Genomic Restructuring in the Tasmanian Devil Facial Tumour: Chromosome Painting and Gene Mapping Provide Clues to Evolution of a Transmissible Tumour

Abstract

Devil facial tumour disease (DFTD) is a fatal, transmissible malignancy that threatens the world's largest marsupial carnivore, the Tasmanian devil, with extinction. First recognised in 1996, DFTD has had a catastrophic effect on wild devil numbers, and intense research efforts to understand and contain the disease have since demonstrated that the tumour is a clonal cell line transmitted by allograft. We used chromosome painting and gene mapping to deconstruct the DFTD karyotype and determine the chromosome and gene rearrangements involved in carcinogenesis. Chromosome painting on three different DFTD tumour strains determined the origins of marker chromosomes and provided a general overview of the rearrangement in DFTD karyotypes. Mapping of 105 BAC clones by fluorescence in situ hybridisation provided a finer level of resolution of genome rearrangements in DFTD strains. Our findings demonstrate that only limited regions of the genome, mainly chromosomes 1 and X, are rearranged in DFTD. Regions rearranged in DFTD are also highly rearranged between different marsupials. Differences between strains are limited, reflecting the unusually stable nature of DFTD. Finally, our detailed maps of both the devil and tumour karyotypes provide a physical framework for future genomic investigations into DFTD.

A second transmissible cancer in Tasmanian devils

“…Despite the absence of cytogenetically identifiable sex chromosomes in DFT1, studies using fluorescence in situ hybridization and DNA sequencing have found evidence for two X chromosome copies in DFT1 (13,14). Furthermore, the number of single point substitution variants mapping to the X chromosome in DFT1 suggested that the two X chromosomes were germ-line homologs rather than recent somatic duplicates (13).…”

“…The DFTD clone has been closely monitored during its epidemic sweep through Tasmania ( Fig. 1A) (13)(14)(15)(16).…”

Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer

“…A devil fibroblast cell line (18) was used as a control. Three cell lines derived from DFTD primary tumors (1426, 4906 and C5065) are described (33,34). Complete medium and cell culture conditions are described in SI Appendix.…”

Catching Cancer

“…Despite no sex chromosomes being in any sample being analyzed, duplicates of 11/14 Xchromosome genes were found scattered amongst the marker chromosomes, suggesting positive selection for these X-chromosome genes [40,41]. Fluorescence hybridization confirmed these findings, and in addition found traces of male genes, suggesting the ancestral donor was female.…”

“…Fluorescence hybridization confirmed these findings, and in addition found traces of male genes, suggesting the ancestral donor was female. This was supported by both the absence of Y chromosome hybridization and the lack of SRY sequence in DFTD tumors [40,41].…”