Additional file 1: of Deletion of the murine ortholog of the 8q24 gene desert has anti-cancer effects in transgenic mammary cancer models
Creators: name: Homer-Bouthiette, Collin
name: Zhao, Yang
name: Shunkwiler, Lauren
name: Peel, Benjamine
name: Garrett-Mayer, Elizabeth
name: Baird, Rachael
name: Rissman, Anna
name: Guest, Stephen
name: Ethier, Stephen
name: John, Manorama
name: Powers, Patricia
name: Haag, Jill
name: Gould, Michael
name: Smits, Bart
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Computational Biology

description: Figure S1: A) The Southern blots of the correctly inserted clones are shown in the panel. B) The MD allele in the mouse is viable in homozygous state and MD-/- mothers produce normal litter size, as compared with MD+/+ mothers. Figure S2: Comparison of tumor parameters for the PyVT (A-D), C3(1)-TAg (E-G) and neu transgenes on the FVB/N genetic background (Jackson Labs) and our MD+/+ genetic background. No differences between the genetic backgrounds were detected. Hence, we added the data for the animals with the FVB/N genetic background to the MD+/+ groups for further analysis. Figure S3: Effect of MD allele on premalignant mammary glands in the PyVT and C3(1)-TAg models. A, B) Representative images of whole mounted mammary glands from PyVT MD+/+ (A) and PyVT MD-/- (B) mice at 46 days of age. The PyVT-induced hyperplastic expansion of the mammary epithelium is clearly visible in the MD+/+ glands, but strongly reduced in the MD-/- gland. C, D) Images of whole mounted mammary glands from C3(1)-TAg MD+/+ (A) and C3(1)-TAg MD-/- (B) mice at 5 months of age. Premalignant and malignant lesions are visible in both glands. E, F) Quantification of premalignant nodules and lesions on whole mounted mammary glands from PyVT MD+/+ (n = 9) and PyVT MD-/- (n = 4) mice (E), or C3(1)-TAg MD+/+ (n = 3) and C3(1)-TAg MD-/- (n = 4) mice (F), respectively. Graphed are averages +/- sem. Figure S4: Additional gene expression analysis. A) Comparison of housekeeping gene ActB transcript levels (normalized to 18S) between MD+/+ and MD-/- tissue samples. B) Comparison of PyVT or C3(1)-TAg transgene expression (normalized to 18S) between MD+/+ and MD-/- tumor tissue samples. Averages are shown, error bars are s.e.m. Significance (p &lt; 0.05) is indicated by an asterisk. Figure S5: Higher-order chromatin interactions in the cancer-associated human and mouse gene desert. A) Higher-order chromatin interaction heat map of the 8q24 locus in human mammary epithelial cell line HMEC generated using the Jukebox tool. The positions of genes FAM84B, MYC and PVT1 are indicated. B) Chromatin interactions in the MD interval with the MYC promoter. The human interactions are shown in purple, the mouse in pink. The human interactions are derived from the vertical blue line in the heat map in panel A. The mouse interactions were determined experimentally, using the 3C assay on formaldehyde-fixed, restriction/ligation-treated MEC chromatin isolated from the mammary gland (MG) from MD+/+ mice. Figure S6: The association of MYC and FAM84B gene copy number increase and overexpression with clinical outcomes in 1105 primary breast cancers of the TCGA data set. (A) Frequency of MYC and FAM84B copy number amplification in 35 cancer types from the TCGA bioportal database. (B, C) Oncoprint showing cases from the TCGA database with MYC or FAM84B gene amplification (B) or gene expression greater than 2 standard deviations (SD) above the mean (C). (D, E) Overall survival plots from the TCGA bioportal for breast cancer patients with (red plot) or without (blue plot) FAM84B (D) or MYC (E) gene overexpression (&gt; 2 SD). Figure S7: A, B) Overall survival plots from the TCGA cancer bioportal for breast cancer patients (n = 1105), with (red plot) or without (blue plot) FAM84B (A) or MYC (B) gene overexpression at &gt; 1.5 SD. C) Disease-free survival plots from the TCGA bioportal for breast cancer patients with (red plot) or without (blue plot) FAM84B gene overexpression at &gt; 2 SD. (DOCX 9763 kb)