MOESM1 of Regional methylome profiling reveals dynamic epigenetic heterogeneity and convergent hypomethylation of stem cell quiescence-associated genes in breast cancer following neoadjuvant chemotherapy
Creators: name: Luo, Yumei
name: Huang, Juan
name: Tang, Yi
name: Luo, Xitu
name: Ge, Lingxia
name: Sheng, Xiujie
name: Sun, Xiaofang
name: Chen, Yaoyong
name: Zhu, Detu
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: Virology

description: Additional file 1: Table S1. Clinical Characteristics of Selected Breast Cancer Patients. Table S2. Primers and probes used in ddPCR MethyLight assays. Figure S1. Unsupervised clustering of top 1% most variable probes of all the 870 TCGA-BRCA 450K samples. Figure S2. Unsupervised clustering of top 1% most variable probes of all the 870 TCGA-BRCA 450K samples with PR/ER/HER2 annotations. Figure S3. Unsupervised clustering of top 1% most variable probes of all the 870 TCGA-BRCA 450K samples with TNM annotations. Figure S4. Histopathological analysis of selected breast cancer patients. Figure S5. Sampling procedures. (A) Breast cancer patients were selected who underwent core needle biopsy sampling, followed by CET neoadjuvant chemotherapy regimens, and finally surgical removal of the breast tumors. Each patient derived 3-4 core needle biopsy specimens prior to NAC, and each post-NAC tumor tissue was spatially dissected into 6-7 sectors; (B) Breast cancer patients were selected whose breast tumors were surgically removed without neoadjuvant chemotherapy treatment. Each tumor tissue was spatially dissected into 6 sectors. Figure S6. Unsupervised clustering of top 1% most variable probes of samples from 5 patients without chemotherapy separately. Figure S7. Unsupervised clustering of 450K array probes mapped to known genes associated to chemotherapy resistant: ABCB1, DUSP4, ETS1, FOXC1, GSTP1, PTEN and TGM2. Figure S8. Unsupervised clustering of MeTIL signature probes of all the samples. Figure S9. DM genes in KEGG cAMP signaling pathway in the 3 NAC-treated patients. Red color indicates hypermethylated genes; blue color indicates hypomethylated genes. Figure S10. DM genes in KEGG Pathways in Cancer in the 3 NAC-treated patients. Red color indicates hypermethylated genes; blue color indicates hypomethylated genes. Figure S11. Establishment of multiplexed Methylight ddPCR. (A) Locations of CpGs in the MethyLight primers and probes and the amplicons for methylated loci of interest, and the C-LESS-C1 assay that amplifies a DNA strand without any cytosine to determine the total DNA amounts in each sample. Genomic coordinate is referred to UCSC hg19; (B) The C- LESS-C1 assay is measured by the HEX-labelled probe, meanwhile 2 genes of interest are measured by the 2 genespecific FAM-labelled probes adjusted at different concentrations. The accuracy of ddPCR is sufficient to display the 2 gene-specific FAM-positive droplets at 2 distinctively separated FAM altitudes, enabling quantification of the 2 genes with 1 fluorescent channel. For the first assay, Gene A = ALDH1L1, Gene B = SOX9; for the second assay, Gene A = HOPX, Gene B = WNT5A. Thus, the 4 genes can be measured with only 2 assays.