Human archival tissues provide a valuable source for the analysis of spatial genome organization

Abstract

Sections from archival formalin-fixed, paraffin wax-embedded human tissues are a valuable source for the study of the nuclear architecture of specific tissue types in terms of the three-dimensional spatial positioning and architecture of chromosome territories and sub-chromosomal domains. Chromosome painting, centromeric, and locus-specific probes were hybridized to tissue microarrays prepared from formalin-fixed paraffin wax-embedded samples of pancreas and breast. The cell nuclei were analyzed using quantitative three-dimensional image microscopy. The results obtained from non-neoplastic pancreatic cells of randomly selected individuals indicated that the radial arrangement of the chromosome 8 territories as well as their shape (roundness) did not significantly differ between the individuals and were in accordance with assumptions of a probabilistic model for computer simulations. There were considerable differences between pancreatic tumor and non-neoplastic cells. In non-neoplastic ductal epithelium of the breast there was a larger, but insignificant, variability in the three-dimensional positioning of the centromere 17 and HER2 domains between individuals. In neoplastic epithelial breast cells, however, the distances between centromere and gene domains were, on average, smaller than in non-neoplastic cells. In conclusion, our results demonstrate the feasibility of studying the genome architecture in archival, formalin-fixed, paraffin wax-embedded human tissues, opening new directions in tumor research and cell classification.

Disease-specific gene repositioning in breast cancer

“…Spatial reorganization of the genome has previously been linked to cancer and genomic instability (Cremer et al, 2003;Taslerová et al, 2003Taslerová et al, , 2006Murmann et al, 2005;Wiech et al, 2005Wiech et al, , 2009Petrova et al, 2007;Sengupta et al, 2007;Meaburn and Misteli, 2008). With the exceptions of a few chromosomal translocations, however, the previously described cancerassociated spatial genome repositioning events are relatively minor and often involve large genome regions (Cremer et al, 2003;Wiech et al, 2005;Meaburn and Misteli, 2008;Wiech et al, 2009).…”

The actin family member Arp6 and the histone variant H2A.Z are required for spatial positioning of chromatin in chicken cell nuclei.

“…Possible contribution of Arp6 and H2A.Z to development and tumorigenesis through nuclear organization Previous studies have shown that the intranuclear repositioning of chromosomal loci is linked to the differentiation of normal and tumorigenic cells (Cremer et al, 2003;Meaburn et al, 2009;Wiblin et al, 2005;Wiech et al, 2005). It has been observed that Arp6 and H2A.Z show dynamic behavior during development (Kato et al, 2001;Matsuda et al, 2010;Nashun et al, 2010).…”

“…In chicken cells, the territories of gene-rich microchromosomes and gene-poor macrochromosomes are positioned in the center and periphery of the nucleus, respectively. The physiological significance of the radial distribution of CTs is supported by evidence that their arrangement is specific to cell and tissue types, and is altered during development (Meaburn and Misteli, 2007;Meshorer and Misteli, 2006), and in multiple types of cancer cells (Cremer et al, 2003;Meaburn and Misteli, 2008;Wiech et al, 2005).…”

Spatial genome organization in the formation of chromosomal translocations

“…In addition to tissue specific genome organisation, changes in the spatial organisation of the genome have been observed in several diseases, including cancer [10,25,[33][34][35][36], epilepsy [37], and laminopathies, a group of diseases caused by mutation in the nuclear proteins lamin A/C [16], further suggesting a link between positioning and genome activity rather than simply gene density.…”