MATERIALS AND METHODS Time course study The number of experimental (CERM D1 -/-) and control (non-transgenic, CERM, CERM D1 +/-, cyclin D1 +/- and cyclin D1 -/-) mice included in the study was as follows: CERM D1 -/- (n=10), non-transgenic (n=16), CERM (n=11), CERM cyclin D1 +/- (n=9), cyclin D1 +/- (n=15), cyclin D1 -/- (n=9). The following time points throughout mammary gland development were studied: 1-, 3-, 6-, 8- and 12-weeks. It is important to note that CERM D1 -/- mice showed relatively normal development at one week of age and that all CERM D1 -/- mice showed abnormal development at 3, 6, 8 and 12 weeks of age. Abnormal mammary gland development was defined in whole mounts as absence of a ductal tree and/or abnormal stroma, and in H&E sections as significantly reduced number of epithelial cells composing the TEBs and/or disorganization of the myoepithelial cell layer of the TEB and/or absence of fat cells and/or increased number of fibroblasts and collagen deposition in the stroma. A contingency table was created with the number of control (n=0) and CERM D1 -/- (n=8) mice showing abnormal development and the number of control (n=60) and CERM D1 -/- (n=2) mice without abnormal development. Morphological and histological analyses of mammary glands The number of TEBs per gland was counted on whole mounts at 1X and then the mean and standard error of the mean (SEM) were calculated. Four H&E slides, 6 slides apart from each other, from 6-week-old CERM (n=4) and CERM D1 -/- (n=4) were randomly selected from the middle part of the gland (estimated by lymph node diameter); the number of MECs composing the TEB was determined by counting epithelial cells in all TEB present in those four slides and then calculating the mean number of epithelial cells and SEM per TEB. Sirius Red Staining Tissue sections were deparaffinized, rehydrated and a small volume of Picro-Sirius Red (American Master Tech Scientific, Lodi, CA) solution was added onto the slides. Slides were incubated overnight at room temperature, and washed twice with acidified water (5ml of glacial acetic acid glacial in 1 liter of distiled water) the next day. Slides were then dehydrated in butanol and xylene, mounted using a xylene-based permount solution, and examined with polarized light microscopy. Sirius Red staining was performed on mammary glands from experimental CERM D1 -/- (n=10) and control mice (n=10). Immunohistochemistry Primary antibodies used for immunohistochistry on mouse mammary gland tissue: mouse cyclin D1, rabbit cyclin D2, rabbit cyclin D3, and rabbit cyclin E (Santa Cruz Biotechnology Inc., Santa Cruz, CA); rabbit polyclonal P-cadherin (Santa Cruz Biotechnology Inc., Santa Cruz, CA); mouse monoclonal Ki67 antibody clone MM1 (Novocastra, United Kingdom); mouse polyclonal E-cadherin (BD Transduction Labs); mouse monoclonal p63 (Neomarkers/Lab Vision, Fremont, CA); mouse monoclonal SMA (Neomarkers/Lab Vision, Fremont, CA); rabbit monoclonal H2AX (Cell Signaling, Danvers, MA); rabbit polyclonal pS-p53 (Abcam Inc., Cambridge, MA); rabbit polyclonal pT-Chk2 (Abcam Inc., Cambridge, MA). Detection of apoptosis by terminal deoxytransferase-mediated deoxy uridine nick end-labelling (TUNEL) assay was carried out utilizing the Apoptag®peroxidase in situ apoptosis detection kit (Chemicon International, Temecula, CA) according to manufacturer’s instructions. All inmunohistochemical procedures were performed in 6-week-old CERM (n=4) and CERM D1 -/- (n=4) mammary glands and in transplanted CERM and CERM D1 -/mammary epithelium. For cyclin D2, D3 and E immunohistochemistry cell counting: a total of 1000 ductal MECs per section were counted to determine the percentage of ductal MECs demonstrating nuclear localized cyclin D2, D3 and E. For Ki67 and TUNEL immunohistochemistry cell counting: the number of MECs within each TEB demonstrating positively-stained nuclei was counted and proliferative/apoptotic rates were calculated. All the TEBs present in each section were counted. For H2AX and pTChk2 immunohistochemistry cell counting: the number of MECs within the TEBs demonstrating positively-stained nuclei was counted and the percentage of cells showing positive staining was calculated. For pS-p53 immunohistochemistry cell counting: a contingency table was created with the number of CERM TEBs with no positive cells (n=8) or 1 to 10% positive cells (n=0) and the number of CERM D1-/- TEB with no positive cells (n=7) or 1 to 10% positive cells (n=4). All the TEBs present in each section were counted. In all cases, negative control slides in which the primary antibody was omitted were analyzed in parallel; no nuclear specific staining was observed in the absence of primary antibody. Cyclicity Measurements Estrous cycles were monitored in 6-week-old CERM D1 -/- mice (n=4) by analysis of vaginal cytology beginning on postnatal day 35. A plastic pipette was inserted into the vagina, with care not to stimulate the cervix, and the area was gently flushed with PBS. Vaginal cells were analyzed by light microscopy according to standard morphological criteria. Hormonal supplementation and whole organ culture Twenty-one-day-release 17-estradiol (0.01 mg) + progesterone (10 mg) pellets (Innovative Research of America) were inserted in 3-week-old CERM D1 -/- and control mice (n=3). After 7 days of priming with estradiol and progesterone pellet, the abdominal number 4 mammary glands were removed aseptically, temporarily placed in a sterile dish with a small amount of sterile media without hormones in order to keep the glands moist, stretched on a dry fluorcarbon spectrum mesh, and then placed on a 6 well culture dish containing Waymouth’s MB 752/1 media (Invitrogen, Carlsbad, CA) plus all the necessary hormones: 0.1 g/ml hydrocortisone , 5 g/ml bovine insulin, 1 g/ml prolactin, 0.1 g/ml aldosterone (HIPA media). Glands were maintained in a tri-gas incubator in an atmosphere of 50% O2 and 5% CO2 in air. The medium was replaced every 24 hours initially and every other day for a total of seven days. After 7 days, glands were whole mounted for morphological examination. Mammary gland transplantation For clearing of the endogenous mammary epithelium, the tissue between the nipple and the lymph node was excised from 3-week-old female nude mice and mammary anlagen from E13.5 embryos were implanted into the center of the remaining fat pad. The transplants were harvested six weeks after the surgery. The number of transplants per genotype was as follows: D1 -/- (n=1), MMTV-rtTA D1 +/- (n=2), tet-op-ERD1 -/(n=2), tet-op-ERD1 +/- (n=2), CERMD1 -/- (n=2), CERMD1 +/- (n=1), CERM (n=1). SUPPLEMENTARY EXPERIMENTS Experiments performed to test whether alterations in ovarian function were responsible for the phenotype CERM D1 -/- mice showed vaginal opening at day 30 on average, which is within normal range for C57BL/6 mice, and completed at least one documented complete estrous cycle by day 46 on average indicating that loss of cyclin D1 in CERM mice did neither retard the onset of puberty nor prevent normal estrous cyclicity. In addition, normal antral follicles, responsible for estrogen production, were found in 12-week-old CERM D1 -/mice. The phenotype was not rescued by estrogen and progesterone supplementation of intact CERM D1-/- mice. CERM D1-/- mammary glands failed to undergo alveolar differentiation following exposure to prolactin in vitro in whole mammary gland organ culture. These results suggest that the phenotype was not due to alterations in ovarian function or to estrogen, progesterone or prolactin deficiency. TITLES AND LEGENDS TO SUPPLEMENTARY FIGURES Figure 1: CERM D1 -/- mice showed abnormally increased collagen I/III deposition Sirius Red Staining of collagen I and III in mammary glands from 12-week-old nulliparous female CERM (a) and CERM D1 -/- (b) mice. Figure 2: CERM D1 -/- mice demonstrated normal ovarian function H&E stained section of ovary from a 12-week-old nulliparous female CERM D1 -/mouse (a). Mammary gland whole mounts from 4-week-old nulliparous female CERM D1 -/- mice treated with Estrogen and Progesterone pellets for 7 days (b) and then cultured in media containing prolactin, insulin, aldosterone and hydrocortisone (c). Black arrow indicates the presence of antral follicles (a). CERM D1 -/- mammary gland failed to develop normally even after estrogen and progesterone (b) and prolactin (c) supplementation.