aging; breast cancer risk; breast tumorigenesis; mammary tumors; midkine; single-cell profiling; Midkine; MDK protein, human; Methylnitrosourea; Animals; Female; Humans; Rats; Carcinogenesis/genetics; Mammary Glands, Animal/pathology; Mammary Glands, Animal/metabolism; Cell Proliferation; Mammary Neoplasms, Experimental/pathology; Mammary Neoplasms, Experimental/genetics; Mammary Neoplasms, Experimental/chemically induced; Mammary Neoplasms, Experimental/metabolism; Cell Transformation, Neoplastic/genetics; Cell Transformation, Neoplastic/metabolism; Cell Transformation, Neoplastic/pathology; Signal Transduction; Methylnitrosourea/toxicity; Midkine/metabolism; Midkine/genetics; Breast Neoplasms/pathology; Breast Neoplasms/metabolism; Breast Neoplasms/etiology; Breast Neoplasms/genetics; Aging/pathology; Breast Neoplasms; Carcinogenesis; Cell Transformation, Neoplastic; Mammary Glands, Animal; Mammary Neoplasms, Experimental; Oncology; Cancer Research
Abstract :
[en] Aging is a pivotal risk factor for cancer, yet the underlying mechanisms remain poorly defined. Here, we explore age-related changes in the rat mammary gland by single-cell multiomics. Our findings include increased epithelial proliferation, loss of luminal identity, and decreased naive B and T cells with age. We discover a luminal progenitor population unique to old rats with profiles reflecting precancerous changes and identify midkine (Mdk) as a gene upregulated with age and a regulator of age-related luminal progenitors. Midkine treatment of young rats mimics age-related changes via activating PI3K-AKT-SREBF1 pathway and promotes nitroso-N-methylurea-induced mammary tumorigenesis. Midkine levels increase with age in human blood and mammary epithelium, and higher MDK in normal breast tissue is associated with higher breast cancer risk in younger women. Our findings reveal a link between aging and susceptibility to tumor initiation and identify midkine as a mediator of age-dependent increase in breast tumorigenesis.
Disciplines :
Oncology
Author, co-author :
Yan, Pengze; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
Jimenez, Ernesto Rojas; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
Li, Zheqi; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
Bui, Triet; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
Seehawer, Marco; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
Nishida, Jun; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
Foidart, Pierre ; Université de Liège - ULiège > Département des sciences cliniques ; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
Stevens, Laura E; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
Xie, Yingtian; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
Gomez, Miguel Munoz; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
Park, So Yeon; Department of Pathology, Seoul National University, Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea
Long, Henry W; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
Polyak, Kornelia ; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA, Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA, Department of Pathology, Seoul National University, Bundang Hospital, Seoul National University College of Medicine, Seongnam, Republic of Korea, Harvard Stem Cell Institute, Cambridge, MA 02142, USA. Electronic address: kornelia_polyak@dfci.harvard.edu
SWCRF - Samuel Waxman Cancer Research Foundation Susan G. Komen Breast Cancer Foundation Mark Foundation for Cancer Research ACS - American Cancer Society NCI - National Cancer Institute
Funding text :
We thank members of our laboratories for critical reading of the manuscript and discussions. We thank the Dana-Farber Cancer Institute Molecular Biology, Molecular Imaging Core, Flow Cytometry Core Facilities, Dana-Farber/Harvard Cancer Center Rodent Histopathology Core facility, Dana-Farber Cancer Institute Animal Resource Facilities, and Translational Immunogenomics Laboratory for outstanding services. We thank the National Institute of Aging for providing aged rats. This research was supported by the National Cancer Institute R35 CA197623 (K.P.) and P01 CA250959 (K.P. and H.L.), the Susan G. Komen Foundation (K.P.), and a joint grant by the Samuel Waxman Cancer Research Foundation and The Mark Foundation For Cancer Research (K.P.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health/NCI.We thank members of our laboratories for critical reading of the manuscript and discussions. We thank the Dana-Farber Cancer Institute Molecular Biology, Molecular Imaging Core, Flow Cytometry Core Facilities, Dana-Farber/Harvard Cancer Center Rodent Histopathology Core facility, Dana-Farber Cancer Institute Animal Resource Facilities, Translational Immunogenomics Laboratory and Neurobiology Imaging Facility, HMS for outstanding services. We thank the National Institute of Aging for providing aged rats. This research was supported by the National Cancer Institute R35 CA197623 (K.P.) and P01 CA250959 (K.P. and H.L.), the Susan G. Komen Foundation (K.P.), and a joint grant by the Samuel Waxman Cancer Research Foundation and The Mark Foundation For Cancer Research (K.P.). K.P.. is an American Cancer Society Research Professor. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health / NCI .
Peto, J., Cancer epidemiology in the last century and the next decade. Nature 411 (2001), 390–395, 10.1038/35077256.
Edwards, B.K., Howe, H.L., Ries, L.A.G., Thun, M.J., Rosenberg, H.M., Yancik, R., Wingo, P.A., Jemal, A., Feigal, E.G., Annual report to the nation on the status of cancer, 1973-1999, featuring implications of age and aging on U.S. cancer burden. Cancer 94 (2002), 2766–2792, 10.1002/cncr.10593.
Bidoli, E., Virdone, S., Hamdi-Cherif, M., Toffolutti, F., Taborelli, M., Panato, C., Serraino, D., Worldwide Age at Onset of Female Breast Cancer: A 25-Year Population-Based Cancer Registry Study. Sci. Rep., 9, 2019, 14111, 10.1038/s41598-019-50680-5.
Azam, S., Sjölander, A., Eriksson, M., Gabrielson, M., Czene, K., Hall, P., Determinants of Mammographic Density Change. JNCI Cancer Spectr., 3, 2019, pkz004, 10.1093/jncics/pkz004.
McCormack, V.A., Perry, N.M., Vinnicombe, S.J., Dos Santos Silva, I., Changes and tracking of mammographic density in relation to Pike's model of breast tissue aging: a UK longitudinal study. Int. J. Cancer 127 (2010), 452–461, 10.1002/ijc.25053.
Zhang, M., Lee, A.V., Rosen, J.M., The Cellular Origin and Evolution of Breast Cancer. Cold Spring Harb. Perspect. Med., 7, 2017, a027128, 10.1101/cshperspect.a027128.
Li, C.M.C., Shapiro, H., Tsiobikas, C., Selfors, L.M., Chen, H., Rosenbluth, J., Moore, K., Gupta, K.P., Gray, G.K., Oren, Y., et al. Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing. Cell Rep., 33, 2020, 108566, 10.1016/j.celrep.2020.108566.
Gray, G.K., Li, C.M.C., Rosenbluth, J.M., Selfors, L.M., Girnius, N., Lin, J.R., Schackmann, R.C.J., Goh, W.L., Moore, K., Shapiro, H.K., et al. A human breast atlas integrating single-cell proteomics and transcriptomics. Dev. Cell 57 (2022), 1400–1420.e7, 10.1016/j.devcel.2022.05.003.
Bai, H., Liu, X., Lin, M., Meng, Y., Tang, R., Guo, Y., Li, N., Clarke, M.F., Cai, S., Progressive senescence programs induce intrinsic vulnerability to aging-related female breast cancer. Nat. Commun., 15, 2024, 5154, 10.1038/s41467-024-49106-2.
Reed, A.D., Pensa, S., Steif, A., Stenning, J., Kunz, D.J., Porter, L.J., Hua, K., He, P., Twigger, A.J., Siu, A.J.Q., et al. A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast. Nat. Genet. 56 (2024), 652–662, 10.1038/s41588-024-01688-9.
Polyak, K., Kalluri, R., The role of the microenvironment in mammary gland development and cancer. Cold Spring Harb. Perspect. Biol., 2, 2010, a003244, 10.1101/cshperspect.a003244.
Tharmapalan, P., Mahendralingam, M., Berman, H.K., Khokha, R., Mammary stem cells and progenitors: targeting the roots of breast cancer for prevention. EMBO J., 38, 2019, e100852, 10.15252/embj.2018100852.
Shackleton, M., Vaillant, F., Simpson, K.J., Stingl, J., Smyth, G.K., Asselin-Labat, M.L., Wu, L., Lindeman, G.J., Visvader, J.E., Generation of a functional mammary gland from a single stem cell. Nature 439 (2006), 84–88, 10.1038/nature04372.
Dong, Q., Gao, H., Shi, Y., Zhang, F., Gu, X., Wu, A., Wang, D., Chen, Y., Bandyopadhyay, A., Yeh, I.T., et al. Aging is associated with an expansion of CD49f(hi) mammary stem cells that show a decline in function and increased transformation potential. Aging (Albany NY) 8 (2016), 2754–2776, 10.18632/aging.101082.
Russo, J., Gusterson, B.A., Rogers, A.E., Russo, I.H., Wellings, S.R., van Zwieten, M.J., Comparative study of human and rat mammary tumorigenesis. Lab. Invest. 62 (1990), 244–278.
Miyano, M., Sayaman, R.W., Shalabi, S.F., Senapati, P., Lopez, J.C., Angarola, B.L., Hinz, S., Zirbes, A., Anczukow, O., Yee, L.D., et al. Breast-Specific Molecular Clocks Comprised of ELF5 Expression and Promoter Methylation Identify Individuals Susceptible to Cancer Initiation. Cancer Prev. Res. 14 (2021), 779–794, 10.1158/1940-6207.CAPR-20-0635.
Miyano, M., Sayaman, R.W., Stoiber, M.H., Lin, C.H., Stampfer, M.R., Brown, J.B., LaBarge, M.A., Age-related gene expression in luminal epithelial cells is driven by a microenvironment made from myoepithelial cells. Aging (Albany NY) 9 (2017), 2026–2051, 10.18632/aging.101298.
Russo, J., Russo, I.H., Atlas and histologic classification of tumors of the rat mammary gland. J. Mammary Gland Biol. Neoplasia 5 (2000), 187–200, 10.1023/a:1026443305758.
Alečković, M., Cristea, S., Gil Del Alcazar, C.R., Yan, P., Ding, L., Krop, E.D., Harper, N.W., Rojas Jimenez, E., Lu, D., Gulvady, A.C., et al. Breast cancer prevention by short-term inhibition of TGFβ signaling. Nat. Commun., 13, 2022, 7558, 10.1038/s41467-022-35043-5.
Gil Del Alcazar, C.R., Trinh, A., Alečković, M., Rojas Jimenez, E., Harper, N.W., Oliphant, M.U.J., Xie, S., Krop, E.D., Lulseged, B., Murphy, K.C., et al. Insights into Immune Escape During Tumor Evolution and Response to Immunotherapy Using a Rat Model of Breast Cancer. Cancer Immunol. Res. 10 (2022), 680–697, 10.1158/2326-6066.CIR-21-0804.
Thompson, T.A., Haag, J.D., Gould, M.N., ras gene mutations are absent in NMU-induced mammary carcinomas from aging rats. Carcinogenesis 21 (2000), 1917–1922, 10.1093/carcin/21.10.1917.
Bhowmick, N.A., Neilson, E.G., Moses, H.L., Stromal fibroblasts in cancer initiation and progression. Nature 432 (2004), 332–337, 10.1038/nature03096.
Howell, A., Landberg, G., Bergh, J., Breast tumour stroma is a prognostic indicator and target for therapy. Breast Cancer Res., 11, 2009, S16, 10.1186/bcr2435.
Elyahu, Y., Monsonego, A., Thymus involution sets the clock of the aging T-cell landscape: Implications for declined immunity and tissue repair. Ageing Res. Rev., 65, 2021, 101231, 10.1016/j.arr.2020.101231.
López-Otín, C., Pietrocola, F., Roiz-Valle, D., Galluzzi, L., Kroemer, G., Meta-hallmarks of aging and cancer. Cell Metabol. 35 (2023), 12–35, 10.1016/j.cmet.2022.11.001.
Shalabi, S.F., Miyano, M., Sayaman, R.W., Lopez, J.C., Jokela, T.A., Todhunter, M.E., Hinz, S., Garbe, J.C., Stampfer, M.R., Kessenbrock, K., et al. Evidence for accelerated aging in mammary epithelia of women carrying germline BRCA1 or BRCA2 mutations. Nat. Aging 1 (2021), 838–849, 10.1038/s43587-021-00104-9.
Zou, M.R., Cao, J., Liu, Z., Huh, S.J., Polyak, K., Yan, Q., Histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) controls mammary gland development by regulating key developmental and lineage specification genes. J. Biol. Chem. 289 (2014), 17620–17633, 10.1074/jbc.M114.570853.
Hinohara, K., Wu, H.J., Vigneau, S., McDonald, T.O., Igarashi, K.J., Yamamoto, K.N., Madsen, T., Fassl, A., Egri, S.B., Papanastasiou, M., et al. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell 34 (2018), 939–953.e9, 10.1016/j.ccell.2018.10.014.
Agredo, A., Kasinski, A.L., Histone 4 lysine 20 tri-methylation: a key epigenetic regulator in chromatin structure and disease. Front. Genet., 14, 2023, 1243395, 10.3389/fgene.2023.1243395.
Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D.M., Hill, A.J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F.J., et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566 (2019), 496–502, 10.1038/s41586-019-0969-x.
Chaffer, C.L., Weinberg, R.A., Cancer cell of origin: spotlight on luminal progenitors. Cell Stem Cell 7 (2010), 271–272, 10.1016/j.stem.2010.08.008.
Forster, N., Saladi, S.V., van Bragt, M., Sfondouris, M.E., Jones, F.E., Li, Z., Ellisen, L.W., Basal cell signaling by p63 controls luminal progenitor function and lactation via NRG1. Dev. Cell 28 (2014), 147–160, 10.1016/j.devcel.2013.11.019.
Faraldo, M.M., Teulière, J., Deugnier, M.A., Taddei-De La Hosseraye, I., Thiery, J.P., Glukhova, M.A., Myoepithelial cells in the control of mammary development and tumorigenesis: data from genetically modified mice. J. Mammary Gland Biol. Neoplasia 10 (2005), 211–219, 10.1007/s10911-005-9582-8.
Browaeys, R., Saelens, W., Saeys, Y., NicheNet: modeling intercellular communication by linking ligands to target genes. Nat. Methods 17 (2020), 159–162, 10.1038/s41592-019-0667-5.
Filippou, P.S., Karagiannis, G.S., Constantinidou, A., Midkine (MDK) growth factor: a key player in cancer progression and a promising therapeutic target. Oncogene 39 (2020), 2040–2054, 10.1038/s41388-019-1124-8.
Ibusuki, M., Fujimori, H., Yamamoto, Y., Ota, K., Ueda, M., Shinriki, S., Taketomi, M., Sakuma, S., Shinohara, M., Iwase, H., Ando, Y., Midkine in plasma as a novel breast cancer marker. Cancer Sci. 100 (2009), 1735–1739, 10.1111/j.1349-7006.2009.01233.x.
Tanaka, T., Biancotto, A., Moaddel, R., Moore, A.Z., Gonzalez-Freire, M., Aon, M.A., Candia, J., Zhang, P., Cheung, F., Fantoni, G., et al. Plasma proteomic signature of age in healthy humans. Aging Cell, 17, 2018, e12799, 10.1111/acel.12799.
Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490 (2012), 61–70, 10.1038/nature11412.
Cai, Y.Q., Lv, Y., Mo, Z.C., Lei, J., Zhu, J.L., Zhong, Q.Q., Multiple pathophysiological roles of midkine in human disease. Cytokine, 135, 2020, 155242, 10.1016/j.cyto.2020.155242.
Gail, M.H., Brinton, L.A., Byar, D.P., Corle, D.K., Green, S.B., Schairer, C., Mulvihill, J.J., Projecting individualized probabilities of developing breast cancer for white females who are being examined annually. J. Natl. Cancer Inst. 81 (1989), 1879–1886, 10.1093/jnci/81.24.1879.
Kang, T., Yau, C., Wong, C.K., Sanborn, J.Z., Newton, Y., Vaske, C., Benz, S.C., Krings, G., Camarda, R., Henry, J.E., et al. A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population. Breast Cancer Res., 22, 2020, 81, 10.1186/s13058-020-01322-6.
Brown, M.S., Goldstein, J.L., The SREBP pathway: regulation of cholesterol metabolism by proteolysis of a membrane-bound transcription factor. Cell 89 (1997), 331–340, 10.1016/s0092-8674(00)80213-5.
Tang, J.J., Li, J.G., Qi, W., Qiu, W.W., Li, P.S., Li, B.L., Song, B.L., Inhibition of SREBP by a small molecule, betulin, improves hyperlipidemia and insulin resistance and reduces atherosclerotic plaques. Cell Metabol. 13 (2011), 44–56, 10.1016/j.cmet.2010.12.004.
Shao, W., Machamer, C.E., Espenshade, P.J., Fatostatin blocks ER exit of SCAP but inhibits cell growth in a SCAP-independent manner. J. Lipid Res. 57 (2016), 1564–1573, 10.1194/jlr.M069583.
Porstmann, T., Santos, C.R., Griffiths, B., Cully, M., Wu, M., Leevers, S., Griffiths, J.R., Chung, Y.L., Schulze, A., SREBP activity is regulated by mTORC1 and contributes to Akt-dependent cell growth. Cell Metabol. 8 (2008), 224–236, 10.1016/j.cmet.2008.07.007.
Böttcher, J.P., Bonavita, E., Chakravarty, P., Blees, H., Cabeza-Cabrerizo, M., Sammicheli, S., Rogers, N.C., Sahai, E., Zelenay, S., Reis e Sousa, C., NK Cells Stimulate Recruitment of cDC1 into the Tumor Microenvironment Promoting Cancer Immune Control. Cell 172 (2018), 1022–1037.e14, 10.1016/j.cell.2018.01.004.
Nicotra, R., Lutz, C., Messal, H.A., Jonkers, J., Rat Models of Hormone Receptor-Positive Breast Cancer. J. Mammary Gland Biol. Neoplasia, 29, 2024, 12, 10.1007/s10911-024-09566-0.
Jenkins, E.O., Deal, A.M., Anders, C.K., Prat, A., Perou, C.M., Carey, L.A., Muss, H.B., Age-specific changes in intrinsic breast cancer subtypes: a focus on older women. Oncologist 19 (2014), 1076–1083, 10.1634/theoncologist.2014-0184.
Kumar, T., Nee, K., Wei, R., He, S., Nguyen, Q.H., Bai, S., Blake, K., Pein, M., Gong, Y., Sei, E., et al. A spatially resolved single-cell genomic atlas of the adult human breast. Nature 620 (2023), 181–191, 10.1038/s41586-023-06252-9.
Lu, J., Ahmad, R., Nguyen, T., Cifello, J., Hemani, H., Li, J., Chen, J., Li, S., Wang, J., Achour, A., et al. Heterogeneity and transcriptome changes of human CD8(+) T cells across nine decades of life. Nat. Commun., 13, 2022, 5128, 10.1038/s41467-022-32869-x.
Castillo-Fernandez, J., Herrera-Puerta, E., Demond, H., Clark, S.J., Hanna, C.W., Hemberger, M., Kelsey, G., Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis. Aging Cell, 19, 2020, e13278, 10.1111/acel.13278.
Wang, K., Liu, H., Hu, Q., Wang, L., Liu, J., Zheng, Z., Zhang, W., Ren, J., Zhu, F., Liu, G.H., Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct. Targeted Ther., 7, 2022, 374, 10.1038/s41392-022-01211-8.
Lu, Y., Brommer, B., Tian, X., Krishnan, A., Meer, M., Wang, C., Vera, D.L., Zeng, Q., Yu, D., Bonkowski, M.S., et al. Reprogramming to recover youthful epigenetic information and restore vision. Nature 588 (2020), 124–129, 10.1038/s41586-020-2975-4.
Berdyshev, G.D., Korotaev, G.K., Boiarskikh, G.V., Vaniushin, B.F., [Nucleotide composition of DNA and RNA from somatic tissues of humpback and its changes during spawning]. Biokhimiia 32 (1967), 988–993.
Feinberg, A.P., Vogelstein, B., Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301 (1983), 89–92, 10.1038/301089a0.
Sun, D., Luo, M., Jeong, M., Rodriguez, B., Xia, Z., Hannah, R., Wang, H., Le, T., Faull, K.F., Chen, R., et al. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal. Cell Stem Cell 14 (2014), 673–688, 10.1016/j.stem.2014.03.002.
Selman, M., Pardo, A., Fibroageing: An ageing pathological feature driven by dysregulated extracellular matrix-cell mechanobiology. Ageing Res. Rev., 70, 2021, 101393, 10.1016/j.arr.2021.101393.
Mogilenko, D.A., Shchukina, I., Artyomov, M.N., Immune ageing at single-cell resolution. Nat. Rev. Immunol. 22 (2022), 484–498, 10.1038/s41577-021-00646-4.
Franklin, R.A., Liao, W., Sarkar, A., Kim, M.V., Bivona, M.R., Liu, K., Pamer, E.G., Li, M.O., The cellular and molecular origin of tumor-associated macrophages. Science 344 (2014), 921–925, 10.1126/science.1252510.
Amens, J.N., Bahçecioglu, G., Zorlutuna, P., Immune System Effects on Breast Cancer. Cell. Mol. Bioeng. 14 (2021), 279–292, 10.1007/s12195-021-00679-8.
Xu, S., Xu, H., Wang, W., Li, S., Li, H., Li, T., Zhang, W., Yu, X., Liu, L., The role of collagen in cancer: from bench to bedside. J. Transl. Med., 17, 2019, 309, 10.1186/s12967-019-2058-1.
Laconi, E., Marongiu, F., DeGregori, J., Cancer as a disease of old age: changing mutational and microenvironmental landscapes. Br. J. Cancer 122 (2020), 943–952, 10.1038/s41416-019-0721-1.
DeGregori, J., Adaptive Oncogenesis: A New Understanding of How Cancer Evolves inside Us. 2018, Harvard University Press.
Kadomatsu, K., Tomomura, M., Muramatsu, T., cDNA cloning and sequencing of a new gene intensely expressed in early differentiation stages of embryonal carcinoma cells and in mid-gestation period of mouse embryogenesis. Biochem. Biophys. Res. Commun. 151 (1988), 1312–1318, 10.1016/s0006-291x(88)80505-9.
Matsubara, S., Tomomura, M., Kadomatsu, K., Muramatsu, T., Structure of a retinoic acid-responsive gene, MK, which is transiently activated during the differentiation of embryonal carcinoma cells and the mid-gestation period of mouse embryogenesis. J. Biol. Chem. 265 (1990), 9441–9443.
Neumaier, E.E., Rothhammer, V., Linnerbauer, M., The role of midkine in health and disease. Front. Immunol., 14, 2023, 1310094, 10.3389/fimmu.2023.1310094.
Velentzis, L.S., Freeman, V., Campbell, D., Hughes, S., Luo, Q., Steinberg, J., Egger, S., Mann, G.B., Nickson, C., Breast Cancer Risk Assessment Tools for Stratifying Women into Risk Groups: A Systematic Review. Cancers, 15, 2023, 1124, 10.3390/cancers15041124.
Lim, E., Vaillant, F., Wu, D., Forrest, N.C., Pal, B., Hart, A.H., Asselin-Labat, M.L., Gyorki, D.E., Ward, T., Partanen, A., et al. Aberrant luminal progenitors as the candidate target population for basal tumor development in BRCA1 mutation carriers. Nat. Med. 15 (2009), 907–913, 10.1038/nm.2000.
Tian, R., Tica, S., Hong, D., Oduyale, O., Zong, X., Ren, D., Govindan, R., Cao, Y., Rising accelerated aging in recent generations associated with elevated risk of early-onset cancers. Proceedings of the 115th Annual Meeting of the American Association for Cancer Research, 2024.
Metcalfe, K., Lynch, H.T., Foulkes, W.D., Tung, N., Olopade, O.I., Eisen, A., Lerner-Ellis, J., Snyder, C., Kim, S.J., Sun, P., Narod, S.A., Oestrogen receptor status and survival in women with BRCA2-associated breast cancer. Br. J. Cancer 120 (2019), 398–403, 10.1038/s41416-019-0376-y.
Zhao, S., Wang, H., Nie, Y., Mi, Q., Chen, X., Hou, Y., Midkine upregulates MICA/B expression in human gastric cancer cells and decreases natural killer cell cytotoxicity. Cancer Immunol. Immunother. 61 (2012), 1745–1753, 10.1007/s00262-012-1235-3.
Bankhead, P., Loughrey, M.B., Fernández, J.A., Dombrowski, Y., McArt, D.G., Dunne, P.D., McQuaid, S., Gray, R.T., Murray, L.J., Coleman, H.G., et al. QuPath: Open source software for digital pathology image analysis. Sci. Rep., 7, 2017, 16878, 10.1038/s41598-017-17204-5.
Zhou, Y., Zhou, B., Pache, L., Chang, M., Khodabakhshi, A.H., Tanaseichuk, O., Benner, C., Chanda, S.K., Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun., 10, 2019, 1523, 10.1038/s41467-019-09234-6.
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T., Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13 (2003), 2498–2504, 10.1101/gr.1239303.
Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W.M. 3rd, Zheng, S., Butler, A., Lee, M.J., Wilk, A.J., Darby, C., Zager, M., et al. Integrated analysis of multimodal single-cell data. Cell 184 (2021), 3573–3587.e29, 10.1016/j.cell.2021.04.048.
Villanueva, R.A.M., Chen, Z.J., ggplot2: Elegant Graphics for Data Analysis (2nd ed.). Meas. Interdiscip. Res. Perspect. 17 (2019), 160–167, 10.1080/15366367.2019.1565254.
Morgan, M., Pages, H., Obenchain, V., Hayden, N., Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. 2016, 677–689 R package version 1.
Stuart, T., Srivastava, A., Madad, S., Lareau, C.A., Satija, R., Single-cell chromatin state analysis with Signac. Nat. Methods 18 (2021), 1333–1341, 10.1038/s41592-021-01282-5.
Yu, G., Wang, L.G., Han, Y., He, Q.Y., clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16 (2012), 284–287, 10.1089/omi.2011.0118.
Jin, S., Guerrero-Juarez, C.F., Zhang, L., Chang, I., Ramos, R., Kuan, C.H., Myung, P., Plikus, M.V., Nie, Q., Inference and analysis of cell-cell communication using CellChat. Nat. Commun., 12, 2021, 1088, 10.1038/s41467-021-21246-9.
Love, M.I., Huber, W., Anders, S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 2014, 550, 10.1186/s13059-014-0550-8.