Journal: Breast Cancer Research : BCR

Article Title: A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population

doi: 10.1186/s13058-020-01322-6

Figure Lengend Snippet: Classification of normal breast transcriptomes into Active and Inactive phenotypes and increased adipocyte association with Active samples. a Unsupervised clustering heat map (red = increased gene expression, blue = decreased gene expression) showing batch-specific assignment of Active (orange covariate bar) and Inactive (blue co-variate bar) phenotype samples. Horizontal dendrogram = samples, vertical dendrogram = 1318 classifying genes (gold bars = genes upregulated for Active , gray bars = genes upregulated for Inactive phenotype). b Box plots of normal breast cell composition (% adipocyte, stromal, epithelial nuclei) across all 151 samples relative to their transcriptome phenotype assignments (expression cluster Active or Inactive). c Left panel: two-dimensional TumorMap layouts of all KTB normal breast full transcriptomes after batch-integration and projected relative to 1096 TCGA breast cancer full transcriptomes. Batch-integrated normal breast transcriptome samples colored according to batch (blue = F , yellow = P ), and TCGA breast cancer transcriptomes colored according to their PAM50 subtype . Right panel: normal breast full transcriptome TumorMaps presented in isolation before and after batch-correction, showing good sample set integration of both F and P batch samples and preserved spatial separation of Active and Inactive phenotypes, and overlay of the integrated set with color scores (red = high) of their individual cell compositions (% nuclei)

Article Snippet: Contiguous thick paraffin sections (10 μm each) sufficient to extract ~ 100 ng of total breast RNA per sample were sent to NantOmics, LLC (Culver City, CA 90232) for full transcriptome ribo-deplete RNA sequencing (RNAseq), performed on the Illumina NovaSeq platform.

Techniques: Expressing, Isolation

Journal: Breast Cancer Research : BCR

Article Title: A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population

doi: 10.1186/s13058-020-01322-6

Figure Lengend Snippet: Normal breast adipocyte size and gene expression signatures in relation to Active and Inactive transcriptome phenotypes. a Representative H&E image (sample K102670) showing automated adipocyte delineation for cross-sectional area determination on each sample, and distribution plots of mean adipocyte areas for all 151 samples according to their donor’s BMI ( r = 0.48, p < 0.0001) and the sample’s transcriptome phenotype as either Active or Inactive (** p < 0.01). b Batch-specific (F, P) box plot distributions of a previously reported breast cancer-associated cAMP-dependent lipolysis signature [ , ] according to sample transcriptome phenotype assignment (expression cluster) as either Active or Inactive . c Batch-specific ( F , P ) box plot distributions of a previously reported breast cancer-associated white adipocyte browning signature shown according to sample transcriptome phenotype assignment (expression cluster) as either Active or Inactive

Article Snippet: Contiguous thick paraffin sections (10 μm each) sufficient to extract ~ 100 ng of total breast RNA per sample were sent to NantOmics, LLC (Culver City, CA 90232) for full transcriptome ribo-deplete RNA sequencing (RNAseq), performed on the Illumina NovaSeq platform.

Techniques: Expressing

Journal: Breast Cancer Research : BCR

Article Title: A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population

doi: 10.1186/s13058-020-01322-6

Figure Lengend Snippet: Normal breast expression of genes representing fat activation, remodeling, pro-inflammatory signaling, and growth factor expression. F batch-specific box plot distributions of single genes reflecting adipocyte activation (leptin, leptin receptor, adiponectin), adipocyte pro-inflammatory signaling (IKBKG, CCL13), remodeling (CAV1, BNIP3), and adipokine growth factor expression (IGF1 score, FGF2) shown according to sample transcriptome phenotype assignment, Active or Inactive . Comparable P batch-specific box plot distributions are shown in Supplement Figure

Article Snippet: Contiguous thick paraffin sections (10 μm each) sufficient to extract ~ 100 ng of total breast RNA per sample were sent to NantOmics, LLC (Culver City, CA 90232) for full transcriptome ribo-deplete RNA sequencing (RNAseq), performed on the Illumina NovaSeq platform.

Techniques: Expressing, Activation Assay