic hypertension, Mol. Med. Rep., 2016, vol. 14, pp. 22-32. doi 10.3892/mmr.2016.5268 Canis, M., Donnez, J.G., Guzick, D.S., et al., Revised American Society for Reproductive Medicine classification of endometriosis: 1996, Fertil. Steril., 1997, vol. 67, pp. 817-821. Dobin, A., Davis, C.A., Schlesinger, F., et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 2013, vol. 29, pp. 15-21. doi 10.1093/bioinformatics/bts635 Harrow, J., Frankish, A., Gonzalez, J.M., et al., GENCODE: the reference human genome annotation for The ENCODE Project, Genome Res., 2012, vol. 22, pp. 1760-1774. doi 10.1101/gr.135350.111 Li, B. and Dewey, C.N., RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinf., 2011, vol. 12, p. 323. doi 10.1186/1471-2105-12-323 Love, M.I., Huber, W., and Anders, S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 2014, vol. 15, p. 550. doi 10.1186/s13059-014-0550-8 Wickham, H., ggplot2: Elegant Graphics for Data Analysis, New York: Springer-Verlag, 2016. Sergushichev, A., An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation, bioRxiv, 2016. http://dx.org/10.1101/060012. Eden, E., Navon, R., Steinfeld, I., et al., GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists, BMC Bioinf., 2009, vol. 10, p. 48. doi 10.1186/1471-2105-10-48 Kidder, B.L., Stem Cell Transcriptional Networks, New York: Springer-Verlag, 2014. Livak, K.J. and Schmittgen, T.D., Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method, Methods, 2001, vol. 25, pp. 402-408. Liberzon, A., Birger, C., Thorvaldsdóttir H., et al., The molecular signatures database hallmark gene set collection, Cell Syst., 2015, vol. 1, pp. 417-425. Leek, J.T. and Storey, J.D., Capturing heterogeneity in gene expression studies by surrogate variable analysis, PLoS Genet., 2007, vol. 3, pp. 1724-1735. Subramanian, A., Tamayo, P., Mootha, V.K., et al., Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. U.S.A., 2005, vol. 102, pp. 15545-15550. Chase, J.R., Poolman, M.G., and Fell, D.A., Contribution of NADH increases to ethanol’s inhibition of retinol oxidation by human ADH isoforms, Alcohol Clin. Exp. Res., 2009, vol. 33, pp. 571-580. doi 10.1111/j.1530-0277.2008.00871.x Hotamisligil, G.S. and Bernlohr, D.A., Metabolic functions of FABPs—mechanisms and therapeutic implications, Nat. Rev. Endocrinol., 2015, vol. 11, pp. 592-605. doi 10.1038/nrendo.2015.122 Goetz, L.G., Mamillapalli, R. and Taylor, H.S, Low body mass index in endometriosis is promoted by hepatic metabolic gene dysregulation in mice, Biol. Reprod., 2016, vol. 95, p. 115. Ahn, J.H., Choi, Y.S. and Choi, J.H., Leptin promotes human endometriotic cell migration and invasion by up-regulating MMP-2 through the JAK2/STAT3 signaling pathway, Mol. Hum. Reprod., 2015, vol. 21, pp. 792–802. doi 10.1093/molehr/gav039 Gonçalves, H.F., Zendron, C., Cavalcante, F.S., et al., Leptin, its receptor and aromatase expression in deep infiltrating endometriosis, J. Ovarian Res., 2015, vol. 8, p. 53. doi 10.1186/s13048-015-0180-0 Wu, L.L., Pang, R.P., Yin, Y.Z., et al., Human chorionic gonadotropin improves endometriosis through downregulation of leptin expression in rats, Gynecol. Obstet. Invest., 2015, vol. 79, pp. 189-194. doi 10.1159/000367655 Frank, S., Stallmeyer, B., Kämpfer, H., et al., Leptin enhances wound re-epithelialization and constitutes a direct function of leptin in skin repair, J. Clin. Invest., 2000, vol. 106, pp. 501-509. Müller, W.E.G., Tolba, E., Dorweiler, B., et al., Electrospun bioactive mats enriched with Ca-polyphosphate/retinol nanospheres as potential wound dressing, Biochem. Biophys. Rep., 2015, vol. 3, pp. 150-160. doi 10.1016/j.bbrep.2015.08.007 Kim, H.S., Yoon, G., Ha, S.Y. and Song, S.Y., Nodular smooth muscle metaplasia in multiple peritoneal endometriosis, Int. J. Clin. Exp. Pathol., 2015, vol. 8, pp. 3370-3373. Suryawanshi, S., Huang, X., Elishaev, E., et al., Complement pathway is frequently altered in endometriosis and endometriosis-associated ovarian cancer, Clin. Cancer Res., 2014, vol. 20, pp. 6163-6174. doi 10.1158/1078-0432.CCR-14-1338 Monsivais, D., Bray, J.D., Su, E., et al., Activated glucocorticoid and eicosanoid pathways in endometriosis, Fertil. Steril., 2012, vol. 98, pp. 117-125. doi 10.1016/j.fertnstert.2012.03.030 Proestling, K., Birner, P., Gamperl, S., et al., Enhanced epithelial to mesenchymal cell transition (EMT) and upregulated MYC in ectopic lesions contribute independently to endometriosis, Reprod. Biol. Endocrinol., 2015, vol. 13, pp. 75-87. doi 10.1186/s12958-015-0063-7 ACKNOWLEDGMENTS The work was supported by Russian Science Foundation (grant no. 14-15-00737). Author information Authors and Affiliations Corresponding author Additional information The article is published in the original. Rights and permissions About this article Cite this article Predeus, A.V., Vashukova, E.S., Glotov, A.S. et al. Next-Generation Sequencing of Matched Ectopic and Eutopic Endometrium Identifies Novel Endometriosis-Related Genes. Russ J Genet 54, 1358–1365 (2018). https://doi.org/10.1134/S1022795418110133 Received: Accepted: Published: Version of record: Issue date: DOI: https://doi.org/10.1134/S1022795418110133