Additional file 2: Figures S1–S6. of Integrative genomic analysis reveals functional diversification of APOBEC gene family in breast cancer

Figure S1. Expression profiles of APOBEC family genes in breast tumor tissues and adjacent normal tissues in relation to ER status. Figure S2. Comparison of chromatin states in APOBEC1 (A), APOBEC2 (B), APOBEC4 (C), and AICDA (D) genes in ER+ (MCF-7), ER− (HCC1954) breast cancer cells, and normal cells (HMEC). Chromatin states characterized by the ChromHMM algorithm are represented by different colors shown in the bottom. Figure S3. Kaplan-Meier curve for overall survival of four patient groups with higher (top 50 %) or lower (bottom 50 %) expression of APOBEC3B and APOBEC3C genes in breast cancer. Figure S4. Distribution of the number of somatic mutations (A) and C>T/G>A mutations (B) per tumor exome. The red curve is a kernel density estimate. Figure S5. Relationship between mRNA levels of APOBEC3B (upper panel) and APOBEC3C (lower panel) and number of somatic SNVs per tumor exome stratified by the ER status. The black lines and red curves are drawn from the linear regression model and local regression smoothing, respectively. Figure S6. Expression profiles of APOBEC family genes in breast tumor tissues in relation with copy numbers of APOBEC3B. (ZIP 559 kb

The Circadian Rhythm Gene <i>Arntl2</i> Is a Metastasis Susceptibility Gene for Estrogen Receptor-Negative Breast Cancer

<div><p>Breast cancer mortality is primarily due to metastasis rather than primary tumors, yet relatively little is understood regarding the etiology of metastatic breast cancer. Previously, using a mouse genetics approach, we demonstrated that inherited germline polymorphisms contribute to metastatic disease, and that these single nucleotide polymorphisms (SNPs) could be used to predict outcome in breast cancer patients. In this study, a backcross between a highly metastatic (FVB/NJ) and low metastatic (MOLF/EiJ) mouse strain identified <i>Arntl2</i>, a gene encoding a circadian rhythm transcription factor, as a metastasis susceptibility gene associated with progression, specifically in estrogen receptor-negative breast cancer patients. Integrated whole genome sequence analysis with DNase hypersensitivity sites reveals SNPs in the predicted promoter of <i>Arntl2</i>. Using CRISPR/Cas9-mediated substitution of the MOLF promoter, we demonstrate that the SNPs regulate <i>Arntl2</i> transcription and affect metastatic burden. Finally, analysis of SNPs associated with <i>ARNTL2</i> expression in human breast cancer patients revealed reproducible associations of <i>ARNTL2</i> expression quantitative trait loci (eQTL) SNPs with disease-free survival, consistent with the mouse studies.</p></div

Additional file 1: of Integrative genomic analysis reveals functional diversification of APOBEC gene family in breast cancer

Tables S1 and S2. Table S1. Data characteristics in this study. Table S2. Expression levels of APOBEC family genes across ten breast cell lines. (XLSX 14 kb

Distal chromosome 6 is a metastasis modifier.

<p>(A) Survival plot of FVB/NJ x (MOLF/EiJ x MMTV-PyMT) mice. p-value calculated by Log-Rank test. FVB = FVB/NJ x MMTV-PyMT; MOLF = MOLF/EiJ x MMTV-PyMT. (B) Surface metastasis count of FVB/NJ x (MOLF/EiJ x MMTV-PyMT) mice. p-value calculated by Mann-Whitney test. FVB = FVB/NJ x MMTV-PyMT; MOLF = MOLF/EiJ x MMTV-PyMT. (C) Depiction of breeding scheme. (D) LOD score plot for metastasis susceptibility, latency and tumor burden loci in the backcross. The y-axis represents the LOD score observed across the genome. The mouse chromosomes are presented head-to-tail on the x-axis. The lower horizontal dashed line represents the suggestive LOD score for a quantitative trait locus after correction for multiple testing by permutation testing. The upper dashed line is the significance threshold after permutation testing. (E) Approximate location of metastasis-associated eQTL candidate genes on distal chromosome 6. (F) The Gene expression-based Outcome for Breast Cancer Online (GOBO) database was queried for the eQTL genes on distal chromosome 6. Distant metastasis-free survival (DMFS) plotted as Kaplan-Meier curves for patients with ER+ and ER- tumors expressing high (blue), intermediate (red), or low (gray) levels of the eQTL genes.</p

Tumor-autonomous effect of Arntl2.

<p>(A) <i>Arntl2</i>^+/+ and <i>Arntl2</i>^-/- mice were bred to MMTV-PyMT+ mice to generate spontaneous primary tumors and lung metastases. At the time of euthanasia, autochthonous PyMT-induced tumors were weighed. N.S. = not significant. (B) Surface lung metastasis count of spontaneous metastases from (A). P-value calculated by two-tailed Mann-Whitney test (C) Primary tumor weight of orthotopically injected 4T1 cells into F1 hybrids from <i>Arntl2</i>^+/+ and Arntl2^+/- mice crossed with BALB/cJ mice. N.S. = not significant. (D) Surface lung metastasis count of the injected mice in (C). N.S. = not significant.</p

Human eQTL SNPs associated with ARNTL2 expression that are prognostic for ER- breast cancer.

<p>Human eQTL SNPs associated with ARNTL2 expression that are prognostic for ER- breast cancer.</p

SNPs within the <i>Arntl2</i> promoter modulate chromatin binding.

<p>(A) Differential binding of MOLF and FVB promoter DNA probes to chromatin proteins. Relative densitometry compared to beads only is reported above each sample. Densitometry was calculated using ImageJ. (B) Relative mRNA expression of <i>Stkl3</i> in wildtype and heterozygous CRISPR 6DT1 cells. (C) Working model depicting differential chromatin binding of MOLF and FVB to regions of the nucleus. LADs = laminar-associated domains (repressive state).</p

Genome editing of the <i>Arntl2</i> promoter.

<p>(A) Haplotypes for the <i>Arntl2</i> putative promoter from the FVB, MOLF, PWK and WSB inbred strains. Brain RNAseq data shows that wild-derived PWK/PhJ carries the same haplotype as MOLF/EiJ, and WSB/EiJ shares 9 of the 10 FVB/NJ SNPs at this location. (B) Relative expression of <i>Arntl2</i> in brain RNA from the PWK and WSB strains. (C) Confirmation of genomically-edited 6DT1 cells. (D) Relative mRNA expression of <i>Arntl2</i> in CRISPR-engineered 6DT1 cells as measured by qPCR. (E) Primary tumor weight of injected CRISPR-engineered WT and heterozygous substituted cells in FVB mice. N.S. = not significant. (F) Surface lung metastasis count on injected cells in (E). P-value calculated by two-tailed Mann-Whitney test.</p

Effect of Arntl2 expression <i>in vivo</i>.

<p>(A) Relative <i>Arntl2</i> mRNA expression in 4T1 cells with control (scramble) and <i>Arntl2</i> shRNA cell lines. (B) Protein expression of ARNTL2 in transiently transfected HEK293 cells with shRNA and overexpression vector expressing myc-tag. Actin is the loading control. (C) Weight of primary tumor from orthotopically injected BALB/cJ mice with 4T1 control and C7 and C11 <i>Arntl2</i> shRNA constructs. N.S. = not significant. (D) Count of surface pulmonary nodules from (C). P-value calculated by two-tailed Mann-Whitney test. (E) Primary tumor weight of <i>Arntl2</i> overexpressing 4T1 cells. N.S. = not significant. (F) Lung metastases from (E), p-value calculated by one-tailed Mann-Whitney test.</p

Supplementary_figure_and_Tables - Transcriptome-Wide Association Study Identifies Susceptibility Loci and Genes for Age at Natural Menopause

<p>Supplementary_figure_and_Tables for Transcriptome-Wide Association Study Identifies Susceptibility Loci and Genes for Age at Natural Menopause by Jiajun Shi, Lang Wu, Bingshan Li, Yingchang Lu, Xingyi Guo, Qiuyin Cai, Jirong Long, Wanqing Wen, Wei Zheng, and Xiao-Ou Shu in Reproductive Sciences</p