Mapping Single-Cell Transcriptomes of Endometrium Reveals Potential Biomarkers in Endometrial Cancer

References

• Garrido-Gomez T, Dominguez F, Quinonero A, et al. Defective decidualization during and after severe preeclampsia reveals a possible maternal contribution to the etiology. Proc Natl Acad Sci U S A. 2017;114(40):E8468–E8477. doi:10.1073/pnas.1706546114
   PubMed Web of Science ®Google Scholar
• Salker MS, Christian M, Steel JH, et al. Deregulation of the serum- and glucocorticoid-inducible kinase SGK1 in the endometrium causes reproductive failure. Nat Med. 2011;17(11):1509–1513. doi:10.1038/nm.2498
   PubMed Web of Science ®Google Scholar
• Piergentili R, Zaami S, Cavaliere AF, et al. Non-coding RNAs as prognostic markers for endometrial cancer. Int J Mol Sci. 2021;23(1):22. doi:10.3390/ijms23010022
   PubMedGoogle Scholar
• Cavaliere AF, Perelli F, Zaami S, et al. Towards Personalized medicine: non-coding RNAs and endometrial cancer. Healthcare. 2021;10(1):9. doi:10.3390/healthcare10010009
   Google Scholar
• Wang F, Jia W, Fan M, et al. Single-cell immune landscape of human recurrent miscarriage. Genomics Proteomics Bioinf. 2021;19(2):208–222. doi:10.1016/j.gpb.2020.11.002
   PubMed Web of Science ®Google Scholar
• Liu Z, Sun Z, Liu H, et al. Single-cell transcriptomic analysis of eutopic endometrium and ectopic lesions of adenomyosis. Cell Biosci. 2021;11(1):51. doi:10.1186/s13578-021-00562-z
   PubMed Web of Science ®Google Scholar
• Ma J, Zhang L, Zhan H, et al. Single-cell transcriptomic analysis of endometriosis provides insights into fibroblast fates and immune cell heterogeneity. Cell Biosci. 2021;11(1):125. doi:10.1186/s13578-021-00637-x
   PubMed Web of Science ®Google Scholar
• Garcia-Alonso L, Handfield LF, Roberts K, et al. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nat Genet. 2021;53(12):1698–1711. doi:10.1038/s41588-021-00972-2
   PubMed Web of Science ®Google Scholar
• Guo YE, Li Y, Cai B, et al. Phenotyping of immune and endometrial epithelial cells in endometrial carcinomas revealed by single-cell RNA sequencing. Aging. 2021;13(5):6565–6591. doi:10.18632/aging.202288
   PubMedGoogle Scholar
• Bell DW, Ellenson LH. Molecular genetics of endometrial carcinoma. Annu Rev Pathol. 2019;14(1):339–367. doi:10.1146/annurev-pathol-020117-043609
   PubMed Web of Science ®Google Scholar
• Murali R, Soslow RA, Weigelt B. Classification of endometrial carcinoma: more than two types. Lancet Oncol. 2014;15(7):e268–278. doi:10.1016/S1470-2045(13)70591-6
   PubMed Web of Science ®Google Scholar
• Kandoth C, Schultz N, Cherniack AD, et al.; Cancer Genome Atlas Research N. Integrated genomic characterization of endometrial carcinoma. Nature. 2013;497(7447):67–73. doi:10.1038/nature12113
   PubMed Web of Science ®Google Scholar
• Stuart T, Butler A, Hoffman P, et al. Comprehensive Integration of Single-Cell Data. Cell. 2019;177(7):1888–1902e1821. doi:10.1016/j.cell.2019.05.031
   PubMed Web of Science ®Google Scholar
• McGinnis CS, Murrow LM, Gartner ZJ. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 2019;8(4):329–337e324. doi:10.1016/j.cels.2019.03.003
   PubMed Web of Science ®Google Scholar
• Aran D, Looney AP, Liu L, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019;20(2):163–172. doi:10.1038/s41590-018-0276-y
   PubMed Web of Science ®Google Scholar
• Yoshihara K, Shahmoradgoli M, Martinez E, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4(1):2612. doi:10.1038/ncomms3612
   PubMed Web of Science ®Google Scholar
• Franzen O, Gan LM, Bjorkegren JLM. PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database. 2019;2019:2. doi:10.1093/database/baz046
   Google Scholar
• Zhang X, Lan Y, Xu J, et al. CellMarker: a manually curated resource of cell markers in human and mouse. Nucleic Acids Res. 2019;47(D1):D721–D728. doi:10.1093/nar/gky900
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Gu Z, Hubschmann D, Pei J, Houwing-Duistermaat J, Uh H-W. Make Interactive Complex Heatmaps in R. Bioinformatics. 2021;22(1). doi:10.1186/s12859-021-03958-3
   Google Scholar
• Van de Sande B, Flerin C, Davie K, et al. A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nat Protoc. 2020;15(7):2247–2276. doi:10.1038/s41596-020-0336-2
   PubMed Web of Science ®Google Scholar
• Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–425. doi:10.1016/j.cels.2015.12.004
   PubMed Web of Science ®Google Scholar
• Aibar S, Gonzalez-Blas CB, Moerman T, et al. SCENIC: single-cell regulatory network inference and clustering. Nat Methods. 2017;14(11):1083–1086. doi:10.1038/nmeth.4463
   PubMed Web of Science ®Google Scholar
• Imrichova H, Hulselmans G, Atak ZK, Potier D, Aerts S. i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly. Nucleic Acids Res. 2015;43(W1):W57–64. doi:10.1093/nar/gkv395
   PubMed Web of Science ®Google Scholar
• Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P. Inferring regulatory networks from expression data using tree-based methods. PLoS One. 2010;2:5.
   Google Scholar
• Jin S, Guerrero-Juarez CF, Zhang L, et al. Inference and analysis of cell-cell communication using CellChat. Nat Commun. 2021;12(1):1088. doi:10.1038/s41467-021-21246-9
   PubMed Web of Science ®Google Scholar
• Gaujoux R, Seoighe C. A flexible R package for nonnegative matrix factorization. BMC Bioinf. 2010;11(1):367. doi:10.1186/1471-2105-11-367
   PubMed Web of Science ®Google Scholar
• Zou G, Wang J, Xu X, et al. Cell subtypes and immune dysfunction in peritoneal fluid of endometriosis revealed by single-cell RNA-sequencing. Cell Biosci. 2021;11:98.
   PubMed Web of Science ®Google Scholar
• Owusu-Akyaw A, Krishnamoorthy K, Goldsmith LT, Morelli SS. The role of mesenchymal-epithelial transition in endometrial function. Hum Reprod Update. 2019;25(1):114–133. doi:10.1093/humupd/dmy035
   PubMed Web of Science ®Google Scholar
• Schwab KE, Gargett CE. Co-expression of two perivascular cell markers isolates mesenchymal stem-like cells from human endometrium. Hum Reprod. 2007;22(11):2903–2911. doi:10.1093/humrep/dem265
   PubMed Web of Science ®Google Scholar
• Li Z, Yan G, Diao Q, et al. Transplantation of human endometrial perivascular cells with elevated CYR61 expression induces angiogenesis and promotes repair of a full-thickness uterine injury in rat. Stem Cell Res Ther. 2019;10(1):179. doi:10.1186/s13287-019-1272-3
   PubMedGoogle Scholar
• Li J, Diao S, Yang H, Cao Y, Du J, Yang D. IGFBP5 promotes angiogenic and neurogenic differentiation potential of dental pulp stem cells. Dev Growth Differ. 2019;61(9):457–465. doi:10.1111/dgd.12632
   PubMed Web of Science ®Google Scholar
• Lofqvist C, Willett KL, Aspegren O, et al. Quantification and localization of the IGF/insulin system expression in retinal blood vessels and neurons during oxygen-induced retinopathy in mice. Invest Ophthalmol Vis Sci. 2009;50(4):1831–1837. doi:10.1167/iovs.08-2903
   PubMed Web of Science ®Google Scholar
• He X, Zeng H, Chen ST, et al. Endothelial specific SIRT3 deletion impairs glycolysis and angiogenesis and causes diastolic dysfunction. J Mol Cell Cardiol. 2017;112:104–113. doi:10.1016/j.yjmcc.2017.09.007
   PubMed Web of Science ®Google Scholar
• Deng F, Zhou R, Lin C, et al. Tumor-secreted dickkopf2 accelerates aerobic glycolysis and promotes angiogenesis in colorectal cancer. Theranostics. 2019;9(4):1001–1014. doi:10.7150/thno.30056
   PubMed Web of Science ®Google Scholar
• Lv H, Tong J, Yang J, et al. Dysregulated pseudogene HK2P1 may contribute to preeclampsia as a competing endogenous RNA for hexokinase 2 by impairing decidualization. Hypertension. 2018;71:648–658. doi:10.1161/HYPERTENSIONAHA.117.10084
   PubMed Web of Science ®Google Scholar
• Haider S, Gamperl M, Burkard TR, et al. Estrogen signaling drives ciliogenesis in human endometrial organoids. Endocrinology. 2019;160(10):2282–2297. doi:10.1210/en.2019-00314
   PubMed Web of Science ®Google Scholar
• Fitzgerald HC, Dhakal P, Behura SK, Schust DJ, Spencer TE. Self-renewing endometrial epithelial organoids of the human uterus. Proc Natl Acad Sci U S A. 2019;116(46):23132–23142. doi:10.1073/pnas.1915389116
   PubMed Web of Science ®Google Scholar
• Zhai J, Li S, Hu J, et al. In silico, in vitro, and in vivo analysis identifies endometrial circadian clock genes in recurrent implantation failure. J Clin Endocrinol Metab. 2021;106(7):2077–2091. doi:10.1210/clinem/dgab119
   PubMed Web of Science ®Google Scholar
• Hu S, Yao G, Wang Y, et al. Transcriptomic changes during the pre-receptive to receptive transition in human endometrium detected by RNA-Seq. J Clin Endocrinol Metab. 2014;99(12):E2744–2753. doi:10.1210/jc.2014-2155
   PubMed Web of Science ®Google Scholar
• Moskalev AA, Smit-McBride Z, Shaposhnikov MV, et al. Gadd45 proteins: relevance to aging, longevity and age-related pathologies. Ageing Res Rev. 2012;11(1):51–66. doi:10.1016/j.arr.2011.09.003
   PubMed Web of Science ®Google Scholar
• Barabasi AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet. 2011;12(1):56–68. doi:10.1038/nrg2918
   PubMed Web of Science ®Google Scholar
• Ma CZ, Brent MR, Pier Luigi M. Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data. Bioinformatics. 2021;37(9):1234–1245. doi:10.1093/bioinformatics/btaa947
   PubMed Web of Science ®Google Scholar
• Zhang J, Xiao C, Feng Z, et al. SOX4 promotes the growth and metastasis of breast cancer. Cancer Cell Int. 2020;20(1):468. doi:10.1186/s12935-020-01568-2
   PubMed Web of Science ®Google Scholar
• Brooimans RA, Van der Ark AA, Tomita M, Daha MR, Daha MR. CD59 expressed by human endothelial cells functions as a protective molecule against complement-mediated lysis. Eur J Immunol. 1992;22(3):791–797. doi:10.1002/eji.1830220324
   PubMed Web of Science ®Google Scholar
• Stubbs MC, Hall DJ. The amino-terminus of the E2F-1 transcription factor inhibits DNA replication of autonomously replicating plasmids in mammalian cells. Oncogene. 2002;21(23):3715–3726. doi:10.1038/sj.onc.1205473
   PubMed Web of Science ®Google Scholar
• Lund K, Adams PD, Copland M. EZH2 in normal and malignant hematopoiesis. Leukemia. 2014;28(1):44–49. doi:10.1038/leu.2013.288
   PubMed Web of Science ®Google Scholar
• Li J, Gong L, Zhang R, et al. Fibroblast growth factor 21 inhibited inflammation and fibrosis after myocardial infarction via EGR1. Eur J Pharmacol. 2021;910:174470. doi:10.1016/j.ejphar.2021.174470
   PubMed Web of Science ®Google Scholar
• Wang E, Lee MJ, Pandey S. Control of fibroblast senescence and activation of programmed cell death. J Cell Biochem. 1994;54(4):432–439. doi:10.1002/jcb.240540410
   PubMed Web of Science ®Google Scholar
• Calvo F, Sahai E. Cell communication networks in cancer invasion. Curr Opin Cell Biol. 2011;23(5):621–629. doi:10.1016/j.ceb.2011.04.010
   PubMed Web of Science ®Google Scholar
• Mahdian S, Aflatoonian R, Yazdi RS, et al. Macrophage migration inhibitory factor as a potential biomarker of endometriosis. Fertil Steril. 2015;103(1):153–159e153. doi:10.1016/j.fertnstert.2014.09.031
   PubMed Web of Science ®Google Scholar
• Kats R, Al-Akoum M, Guay S, Metz C, Akoum A. Cycle-dependent expression of macrophage migration inhibitory factor in the human endometrium. Hum Reprod. 2005;20(12):3518–3525. doi:10.1093/humrep/dei234
   PubMed Web of Science ®Google Scholar
• Yamada M, Ikeuchi T, Hatanaka H. The neurotrophic action and signalling of epidermal growth factor. Prog Neurobiol. 1997;51(1):19–37. doi:10.1016/S0301-0082(96)00046-9
   PubMed Web of Science ®Google Scholar
• Inoue H, Hattori T, Zhou X, et al. Dysfunctional ErbB2, an EGF receptor family member, hinders repair of airway epithelial cells from asthmatic patients. J Allergy Clin Immunol. 2019;143(6):2075–2085e2010. doi:10.1016/j.jaci.2018.11.046
   PubMed Web of Science ®Google Scholar
• Yoo JY, Kim TH, Shin JH, et al. Loss of MIG-6 results in endometrial progesterone resistance via ERBB2. Nat Commun. 2022;13(1):1101. doi:10.1038/s41467-022-28608-x
   PubMed Web of Science ®Google Scholar
• Yan M, Parker BA, Schwab R, Kurzrock R. HER2 aberrations in cancer: implications for therapy. Cancer Treat Rev. 2014;40(6):770–780. doi:10.1016/j.ctrv.2014.02.008
   PubMed Web of Science ®Google Scholar
• Xie M, Sun M, Ji X, et al. Overexpression of BACH1 mediated by IGF2 facilitates hepatocellular carcinoma growth and metastasis via IGF1R and PTK2. Theranostics. 2022;12(3):1097–1116. doi:10.7150/thno.65775
   PubMedGoogle Scholar
• Wang W, Vilella F, Alama P, et al. Single-cell transcriptomic atlas of the human endometrium during the menstrual cycle. Nat Med. 2020;26(10):1644–1653. doi:10.1038/s41591-020-1040-z
   PubMed Web of Science ®Google Scholar
• Turco MY, Gardner L, Hughes J, et al. Long-term, hormone-responsive organoid cultures of human endometrium in a chemically defined medium. Nat Cell Biol. 2017;19(5):568–577. doi:10.1038/ncb3516
   PubMed Web of Science ®Google Scholar
• Bonser LR, Schroeder BW, Ostrin LA, et al. The endoplasmic reticulum resident protein AGR3. Required for regulation of ciliary beat frequency in the airway. Am J Respir Cell Mol Biol. 2015;53(4):536–543. doi:10.1165/rcmb.2014-0318OC
   PubMed Web of Science ®Google Scholar
• Lala PK, Nandi P. Mechanisms of trophoblast migration, endometrial angiogenesis in preeclampsia: the role of decorin. Cell Adh Migr. 2016;10(1–2):111–125. doi:10.1080/19336918.2015.1106669
   PubMed Web of Science ®Google Scholar
• Goldoni S, Seidler DG, Heath J, et al. An antimetastatic role for decorin in breast cancer. Am J Pathol. 2008;173(3):844–855. doi:10.2353/ajpath.2008.080275
   PubMed Web of Science ®Google Scholar
• Kim M, Park J, Bouhaddou M, et al. A protein interaction landscape of breast cancer. Science. 2021;374(6563):eabf3066. doi:10.1126/science.abf3066
   PubMed Web of Science ®Google Scholar
• Zhou H, Zou X, Li H, Li T, Chen L, Cheng X. Decreased secretoglobin family 2A member 1expression is associated with poor outcomes in endometrial cancer. Oncol Lett. 2020;20(4):24. doi:10.3892/ol.2020.11885
   PubMed Web of Science ®Google Scholar