Disease-specific gene repositioning in breast cancer

Abstract

The nuclear repositioning of specific genes may be a novel diagnostic strategy to distinguish malignant from normal tissue.

Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

“…Following knock-down for 72 hours, the position of LADF , OR5H1 and COL1A1 in each siRNA-treated well was determined using HIPMap. The distribution of each locus in the presence of each siRNA was statistically compared to that of six pooled, non-targeting siRNA wells using the KS-test as previously described (Meaburn et al, 2009; Meaburn and Misteli, 2008) (Figure 2A; see Experimental Procedures for details). The screen was conducted in biological duplicates using an siRNA pool targeting LMNA/LMNB1 as a positive control and non-targeting siRNA as negative control on each replicate plate (Figure 2A).…”

“…For the primary screen analysis, empirical cumulative distribution functions (ECDF) for the normalized radial distance of each FISH spot from the border were generated as described for each well in a 384- well plate (Meaburn et al, 2009; Meaburn and Misteli, 2008). Data from all FISH spots from negative control wells (6 wells/plate for primary screen, 12 wells/plate in validation screen) were combined to generate a single ECDF that was used in a pairwise comparisons to each assay well in a plate using the two-sample Kolmogorov-Smirnov (KS) test (Mitchison, 2005; Perlman et al, 2004; Smellie et al, 2006).…”

Tissue-of-origin-specific gene repositioning in breast and prostate cancer

“…Spatial reorganization of the genome is also associated with disease (Borden and Manuelidis 1988; Meaburn et al 2007; Mehta et al 2011; Mewborn et al 2010; Mikelsaar et al 2014; Paz et al 2015), including cancer (Cremer et al 2003; Leshner et al 2015; Meaburn et al 2009; Meaburn and Misteli 2008; Murata et al 2007; Wiech et al 2009; Zeitz et al 2013). Much like between tissue types, changes in genome organization are not global and only subsets of gene loci alter their nuclear location (Borden and Manuelidis 1988; Leshner et al 2015; Meaburn et al 2007; Meaburn et al 2009; Meaburn and Misteli 2008; Zeitz et al 2013).…”

“…Much like between tissue types, changes in genome organization are not global and only subsets of gene loci alter their nuclear location (Borden and Manuelidis 1988; Leshner et al 2015; Meaburn et al 2007; Meaburn et al 2009; Meaburn and Misteli 2008; Zeitz et al 2013). We have previously identified two sets of genes that repositioned in malignant breast or prostate tissue, respectively, compared to their normal counterparts (Leshner et al 2015; Meaburn et al 2009).…”

“…Much like between tissue types, changes in genome organization are not global and only subsets of gene loci alter their nuclear location (Borden and Manuelidis 1988; Leshner et al 2015; Meaburn et al 2007; Meaburn et al 2009; Meaburn and Misteli 2008; Zeitz et al 2013). We have previously identified two sets of genes that repositioned in malignant breast or prostate tissue, respectively, compared to their normal counterparts (Leshner et al 2015; Meaburn et al 2009). These repositioning events were specific to the malignant state and do not commonly occur in non-malignant disease and they are not accounted for by inter-individual variations, nor do they correlate with numerical genome abnormalities, gene ontology, the local gene density surrounding the loci or changes in gene expression (Leshner et al 2015; Meaburn et al 2009; Meaburn and Misteli 2008).…”