Monkey multi-organ cell atlas exposed to estrogen

Abstract

Awareness of estrogen’s effects on health is broadening rapidly. The effects of long-term high levels of estrogen on the body involve multiple organs. Here, we used both single-cell chromatin accessibility and RNA sequencing data to analyze the potential effect of estrogen on major organs. The integrated cell map enabled in-depth dissection and comparison of molecular dynamics, cell-type compositions, and cellular heterogeneity across multiple tissues and organs under estrogen stimulation. We also inferred pseudotime cell trajectories and cell–cell communications to uncover key molecular signatures underlying their cellular processes in major organs in response to estrogen. For example, estrogen could induce the differentiation of IFIT3⁺ neutrophils into S100A9⁺ neutrophils involved in the function of endosome-to-lysosome transport and the multivesicular body sorting pathway in liver tissues. Furthermore, through integration with human genome-wide association study data, we further identified a subset of risk genes during disease development that were induced by estrogen, such as AKT1 (related to endometrial cancer), CCND1 (related to breast cancer), HSPH1 (related to colorectal cancer), and COVID-19 and asthma-related risk genes. Our work uncovers the impact of estrogen on the major organs, constitutes a useful resource, and reveals the contribution and mechanism of estrogen to related diseases.

Keywords

estrogen / single-cell RNA sequencing / single-cell ATAC sequencing / cynomolgus monkeys

References

[1] Ruggiero RJ , Likis FE . Estrogen: physiology, pharmacology, and formulations for replacement therapy. J Midwifery Womens Health 2002; 47: 130- 8.

[2] Shoham Z , Schachter M . Estrogen biosynthesis—regulation, action, remote effects, and value of monitoring in ovarian stimulation cycles. Fertil Steril 1996; 65: 687- 701.

[3] Dean M , Murphy BT , Burdette JE . Phytosteroids beyond estrogens: regulators of reproductive and endocrine function in natural products. Mol Cell Endocrinol 2017; 442: 98- 105.

[4] Pfaff DW , Gagnidze K , Hunter RG Molecular endocrinology of female reproductive behavior. Mol Cell Endocrinol 2018; 467: 14- 20.

[5] Simm PJ , Bajpai A , Russo VC , et al. Estrogens and growth. Pediatr Endocrinol Rev 2008; 6: 32- 41.

[6] Kiyama R , Wada-Kiyama Y . Estrogenic endocrine disruptors: molecular mechanisms of action. Environ Int 2015; 83: 11- 40.

[7] Pellegrino A , Tiidus PM , Vandenboom R . Mechanisms of estrogen influence on skeletal muscle: mass, regeneration, and mitochondrial function. Sports Med 2022; 52: 2853- 69.

[8] Knowlton AA , Lee AR . Estrogen and the cardiovascular system. Pharmacol Ther 2012; 135: 54- 70.

[9] Dama A , Baggio C , Boscaro C , et al. Estrogen receptor functions and pathways at the vascular immune interface. Int J Mol Sci 2021; 22: 4254.

[10] Hamilton KJ , Hewitt SC , Arao Y , et al. Estrogen hormone biology. Curr Top Dev Biol 2017; 125: 109- 46.

[11] Ring KL , Mills AM , Modesitt SC . Endometrial hyperplasia. Obstet Gynecol 2022; 140: 1061- 75.

[12] Jia M , Dahlman-Wright K , Gustafsson JA . Estrogen receptor alpha and beta in health and disease. Best Pract Res Clin Endocrinol Metab 2015; 29: 557- 68.

[13] Deroo BJ , Korach KS . Estrogen receptors and human disease. J Clin Invest 2006; 116: 561- 70.

[14] Furuminato K , Minatoya S , Senoo E , et al. The role of mesenchymal estrogen receptor 1 in mouse uterus in response to estrogen. Sci Rep 2023; 13: 12293.

[15] Liu S , Hu C , Li M , et al. Estrogen receptor beta promotes lung cancer invasion via increasing CXCR4 expression. Cell Death Dis 2022; 13: 70.

[16] Yi M , Fashe M , Arakawa S , et al. Nuclear receptor CAR-ERalpha signaling regulates the estrogen sulfotransferase gene in the liver. Sci Rep 2020; 10: 5001.

[17] Jacenik D , Beswick EJ , Krajewska WM , et al. G protein-coupled estrogen receptor in colon function, immune regulation and carcinogenesis. World J Gastroenterol 2019; 25: 4092- 104.

[18] Aryan L , Younessi D , Zargari M , et al. The role of estrogen receptors in cardiovascular disease. Int J Mol Sci 2020; 21: 4314.

[19] Patel S , Homaei A , Raju AB , et al. Estrogen: the necessary evil for human health, and ways to tame it. Biomed Pharmacother 2018; 102: 403- 11.

[20] Bhatt DL , Mehta C . Adaptive designs for clinical trials. N Engl J Med 2016; 375: 65- 74.

[21] Phillips KA , Bales KL , Capitanio JP , et al. Why primate models matter. Am J Primatol 2014; 76: 801- 27.

[22] Chappell L , Russell AJC , Voet T . Single-Cell (Multi)omics technologies. Annu Rev Genomics Hum Genet 2018; 19: 15- 41.

[23] Qu J et al. A reference single-cell regulomic and transcriptomic map of cynomolgus monkeys. Nat Commun 2022; 13: 4069.

[24] Han X , Zhou Z , Fei L , et al. Construction of a human cell landscape at single-cell level. Nature 2020; 581: 303- 9.

[25] Xu W , Huang Y , Mei Y , et al. High expression of POGK predicts poor prognosis in patients with hepatocellular carcinoma. Curr Oncol 2022; 29: 8650- 67.

[26] Baltrunaite K , Craig MP , Palencia Desai S , et al. ETS transcription factors Etv2 and Fli1b are required for tumor angiogenesis. Angiogenesis 2017; 20: 307- 23.

[27] Tang J , Tian Z , Liao X , et al. SOX13/TRIM11/YAP axis promotes the proliferation, migration and chemoresistance of anaplastic thyroid cancer. Int J Biol Sci 2021; 17: 417- 29.

[28] Feng M , Fang F , Fang T , et al. Sox13 promotes hepatocellular carcinoma metastasis by transcriptionally activating Twist1. Lab Invest 2020; 100: 1400- 10.

[29] Kumawat K , Gosens R . WNT-5A: signaling and functions in health and disease. Cell Mol Life Sci 2016; 73: 567- 87.

[30] Wasniewski T , Kiezun J , Krazinski BE , et al. WNT5A gene and protein expression in endometrial cancer. Folia Histochem Cytobiol 2019; 57: 84- 93.

[31] WX Jiang , Cai GQ , Hu P , et al. Personalized medicine of non-genespecific chemotherapies for non-small cell lung cancer. Acta Pharm Sin B 2021; 11: 3406- 16.

[32] Richart L , Carrillo-de Santa Pau E , Río-Machín A , et al. BPTF is required for c-MYC transcriptional activity and tumorigenesis. Nat Commun 2016; 7: 10153.

[33] Buganim Y , Goldstein I , Lipson D , et al. A novel translocation breakpoint within the BPTF gene is associated with a pre-malignant phenotype. PLoS One 2010; 5: e9657.

[34] Zahid H , Olson NM , Pomerantz WCK . Opportunity knocks for uncovering the new function of an understudied nucleosome remodeling complex member, the bromodomain PHD finger transcription factor, BPTF. Curr Opin Chem Biol 2021; 63: 57- 67.

[35] Montaudon E , Nikitorowicz-Buniak J , Sourd L , et al. PLK1 inhibition exhibits strong anti-tumoral activity in CCND1-driven breast cancer metastases with acquired palbociclib resistance. Nat Commun 2020; 11: 4053.

[36] Luo L , Zhang Z , Qiu N , et al. Disruption of FOXO3a-miRNA feedback inhibition of IGF2/IGF-1R/IRS1 signaling confers Herceptin resistance in HER2-positive breast cancer. Nat Commun 2021; 12: 2699.

[37] Xu S et al. The role of collagen in cancer: from bench to bedside. J Transl Med 2019; 17: 309.

[38] Liang Z et al. Identification of candidate diagnostic and prognostic biomarkers for human prostate cancer: RPL22L1 and RPS21. Med Oncol 2019; 36: 56.

[39] Zappasodi R , Ruggiero G , Guarnotta C , et al. HSPH1 inhibition downregulates Bcl-6 and c-Myc and hampers the growth of human aggressive B-cell non-Hodgkin lymphoma. Blood 2015; 125: 1768- 71.

[40] Osborne AR , Zhang H , Fejer G , et al. Oct-1 maintains an intermediate, stable state of HLA-DRA promoter repression in Rb-defective cells: an Oct-1-containing repressosome that prevents NF-Y binding to the HLA-DRA promoter. J Biol Chem 2004; 279: 28911- 9.

[41] Fugger L , Michie SA , Rulifson I , et al. Expression of HLA-DR4 and human CD4 transgenes in mice determines the variable region betachain T-cell repertoire and mediates an HLA-DR-restricted immune response. Proc Natl Acad Sci U S A 1994; 91: 6151- 5.

[42] Herriges M , Morrisey EE . Lung development: orchestrating the generation and regeneration of a complex organ. Development 2014; 141: 502- 13.

[43] Wang S , Song R , Wang Z , et al. S100A8/A9 in inflammation. Front Immunol 2018; 9: 1298.

[44] Jiang C , He C , Kan J , et al. Integrative bulk and single-cell transcriptome profiling analysis reveals IFI27 as a novel interferon-stimulated gene in dengue. J Med Virol 2023; 95: e28706.

[45] Śledzińska A , Vila de Mucha M , Bergerhoff K , et al. Regulatory T cells restrain interleukin-2- and blimp-1-dependent acquisition of cytotoxic function by CD4(+) T cells. Immunity 2020; 52: 151- 66.e6.

[46] Ebert S , Zang L , Ismail N , et al. Tissue inhibitor of metalloproteinases-1 interacts with CD74 to promote AKT signaling, monocyte recruitment responses, and vascular smooth muscle cell proliferation. Cells-Basel 2023; 12: 1899.

[47] Stabile LP , Davis ALG , Gubish CT , et al. Human non-small cell lung tumors and cells derived from normal lung express both estrogen receptor alpha and beta and show biological responses to estrogen. Cancer Res 2002; 62: 2141- 50.

[48] Ganti AK , Sahmoun AE , Panwalkar AW , et al. Hormone replacement therapy is associated with decreased survival in women with lung cancer. J Clin Oncol 2006; 24: 59- 63.

[49] Zhang SY et al. Multi-omics approaches identify and as candidate autophagic regulators and druggable targets in invasive breast carcinoma. Acta Pharm Sin B 2021; 11: 1227- 45.

[50] Palmisano BT , Zhu L , Stafford JM . Role of estrogens in the regulation of liver lipid metabolism. Adv Exp Med Biol 2017; 1043: 227- 56.

[51] Besse-Patin A , Léveillé M , Oropeza D , et al. Estrogen signals through peroxisome proliferator-activated receptor-gamma coactivator 1alpha to reduce oxidative damage associated with diet-induced fatty liver disease. Gastroenterology 2017; 152: 243- 56.

[52] Mathewson ND , Ashenberg O , Tirosh I , et al. Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis. Cell 2021; 184: 1281- 98.e26.

[53] Hipolito Rodrigues MA , Carneiro MM . Estrogen in female health: friend or foe? Women Health 2022; 62: 95- 7.

[54] Merlo S , Spampinato SF , Sortino MA . Estrogen and Alzheimer’s disease: still an attractive topic despite disappointment from early clinical results. Eur J Pharmacol 2017; 817: 51- 8.

[55] Rizner TL . Estrogen metabolism and action in endometriosis. Mol Cell Endocrinol 2009; 307: 8- 18.

[56] Aibar S , González-Blas CB , Moerman T , et al. SCENIC: single-cell regulatory network inference and clustering. Nat Methods 2017; 14: 1083- 6.

[57] Garry DJ . Etv2 is a master regulator of hematoendothelial lineages. Trans Am Clin Climatol Assoc 2016; 127: 212- 23.

[58] Shi Y , Xiao Q , Huang S , et al. Poor prognostic biomarker KIAA1522 Is associated with immune infiltrates in hepatocellular carcinoma. J Oncol 2023; 2023: 1- 15.

[59] Du F , Li X , Feng W , et al. SOX13 promotes colorectal cancer metastasis by transactivating SNAI2 and c-MET. Oncogene 2020; 39: 3522- 40.

[60] Kim S , Lee J-Y , Shin SG , et al. ESRRA (estrogen related receptor alpha) is a critical regulator of intestinal homeostasis through activation of autophagic flux via gut microbiota. Autophagy 2021; 17: 2856- 75.

[61] Buniello A , MacArthur JAL , Cerezo M , et al. The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019. Nucleic Acids Res 2019; 47: D1005- 12.

[62] Sanderson PA , Critchley HO , Williams AR , et al. New concepts for an old problem: the diagnosis of endometrial hyperplasia. Hum Reprod Update 2017; 23: 232- 54.

[63] Crosbie EJ , Kitson SJ , McAlpine JN , et al. Endometrial cancer. Lancet 2022; 399: 1412- 28.

[64] Jiang L , Fei H , Yang A , et al. Estrogen inhibits the growth of colon cancer in mice through reversing extracellular vesicle-mediated immunosuppressive tumor microenvironment. Cancer Lett 2021; 520: 332- 43.

[65] Barzi A , Lenz AM , Labonte MJ , et al. Molecular pathways: estrogen pathway in colorectal cancer. Clin Cancer Res 2013; 19: 5842- 8.

[66] Chen J , Iverson D . Estrogen in obesity-associated colon cancer: friend or foe? Protecting postmenopausal women but promoting latestage colon cancer. Cancer Causes Control 2012; 23: 1767- 73.

[67] Kovats S . Estrogen receptors regulate innate immune cells and signaling pathways. Cell Immunol 2015; 294: 63- 9.

[68] Chakraborty B , Byemerwa J , Krebs T , et al. Estrogen receptor signaling in the immune system. Endocr Rev 2023; 44: 117- 41.

[69] Zhao HC , Chen C-Z , Song H-Q , et al. Single-cell RNA sequencing analysis reveals new immune disorder complexities in hypersplenism. Front Immunol 2022; 13: 921900.

[70] Yu Z , Lv Y , Su C , et al. Integrative single-cell analysis reveals transcriptional and epigenetic regulatory features of clear cell renal cell carcinoma. Cancer Res 2023; 83: 700- 19.

[71] Chen GG , Zeng Q , Tse GM . Estrogen and its receptors in cancer. Med Res Rev 2008; 28: 954- 74.

[72] Liang J , Shang Y . Estrogen and cancer. Annu Rev Physiol 2013; 75: 225- 40.

[73] Hess RA , Cooke PS . Estrogen in the male: a historical perspective. Biol Reprod 2018; 99: 27- 44.

[74] O’Donnell L , Robertson KM , Jones ME , et al. Estrogen and spermatogenesis. Endocr Rev 2001; 22: 289- 318.

[75] Grumbach MM . The role of estrogen in the male and female: evidence from mutations in synthesis and action. Horm Res 2000; 53: 23- 4.

[76] Li H , Durbin R . Fast and accurate short read alignment with BurrowsWheeler transform. Bioinformatics 2009; 25: 1754- 60.

[77] Butler A , Hoffman P , Smibert P , et al. , Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol 2018; 36: 411.

[78] McGinnis CS , Murrow LM , Gartner ZJ . DoubletFinder: doublet detection in single-Cell RNA sequencing data using artificial nearest neighbors. Cell Syst 2019; 8: 329.

[79] Lee DD , Seung HS . Learning the parts of objects by non-negative matrix factorization. Nature 1999; 401: 788- 91.

[80] Puram SV , Tirosh I , Parikh AS , et al. Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. Cell 2017; 171: 1611- 24.e24.

[81] Han XP et al. Construction of a human cell landscape at single-cell level. Nature 2020; 581: 303.

[82] Yu GC , Wang LG , Han YY , et al. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics 2012; 16: 284- 7.

[83] Hänzelmann S , Castelo R , Guinney J . GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinf 2013; 14: 7.

[84] Trapnell C , Cacchiarelli D , Grimsby J , et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 2014; 32: 381- 6.

[85] Saelens W , Cannoodt R , Todorov H , et al. A comparison of single-cell trajectory inference methods. Nat Biotechnol 2019; 37: 547- 54.

[86] Efremova M , Vento-Tormo M , Teichmann SA , et al. CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat Protoc 2020; 15: 1484- 506.

[87] Granja JM , Corces MR , Pierce SE , et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat Genet 2021; 53: 403- 11.

[88] Korsunsky I , Millard N , Fan J , et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 2019; 16: 1289- 96.

[89] D van Dijk et al. Recovering gene interactions from single-cell data using data diffusion. Cell 2018; 174: 716.

[90] Zhang Y , Liu T , Meyer CA , et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008; 9: R137.

RIGHTS & PERMISSIONS

2024 The Author(s) 2024. Published by Oxford University Press on behalf of Higher Education Press.