Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing

Abstract

Aging is closely associated with increased susceptibility to breast cancer, yet there have been limited systematic studies of aging-induced alterations in the mammary gland. Here, we leverage high-throughput single-cell RNA sequencing to generate a detailed transcriptomic atlas of young and aged murine mammary tissues. By analyzing epithelial, stromal, and immune cells, we identify age-dependent alterations in cell proportions and gene expression, providing evidence that suggests alveolar maturation and physiological decline. The analysis also uncovers potential pro-tumorigenic mechanisms coupled to the age-associated loss of tumor suppressor function and change in microenvironment. In addition, we identify a rare, age-dependent luminal population co-expressing hormone-sensing and secretory-alveolar lineage markers, as well as two macrophage populations expressing distinct gene signatures, underscoring the complex heterogeneity of the mammary epithelia and stroma. Collectively, this rich single-cell atlas reveals the effects of aging on mammary physiology and can serve as a useful resource for understanding aging-associated cancer risk.

References 155

1. 1.

   Ace CI, and Okulicz WC (1998 ). A progesterone-induced endometrial homolog of a new candidate tumor suppressor, DMBT1. J. Clin. Endocrinol. Metab 83, 3569–3573.

   Not in our library10.1210/jcem.83.10.5150

2. 2.

   Adriance MC, Inman JL, Petersen OW, and Bissell MJ (2005 ). Myoepithelial cells: good fences make good neighbors. Breast Cancer Res. 7, 190–197.

   Not in our library10.1186/bcr1286

3. 3.

   Agarwal AK, Tunison K, Dalal JS, Nagamma SS, Hamra FK, Sankella S, Shao X, Auchus RJ, and Garg A (2017 ). Metabolic, Reproductive, and Neurologic Abnormalities in Agpat1-Null Mice. Endocrinology 158, 3954–3973.

   Not in our library10.1210/en.2017-00511

4. 4.
   Macrophage Cytokines: Involvement in Immunity and Infectious Diseases · 2014

   No notice
5. 5.

   Azam S, Sjölander A, Eriksson M, Gabrielson M, Czene K, and Hall P (2019 ). Determinants of mammographic density change. JNCI Cancer Spectr 3, pkz004.

   Not in our library10.1093/jncics/pkz004

6. 6.
   Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing · 2017

   No notice
7. 7.

   Bazzoni G, and Dejana E (2004 ). Endothelial cell-to-cell junctions: molecular organization and role in vascular homeostasis. Physiol. Rev 84, 869–901.

   Not in our library10.1152/physrev.00035.2003

8. 8.

   Bjørge L, Jensen TS, Kristoffersen EK, Ulstein M, and Matre R (1996 ). Identification of the complement regulatory protein CD59 in human colostrum and milk. Am. J. Reprod. Immunol 35, 43–50.

   Not in our library10.1111/j.1600-0897.1996.tb00007.x

9. 9.

   Blencowe BJ, Issner R, Nickerson JA, and Sharp PA (1998 ). A coactivator of pre-mRNA splicing. Genes Dev. 12, 996–1009.

   Not in our library10.1101/gad.12.7.996

10. 10.

    Booth BW, Boulanger CA, and Smith GH (2007 ). Alveolar progenitor cells develop in mouse mammary glands independent of pregnancy and lactation. J. Cell. Physiol 212, 729–736.

    Not in our library10.1002/jcp.21071

11. 11.

    Brady NJ, Chuntova P, and Schwertfeger KL (2016 ). Macrophages: regulators of the inflammatory microenvironment during mammary gland development and breast cancer. Mediators Inflamm. 2016, 4549676.

    Not in our library10.1155/2016/4549676

12. 12.

    Brisken C, and Ataca D (2015 ). Endocrine hormones and local signals during the development of the mouse mammary gland. Wiley Interdiscip. Rev. Dev. Biol 4, 181–195.

    Not in our library10.1002/wdev.172

13. 13.

    Bronte V, and Zanovello P (2005 ). Regulation of immune responses by L-arginine metabolism. Nat. Rev. Immunol 5, 641–654.

    Not in our library10.1038/nri1668

14. 14.

    Burchfield JS, Li Q, Wang HY, and Wang R-F (2015 ). JMJD3 as an epigenetic regulator in development and disease. Int. J. Biochem. Cell Biol 67, 148–157.

    Not in our library10.1016/j.biocel.2015.07.006

15. 15.

    Butler A, Hoffman P, Smibert P, Papalexi E, and Satija R (2018 ). Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol 36, 411–420.

    Not in our library10.1038/nbt.4096

16. 16.

    Cella M, Döhring C, Samaridis J, Dessing M, Brockhaus M, Lanzavecchia A, and Colonna M (1997 ). A novel inhibitory receptor (ILT3) expressed on monocytes, macrophages, and dendritic cells involved in antigen processing. J. Exp. Med 185, 1743–1751.

    Not in our library10.1084/jem.185.10.1743

17. 17.
    Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM · 2019

    No notice
18. 18.

    Clarke RB, Howell A, Potten CS, and Anderson E (1997 ). Dissociation between steroid receptor expression and cell proliferation in the human breast. Cancer Res. 57, 4987–4991.

    Not in our library

19. 19.

    Cohen B, Shimizu M, Izrailit J, Ng NFL, Buchman Y, Pan JG, Dering J, and Reedijk M (2010 ). Cyclin D1 is a direct target of JAG1-mediated Notch signaling in breast cancer. Breast Cancer Res. Treat 123, 113–124.

    Not in our library10.1007/s10549-009-0621-9

20. 20.

    Crisà A, Ferrè F, Chillemi G, and Moioli B (2016 ). RNA-sequencing for profiling goat milk transcriptome in colostrum and mature milk. BMC Vet. Res 12, 264.

    Not in our library10.1186/s12917-016-0881-7

21. 21.

    Dawson CA, Pal B, Vaillant F, Gandolfo LC, Liu Z, Bleriot C, Ginhoux F, Smyth GK, Lindeman GJ, Mueller SN, (2020 ). Tissue-resident ductal macrophages survey the mammary epithelium and facilitate tissue re-modelling. Nat. Cell Biol 22, 546–558.

    Not in our library10.1038/s41556-020-0505-0

22. 22.

    Deng M, Gui X, Kim J, Xie L, Chen W, Li Z, He L, Chen Y, Chen H, Luo W, (2018 ). LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration. Nature 562, 605–609.

    Not in our library10.1038/s41586-018-0615-z

23. 23.

    Denissov S, Hofemeister H, Marks H, Kranz A, Ciotta G, Singh S, Anastassiadis K, Stunnenberg HG, and Stewart AF (2014 ). Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant. Development 141, 526–537.

    Not in our library10.1242/dev.102681

24. 24.

    Desai TJ, Brownfield DG, and Krasnow MA (2014 ). Alveolar progenitor and stem cells in lung development, renewal and cancer. Nature 507, 190–194.

    Not in our library10.1038/nature12930

25. 25.

    Diaz Brinton R (2012 ). Minireview: translational animal models of human menopause: challenges and emerging opportunities. Endocrinology 153, 3571–3578.

    Not in our library10.1210/en.2012-1340

26. 26.

    Donato AJ, Morgan RG, Walker AE, and Lesniewski LA (2015 ). Cellular and molecular biology of aging endothelial cells. J. Mol. Cell. Cardiol 89 (Pt B), 122–135.

    Not in our library10.1016/j.yjmcc.2015.01.021

27. 27.

    Dong Q, Gao H, Shi Y, Zhang F, Gu X, Wu A, Wang D, Chen Y, Bandyopadhyay A, Yeh I-T, (2016 ). Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential. Aging (Albany NY) 8, 2754–2776.

    Not in our library10.18632/aging.101082

28. 28.

    Dos Santos CO, Dolzhenko E, Hodges E, Smith AD, and Hannon GJ (2015 ). An epigenetic memory of pregnancy in the mouse mammary gland. Cell Rep. 11, 1102–1109.

    Not in our library10.1016/j.celrep.2015.04.015

29. 29.

    Encinas JM, Michurina TV, Peunova N, Park J-H, Tordo J, Peterson DA, Fishell G, Koulakov A, and Enikolopov G (2011 ). Division-coupled astrocytic differentiation and age-related depletion of neural stem cells in the adult hippocampus. Cell Stem Cell 8, 566–579.

    Not in our library10.1016/j.stem.2011.03.010

30. 30.

    Fata JE, Chaudhary V, and Khokha R (2001 ). Cellular turnover in the mammary gland is correlated with systemic levels of progesterone and not 17β-estradiol during the estrous cycle. Biol. Reprod 65, 680–688.

    Not in our library10.1095/biolreprod65.3.680

31. 31.

    Finch CE, Felicio LS, Mobbs CV, and Nelson JF (1984 ). Ovarian and steroidal influences on neuroendocrine aging processes in female rodents. Endocr. Rev 5, 467–497.

    Not in our library10.1210/edrv-5-4-467

32. 32.

    Flurkey K, Currer JM, and Harrison DE (2007 ). The Mouse in Biomedical Research: Normative Biology, Husbandry, and ModelsSecond Edition, Volume 3 (Elsevier).

    Not in our library

33. 33.

    Franklin RA, Liao W, Sarkar A, Kim MV, Bivona MR, Liu K, Pamer EG, and Li MO (2014 ). The cellular and molecular origin of tumor-associated macrophages. Science 344, 921–925.

    Not in our library10.1126/science.1252510

34. 34.

    Frantz C, Stewart KM, and Weaver VM (2010 ). The extracellular matrix at a glance. J. Cell Sci 123, 4195–4200.

    Not in our library10.1242/jcs.023820

35. 35.

    Froimchuk E, Jang Y, and Ge K (2017 ). Histone H3 lysine 4 methyltransferase KMT2D. Gene 627, 337–342.

    Not in our library10.1016/j.gene.2017.06.056

36. 36.

    Fu NY, Nolan E, Lindeman GJ, and Visvader JE (2020 ). Stem cells and the differentiation hierarchy in mammary gland development. Physiol. Rev 100, 489–523.

    Not in our library10.1152/physrev.00040.2018

37. 37.

    Gannon PO, Godin-Ethier J, Hassler M, Delvoye N, Aversa M, Poisson AO, Péant B, Alam Fahmy M, Saad F, Lapointe R, and Mes-Masson AM (2010 ). Androgen-regulated expression of arginase 1, arginase 2 and interleukin-8 in human prostate cancer. PLoS ONE 5, e12107.

    Not in our library10.1371/journal.pone.0012107

38. 38.

    Gantt S, Gervassi A, Jaspan H, and Horton H (2014 ). The role of myeloid-derived suppressor cells in immune ontogeny. Front. Immunol 5, 387.

    Not in our library10.3389/fimmu.2014.00387

39. 39.

    Garbe JC, Pepin F, Pelissier FA, Sputova K, Fridriksdottir AJ, Guo DE, Villadsen R, Park M, Petersen OW, Borowsky AD, (2012 ). Accumulation of multipotent progenitors with a basal differentiation bias during aging of human mammary epithelia. Cancer Res. 72, 3687–3701.

    Not in our library10.1158/0008-5472.can-12-0157

40. 40.

    Gertig DM, Stillman IE, Byrne C, Spiegelman D, Schnitt SJ, Connolly JL, Colditz GA, and Hunter DJ (1999 ). Association of age and reproductive factors with benign breast tissue composition. Cancer Epidemiol. Biomarkers Prev 8, 873–879.

    Not in our library

41. 41.

    Ginger MR, and Rosen JM (2003 ). Pregnancy-induced changes in cell-fate in the mammary gland. Breast Cancer Res. 5, 192–197.

    Not in our library10.1186/bcr603

42. 42.

    Ginhoux F, and Guilliams M (2016 ). Tissue-resident macrophage ontogeny and homeostasis. Immunity 44, 439–449.

    Not in our library10.1016/j.immuni.2016.02.024

43. 43.

    Giraddi RR, Shehata M, Gallardo M, Blasco MA, Simons BD, and Stingl J (2015 ). Stem and progenitor cell division kinetics during postnatal mouse mammary gland development. Nat. Commun 6, 8487.

    Not in our library10.1038/ncomms9487

44. 44.

    Giraddi RR, Chung C-Y, Heinz RE, Balcioglu O, Novotny M, Trejo CL, Dravis C, Hagos BM, Mehrabad EM, Rodewald L-W, (2018 ). Single-cell transcriptomes distinguish stem cell state changes and lineage specification programs in early mammary gland development. Cell Rep. 24, 1653–1666.e1657.

    Not in our library10.1016/j.celrep.2018.07.025

45. 45.

    Gouon-Evans V, Lin EY, and Pollard JW (2002 ). Requirement of macrophages and eosinophils and their cytokines/chemokines for mammary gland development. Breast Cancer Res. 4, 155–164.

    Not in our library10.1186/bcr441

46. 46.

    Greten FR, and Grivennikov SI (2019 ). Inflammation and cancer: triggers, mechanisms, and consequences. Immunity 51, 27–41.

    Not in our library10.1016/j.immuni.2019.06.025

47. 47.

    Gudjonsson T, Rønnov-Jessen L, Villadsen R, Rank F, Bissell MJ, and Petersen OW (2002 ). Normal and tumor-derived myoepithelial cells differ in their ability to interact with luminal breast epithelial cells for polarity and basement membrane deposition. J. Cell Sci 115, 39–50.

    Not in our library10.1242/jcs.115.1.39

48. 48.

    Guerriero JL (2018 ). Macrophages: the road less traveled, changing anticancer therapy. Trends Mol. Med 24, 472–489.

    Not in our library10.1016/j.molmed.2018.03.006

49. 49.

    Gundlah C, Alves SE, Clark JA, Pai L-Y, Schaeffer JM, and Rohrer SP (2005 ). Estrogen receptor-beta regulates tryptophan hydroxylase-1 expression in the murine midbrain raphe. Biol. Psychiatry 57, 938–942.

    Not in our library10.1016/j.biopsych.2005.01.014

50. 50.

    Guo W, Keckesova Z, Donaher JL, Shibue T, Tischler V, Reinhardt F, Itzkovitz S, Noske A, Zürrer-Härdi U, Bell G, (2012 ). Slug and Sox9 cooperatively determine the mammary stem cell state. Cell 148, 1015–1028.

    Not in our library10.1016/j.cell.2012.02.008

51. 51.

    Gusterson BA, Warburton MJ, Mitchell D, Ellison M, Neville AM, and Rudland PS (1982 ). Distribution of myoepithelial cells and basement membrane proteins in the normal breast and in benign and malignant breast diseases. Cancer Res. 42, 4763–4770.

    Not in our library

52. 52.

    Haaksma CJ, Schwartz RJ, and Tomasek JJ (2011 ). Myoepithelial cell contraction and milk ejection are impaired in mammary glands of mice lacking smooth muscle alpha-actin. Biol. Reprod 85, 13–21.

    Not in our library10.1095/biolreprod.110.090639

53. 53.

    Halper J, and Kjaer M (2014 ). Basic components of connective tissues and extracellular matrix: elastin, fibrillin, fibulins, fibrinogen, fibronectin, laminin, tenascins and thrombospondins. Adv. Exp. Med. Biol 802, 31–47.

    Not in our library10.1007/978-94-007-7893-1_3

54. 54.

    Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, (2018 ). Mapping the mouse cell atlas by Microwell-seq. Cell 172, 1091–1107.e17.

    Not in our library10.1016/j.cell.2018.02.001

55. 55.

    Hart BL, Steinbock RT, Mettler FA Jr., Pathak DR, and Bartow SA (1989 ). Age and race related changes in mammographic parenchymal patterns. Cancer 63, 2537–2539.

    Not in our library10.1002/1097-0142(19890615)63:12<2537::aid-cncr2820631230>3.0.co;2-0

56. 56.

    Hickey DK, Fahey JV, and Wira CR (2013 ). Estrogen receptor α antagonists mediate changes in CCL20 and CXCL1 secretions in the murine female reproductive tract. Am. J. Reprod. Immunol 69, 159–167.

    Not in our library10.1111/aji.12021

57. 57.

    Hoeffel G, and Ginhoux F (2018 ). Fetal monocytes and the origins of tissue-resident macrophages. Cell. Immunol 330, 5–15.

    Not in our library10.1016/j.cellimm.2018.01.001

58. 58.

    Holliday H, Baker LA, Junankar SR, Clark SJ, and Swarbrick A (2018 ). Epigenomics of mammary gland development. Breast Cancer Res. 20, 100–111.

    Not in our library10.1186/s13058-018-1031-x

59. 59.

    Hsu J, Hodgins JJ, Marathe M, Nicolai CJ, Bourgeois-Daigneault M-C, Trevino TN, Azimi CS, Scheer AK, Randolph HE, Thompson TW, (2018 ). Contribution of NK cells to immunotherapy mediated by PD-1/PD-L1 blockade. J. Clin. Invest 128, 4654–4668.

    Not in our library10.1172/jci99317

60. 60.

    Hu M, Yao J, Carroll DK, Weremowicz S, Chen H, Carrasco D, Richardson A, Violette S, Nikolskaya T, Nikolsky Y, (2008 ). Regulation of in situ to invasive breast carcinoma transition. Cancer Cell 13, 394–406.

    Not in our library10.1016/j.ccr.2008.03.007

61. 61.

    Huch M, Dorrell C, Boj SF, van Es JH, Li VSW, van de Wetering M, Sato T, Hamer K, Sasaki N, Finegold MJ, (2013 ). In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration. Nature 494, 247–250.

    Not in our library10.1038/nature11826

62. 62.

    Huh SJ, Clement K, Jee D, Merlini A, Choudhury S, Maruyama R, Yoo R, Chytil A, Boyle P, Ran FA, (2015 ). Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells. Stem Cell Reports 4, 297–311.

    Not in our library10.1016/j.stemcr.2014.12.009

63. 63.

    Hutson SW, Cowen PN, and Bird CC (1985 ). Morphometric studies of age related changes in normal human breast and their significance for evolution of mammary cancer. J. Clin. Pathol 38, 281–287.

    Not in our library10.1136/jcp.38.3.281

64. 64.

    Inman JL, Robertson C, Mott JD, and Bissell MJ (2015 ). Mammary gland development: cell fate specification, stem cells and the microenvironment. Development 142, 1028–1042.

    Not in our library10.1242/dev.087643

65. 65.

    Jahchan NS, You Y-H, Muller WJ, and Luo K (2010 ). Transforming growth factor-beta regulator SnoN modulates mammary gland branching morphogenesis, postlactational involution, and mammary tumorigenesis. Cancer Res. 70, 4204–4213.

    Not in our library10.1158/0008-5472.can-10-0135

66. 66.

    Jahchan NS, Wang D, Bissell MJ, and Luo K (2012 ). SnoN regulates mammary gland alveologenesis and onset of lactation by promoting prolactin/Stat5 signaling. Development 139, 3147–3156.

    Not in our library10.1242/dev.079616

67. 67.

    Jäppinen N, Félix I, Lokka E, Tyystjärvi S, Pynttäri A, Lahtela T, Gerke H, Elima K, Rantakari P, and Salmi M (2019 ). Fetal-derived macrophages dominate in adult mammary glands. Nat. Commun 10, 281.

    Not in our library10.1038/s41467-018-08065-1

68. 68.

    Jenkins EO, Deal AM, Anders CK, Prat A, Perou CM, Carey LA, and Muss HB (2014 ). Age-specific changes in intrinsic breast cancer subtypes: a focus on older women. Oncologist 19, 1076–1083.

    Not in our library10.1634/theoncologist.2014-0184

69. 69.

    Joshi PA, Jackson HW, Beristain AG, Di Grappa MA, Mote PA, Clarke CL, Stingl J, Waterhouse PD, and Khokha R (2010 ). Progesterone induces adult mammary stem cell expansion. Nature 465, 803–807.

    Not in our library10.1038/nature09091

70. 70.

    Kamikawa A, Ichii O, Yamaji D, Imao T, Suzuki C, Okamatsu-Ogura Y, Terao A, Kon Y, and Kimura K (2009 ). Diet-induced obesity disrupts ductal development in the mammary glands of nonpregnant mice. Dev. Dyn 238, 1092–1099.

    Not in our library10.1002/dvdy.21947

71. 71.

    Kanaya N, Chang G, Wu X, Saeki K, Bernal L, Shim H-J, Wang J, Warden C, Yamamoto T, Li J, (2019 ). Single-cell RNA-sequencing analysis of estrogen- and endocrine-disrupting chemical-induced reorganization of mouse mammary gland. Commun. Biol 2, 406–415.

    Not in our library10.1038/s42003-019-0618-9

72. 72.

    Kankel KF, and Reinauer H (1976 ). Activity of pyruvate dehydrogenase complex in the mammary gland of normal and diabetic rats. Diabetologia 12, 149–154.

    Not in our library10.1007/bf00428981

73. 73.

    Kim CF, Jackson EL, Woolfenden AE, Lawrence S, Babar I, Vogel S, Crowley D, Bronson RT, and Jacks T (2005 ). Identification of bronchioalveolar stem cells in normal lung and lung cancer. Cell 121, 823–835.

    Not in our library10.1016/j.cell.2005.03.032

74. 74.

    Kim Y-E, Won M, Lee S-G, Park C, Song C-H, and Kim KK (2019 ). RBM47-regulated alternative splicing of TJP1 promotes actin stress fiber assembly during epithelial-to-mesenchymal transition. Oncogene 38, 6521–6536.

    Not in our library10.1038/s41388-019-0892-5

75. 75.

    Kzhyshkowska J, Rusch A, Wolf H, and Dobner T (2003 ). Regulation of transcription by the heterogeneous nuclear ribonucleoprotein E1B-AP5 is mediated by complex formation with the novel bromodomain-containing protein BRD7. Biochem. J 371, 385–393.

    Not in our library10.1042/bj20021281

76. 76.

    LaBarge MA, Mora-Blanco EL, Samson S, and Miyano M (2016 ). Breast cancer beyond the age of mutation. Gerontology 62, 434–442.

    Not in our library10.1159/000441030

77. 77.
    Chronic Inflammation and Cytokines in the Tumor Microenvironment · 2014

    No notice
78. 78.

    Laporta J, Keil KP, Vezina CM, and Hernandez LL (2014 ). Peripheral serotonin regulates maternal calcium trafficking in mammary epithelial cells during lactation in mice. PLoS ONE 9, e110190.

    Not in our library10.1371/journal.pone.0110190

79. 79.

    Li T, Sun L, Miller N, Nicklee T, Woo J, Hulse-Smith L, Tsao M-S, Khokha R, Martin L, and Boyd N (2005 ). The association of measured breast tissue characteristics with mammographic density and other risk factors for breast cancer. Cancer Epidemiol. Biomarkers Prev 14, 343–349.

    Not in our library10.1158/1055-9965.epi-04-0490

80. 80.

    Liberzon A, Birger C, Thorvaldsdóttir H, Ghandi M, Mesirov JP, and Tamayo P (2015 ). The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 1, 417–425.

    Not in our library10.1016/j.cels.2015.12.004

81. 81.

    Lilja AM, Rodilla V, Huyghe M, Hannezo E, Landragin C, Renaud O, Leroy O, Rulands S, Simons BD, and Fre S (2018 ). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nat. Cell Biol 20, 677–687.

    Not in our library10.1038/s41556-018-0108-1

82. 82.

    Lim E, Vaillant F, Wu D, Forrest NC, Pal B, Hart AH, Asselin-Labat M-L, Gyorki DE, Ward T, Partanen A,; kConFab (2009 ). Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nat. Med 15, 907–913.

    Not in our library10.1038/nm.2000

83. 83.

    Littlejohn MD, Walker CG, Ward HE, Lehnert KB, Snell RG, Verkerk GA, Spelman RJ, Clark DA, and Davis SR (2010 ). Effects of reduced frequency of milk removal on gene expression in the bovine mammary gland. Physiol. Genomics 41, 21–32.

    Not in our library10.1152/physiolgenomics.00108.2009

84. 84.

    Lomniczi A, Wright H, Castellano JM, Matagne V, Toro CA, Ramaswamy S, Plant TM, and Ojeda SR (2015 ). Epigenetic regulation of puberty via Zinc finger protein-mediated transcriptional repression. Nat. Commun 6, 10195.

    Not in our library10.1038/ncomms10195

85. 85.

    Lu D, Ni Z, Liu X, Feng S, Dong X, Shi X, Zhai J, Mai S, Jiang J, Wang Z, (2019 ). Beyond T cells: understanding the role of PD-1/PD-L1 in tumor-associated macrophages. J. Immunol. Res 2019, 1919082–1919087.

    Not in our library10.1155/2019/1919082

86. 86.

    Lv Y, Guan W, Qiao H, Wang C, Chen F, Zhang Y, and Liao Z (2015 ). Veterinary medicine and omics (veterinomics): metabolic transition of milk triacylglycerol synthesis in sows from late pregnancy to lactation. OMICS 19, 602–616.

    Not in our library10.1089/omi.2015.0102

87. 87.
    Tumor endothelial cells accelerate tumor metastasis · 2017

    No notice
88. 88.

    Malhotra GK, Zhao X, Edwards E, Kopp JL, Naramura M, Sander M, Band H, and Band V (2014 ). The role of Sox9 in mouse mammary gland development and maintenance of mammary stem and luminal progenitor cells. BMC Dev. Biol 14, 47.

    Not in our library10.1186/s12861-014-0047-4

89. 89.

    Mas G, Blanco E, Ballaré C, Sansó M, Spill YG, Hu D, Aoi Y, Le Dily F, Shilatifard A, Marti-Renom MA, and Di Croce L (2018 ). Promoter bivalency favors an open chromatin architecture in embryonic stem cells. Nat. Genet 50, 1452–1462.

    Not in our library10.1038/s41588-018-0218-5

90. 90.

    Matsuda M, Imaoka T, Vomachka AJ, Gudelsky GA, Hou Z, Mistry M, Bailey JP, Nieport KM, Walther DJ, Bader M, and Horseman ND (2004 ). Serotonin regulates mammary gland development via an autocrine-paracrine loop. Dev. Cell 6, 193–203.

    Not in our library10.1016/s1534-5807(04)00022-x

91. 91.

    McCormack VA, Perry NM, Vinnicombe SJ, and Dos Santos Silva I (2010 ). Changes and tracking of mammographic density in relation to Pike’s model of breast tissue aging: a UK longitudinal study. Int. J. Cancer 127, 452–461.

    Not in our library10.1002/ijc.25053

92. 92.

    McCormick NH, Hennigar SR, Kiselyov K, and Kelleher SL (2014 ). The biology of zinc transport in mammary epithelial cells: implications for mammary gland development, lactation, and involution. J. Mammary Gland Biol. Neoplasia 19, 59–71.

    Not in our library10.1007/s10911-013-9314-4

93. 93.

    McGinnis CS, Murrow LM, and Gartner ZJ (2019 ). DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329–337.e4.

    Not in our library10.1016/j.cels.2019.03.003

94. 94.

    Miyajima A, Tanaka M, and Itoh T (2014 ). Stem/progenitor cells in liver development, homeostasis, regeneration, and reprogramming. Cell Stem Cell 14, 561–574.

    Not in our library10.1016/j.stem.2014.04.010

95. 95.

    Molyneux G, Geyer FC, Magnay F-A, McCarthy A, Kendrick H, Natrajan R, Mackay A, Grigoriadis A, Tutt A, Ashworth A, (2010 ). BRCA1 basal-like breast cancers originate from luminal epithelial progenitors and not from basal stem cells. Cell Stem Cell 7, 403–417.

    Not in our library10.1016/j.stem.2010.07.010

96. 96.

    Muraoka RS, Koh Y, Roebuck LR, Sanders ME, Brantley-Sieders D, Gorska AE, Moses HL, and Arteaga CL (2003 ). Increased malignancy of Neu-induced mammary tumors overexpressing active transforming growth factor beta1. Mol. Cell. Biol 23, 8691–8703.

    Not in our library10.1128/mcb.23.23.8691-8703.2003

97. 97.

    Muraoka-Cook RS, Kurokawa H, Koh Y, Forbes JT, Roebuck LR, Bar-cellos-Hoff MH, Moody SE, Chodosh LA, and Arteaga CL (2004 ). Conditional overexpression of active transforming growth factor beta1 in vivo accelerates metastases of transgenic mammary tumors. Cancer Res. 64, 9002–9011.

    Not in our library10.1158/0008-5472.can-04-2111

98. 98.

    Nakano S, Iyama K, Ogawa M, Yoshioka H, Sado Y, Oohashi T, and Ninomiya Y (1999 ). Differential tissular expression and localization of type IV collagen alpha1(IV), alpha2(IV), alpha5(IV), and alpha6(IV) chains and their mRNA in normal breast and in benign and malignant breast tumors. Lab. Invest 79, 281–292.

    Not in our library

99. 99.

    Natali PG, Giacomini P, Bigotti G, Nicotra MR, Bellocci M, and De Martino C (1984 ). Heterogeneous distribution of actin, myosin, fibronectin and basement membrane antigens in primary and metastatic human breast cancer. Virchows Arch. A Pathol. Anat. Histopathol 405, 69–83.

    Not in our library10.1007/bf00694926

100. 100.
     Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity · 2018

     No notice
101. 101.

     Nishimura EK, Granter SR, and Fisher DE (2005 ). Mechanisms of hair graying: incomplete melanocyte stem cell maintenance in the niche. Science 307, 720–724.

     Not in our library10.1126/science.1099593

102. 102.

     Oakley R, and Tharakan B (2014 ). Vascular hyperpermeability and aging. Aging Dis. 5, 114–125.

     Not in our library10.14336/ad.2014.0500114

103. 103.

     Ono YJ, Terai Y, Tanabe A, Hayashi A, Hayashi M, Yamashita Y, Kyo S, and Ohmichi M (2014 ). Decorin induced by progesterone plays a crucial role in suppressing endometriosis. J. Endocrinol 223, 203–216.

     Not in our library10.1530/joe-14-0393

104. 104.

     Ormerod EJ, Warburton MJ, Hughes C, and Rudland PS (1983 ). Synthesis of basement membrane proteins by rat mammary epithelial cells. Dev. Biol 96, 269–275.

     Not in our library10.1016/0012-1606(83)90328-7

105. 105.
     Construction of developmental lineage relationships in the mouse mammary gland by single-cell RNA profiling · 2017

     No notice
106. 106.

     Pandey PR, Saidou J, and Watabe K (2010 ). Role of myoepithelial cells in breast tumor progression. Front. Biosci 15, 226–236.

     Not in our library10.2741/3617

107. 107.

     Pankov R, and Yamada KM (2002 ). Fibronectin at a glance. J. Cell Sci 115, 3861–3863.

     Not in our library10.1242/jcs.00059

108. 108.
     Age-Related Dysfunction in Mechanotransduction Impairs Differentiation of Human Mammary Epithelial Progenitors · 2014

     Not checked
109. 109.

     Pelissier Vatter FA, Schapiro D, Chang H, Borowsky AD, Lee JK, Parvin B, Stampfer MR, LaBarge MA, Bodenmiller B, and Lorens JB (2018 ). High-dimensional phenotyping identifies age-emergent cells in human mammary epithelia. Cell Rep. 23, 1205–1219.

     Not in our library10.1016/j.celrep.2018.03.114

110. 110.

     Polyak K, and Kalluri R (2010 ). The role of the microenvironment in mammary gland development and cancer. Cold Spring Harb. Perspect. Biol 2, a003244.

     Not in our library10.1101/cshperspect.a003244

111. 111.

     Proia TA, Keller PJ, Gupta PB, Klebba I, Jones AD, Sedic M, Gilmore H, Tung N, Naber SP, Schnitt S, (2011 ). Genetic predisposition directs breast cancer phenotype by dictating progenitor cell fate. Cell Stem Cell 8, 149–163.

     Not in our library10.1016/j.stem.2010.12.007

112. 112.

     Raafat A, Strizzi L, Lashin K, Ginsburg E, McCurdy D, Salomon D, Smith GH, Medina D, and Callahan R (2012 ). Effects of age and parity on mammary gland lesions and progenitor cells in the FVB/N-RC mice. PLoS ONE 7, e43624.

     Not in our library10.1371/journal.pone.0043624

113. 113.

     Robinson MD, McCarthy DJ, and Smyth GK (2010 ). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140.

     Not in our library10.1093/bioinformatics/btp616

114. 114.
     Organoid cultures from normal and cancer-prone human breast tissues preserve complex epithelial lineages · 2020

     No notice
115. 115.

     Russell TD, Schaack J, Orlicky DJ, Palmer C, Chang BH-J, Chan L, and McManaman JL (2011 ). Adipophilin regulates maturation of cytoplasmic lipid droplets and alveolae in differentiating mammary glands. J. Cell Sci 124, 3247–3253.

     Not in our library10.1242/jcs.082974

116. 116.

     Russo J, Balogh GA, and Russo IH (2008 ). Full-term pregnancy induces a specific genomic signature in the human breast. Cancer Epidemiol. Biomarkers Prev 17, 51–66.

     Not in our library10.1158/1055-9965.epi-07-0678

117. 117.

     Sampath D, Winneker RC, and Zhang Z (2002 ). The angiogenic factor Cyr61 is induced by the progestin R5020 and is necessary for mammary adenocarcinoma cell growth. Endocrine 18, 147–159.

     Not in our library10.1385/endo:18:2:147

118. 118.
     Source of Chronic Inflammation in Aging · 2018

     No notice
119. 119.

     Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, (2012 ). Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682.

     Not in our library10.1038/nmeth.2019

120. 120.

     Schultz MB, and Sinclair DA (2016 ). When stem cells grow old: phenotypes and mechanisms of stem cell aging. Development 143, 3–14.

     Not in our library10.1242/dev.130633

121. 121.

     Shackleton M, Vaillant F, Simpson KJ, Stingl J, Smyth GK, Asselin-Labat M-L, Wu L, Lindeman GJ, and Visvader JE (2006 ). Generation of a functional mammary gland from a single stem cell. Nature 439, 84–88.

     Not in our library10.1038/nature04372

122. 122.
     Expression and functional role of sprouty-2 in breast morphogenesis. · 2013

     Not checked
123. 123.

     Singletary KW, and McNary MQ (1992 ). Effect of moderate ethanol consumption on mammary gland structural development and DNA synthesis in the female rat. Alcohol 9, 95–101.

     Not in our library10.1016/0741-8329(92)90018-6

124. 124.

     Sirka OK, Shamir ER, and Ewald AJ (2018 ). Myoepithelial cells are a dynamic barrier to epithelial dissemination. J. Cell Biol 217, 3368–3381.

     Not in our library10.1083/jcb.201802144

125. 125.

     Sopel M (2010 ). The myoepithelial cell: its role in normal mammary glands and breast cancer. Folia Morphol. (Warsz) 69, 1–14.

     Not in our library

126. 126.
     The long noncoding RNA Neat1 is required for mammary gland development and lactation · 2014

     No notice
127. 127.

     Stingl J, Eirew P, Ricketson I, Shackleton M, Vaillant F, Choi D, Li HI, and Eaves CJ (2006 ). Purification and unique properties of mammary epithelial stem cells. Nature 439, 993–997.

     Not in our library10.1038/nature04496

128. 128.

     Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, and Satija R (2019 ). Comprehensive integration of single-cell data. Cell 177, 1888–1902.e21.

     Not in our library10.1016/j.cell.2019.05.031

129. 129.

     Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, and Mesirov JP (2005 ). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550.

     Not in our library10.1073/pnas.0506580102

130. 130.

     Suciu-Foca N, and Cortesini R (2007 ). Central role of ILT3 in the T suppressor cell cascade. Cell. Immunol. 248, 59–67.

     Not in our library10.1016/j.cellimm.2007.01.013

131. 131.

     Tabula Muris Consortium (2020 ). A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 583, 590–595. https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=32669714&dopt=Abstract.

     Not in our library10.1038/s41586-020-2496-1

132. 132.

     Tabula Muris Consortium; Overall coordination; Logistical coordination; Organ collection and processing; Library preparation and sequencing; Computational data analysis; Cell type annotation; Writing group; Supplemental text writing group; Principal investigators (2018 ). Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 562, 367–372.

     Not in our library10.1038/s41586-018-0590-4

133. 133.

     Theocharis AD, Skandalis SS, Gialeli C, and Karamanos NK (2016 ). Extracellular matrix structure. Adv. Drug Deliv. Rev 97, 4–27.

     Not in our library10.1016/j.addr.2015.11.001

134. 134.

     Tsai M-S, Bogart DF, Li P, Mehmi I, and Lupu R (2002 ). Expression and regulation of Cyr61 in human breast cancer cell lines. Oncogene 21, 964–973.

     Not in our library10.1038/sj.onc.1205131

135. 135.

     Tsubura A, Shikata N, Inui T, Morii S, Hatano T, Oikawa T, and Matsuzawa A (1988 ). Immunohistochemical localization of myoepithelial cells and basement membrane in normal, benign and malignant human breast lesions. Virchows Arch. A Pathol. Anat. Histopathol 413, 133–139.

     Not in our library10.1007/bf00749674

136. 136.

     Tynan S, Pacia E, Haynes-Johnson D, Lawrence D, D’Andrea MR, Guo J-Z, Lundeen S, and Allan G (2005 ). The putative tumor suppressor deleted in malignant brain tumors 1 is an estrogen-regulated gene in rodent and primate endometrial epithelium. Endocrinology 146, 1066–1073.

     Not in our library10.1210/en.2004-1304

137. 137.

     Unsworth A, Anderson R, and Britt K (2014 ). Stromal fibroblasts and the immune microenvironment: partners in mammary gland biology and pathology? J. Mammary Gland Biol. Neoplasia 19, 169–182.

     Not in our library10.1007/s10911-014-9326-8

138. 138.
     Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications · 2018

     No notice
139. 139.
     Lineage-Restricted Mammary Stem Cells Sustain the Development, Homeostasis, and Regeneration of the Estrogen Receptor Positive Lineage · 2017

     Not checked
140. 140.

     Vaughan AE, Brumwell AN, Xi Y, Gotts JE, Brownfield DG, Treutlein B, Tan K, Tan V, Liu FC, Looney MR, (2015 ). Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury. Nature 517, 621–625.

     Not in our library10.1038/nature14112

141. 141.
     Cell state plasticity, stem cells, EMT, and the generation of intra-tumoral heterogeneity · 2017

     No notice
142. 142.

     Wahle E, and Winkler GS (2013 ). RNA decay machines: deadenylation by the Ccr4-not and Pan2-Pan3 complexes. Biochim. Biophys. Acta 1829, 561–570.

     Not in our library10.1016/j.bbagrm.2013.01.003

143. 143.

     Wang C, Christin JR, Oktay MH, and Guo W (2017 ). Lineage-biased stem cells maintain estrogen-receptor-positive and -negative mouse mammary luminal lineages. Cell Rep. 18, 2825–2835.

     Not in our library10.1016/j.celrep.2017.02.071

144. 144.

     Wang Y, Chaffee TS, LaRue RS, Huggins DN, Witschen PM, Ibrahim AM, Nelson AC, Machado HL, and Schwertfeger KL (2020 ). Tissue-resident macrophages promote extracellular matrix homeostasis in the mammary gland stroma of nulliparous mice. eLife 9, 1399.

     Not in our library10.7554/elife.57438

145. 145.

     Warburton MJ, Ormerod EJ, Monaghan P, Ferns S, and Rudland PS (1981 ). Characterization of a myoepithelial cell line derived from a neonatal rat mammary gland. J. Cell Biol 91, 827–836.

     Not in our library10.1083/jcb.91.3.827

146. 146.

     Warburton MJ, Mitchell D, Ormerod EJ, and Rudland P (1982 ). Distribution of myoepithelial cells and basement membrane proteins in the resting, pregnant, lactating, and involuting rat mammary gland. J. Histochem. Cytochem 30, 667–676.

     Not in our library10.1177/30.7.6179984

147. 147.

     Wolock SL, Lopez R, and Klein AM (2019 ). Scrublet: computational identification of cell doublets in single-cell transcriptomic data. Cell Syst. 8, 281–291.e9.

     Not in our library10.1016/j.cels.2018.11.005

148. 148.

     Wuidart A, Sifrim A, Fioramonti M, Matsumura S, Brisebarre A, Brown D, Centonze A, Dannau A, Dubois C, Van Keymeulen A, (2018 ). Early lineage segregation of multipotent embryonic mammary gland progenitors. Nat. Cell Biol 20, 666–676.

     Not in our library10.1038/s41556-018-0095-2

149. 149.

     Yamazaki T, Akiba H, Iwai H, Matsuda H, Aoki M, Tanno Y, Shin T, Tsuchiya H, Pardoll DM, Okumura K, (2002 ). Expression of programmed death 1 ligands by murine T cells and APC. J. Immunol 169, 5538–5545.

     Not in our library10.4049/jimmunol.169.10.5538

150. 150.
     VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation · 2018

     No notice
151. 151.

     Zhang X, Qiao G, and Lu P (2014 ). Modulation of fibroblast growth factor signaling is essential for mammary epithelial morphogenesis. PLoS ONE 9, e92735.

     Not in our library10.1371/journal.pone.0092735

152. 152.

     Zhang S, Yang X, Wang L, and Zhang C (2018a ). Interplay between inflammatory tumor microenvironment and cancer stem cells. Oncol. Lett 16, 679–686.

     Not in our library10.3892/ol.2018.8716

153. 153.

     Zhang Y, Zhang S, Guan W, Chen F, Cheng L, Lv Y, and Chen J (2018b ). GLUT1 and lactose synthetase are critical genes for lactose synthesis in lactating sows. Nutr. Metab. (Lond.) 15, 40.

     Not in our library10.1186/s12986-018-0276-9

154. 154.

     Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang C-M, Li CJ, Vågbø CB, Shi Y, Wang W-L, Song S-H, (2013 ). ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29.

     Not in our library10.1016/j.molcel.2012.10.015

155. 155.

     Zhu W, and Nelson CM (2013 ). PI3K regulates branch initiation and extension of cultured mammary epithelia via Akt and Rac1 respectively. Dev. Biol 379, 235–245.

     Not in our library10.1016/j.ydbio.2013.04.029

Cited by papers we hold 2

• Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data · 2022
  No notice
• Transcriptional changes in the mammary gland during lactation revealed by single cell sequencing of cells from human milk · 2022
  No notice

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