A Deterministic Analysis of Genome Integrity during Neoplastic Growth in Drosophila

Abstract

The development of cancer has been associated with the gradual acquisition of genetic alterations leading to a progressive increase in malignancy. In various cancer types this process is enabled and accelerated by genome instability. While genome sequencing-based analysis of tumor genomes becomes increasingly a standard procedure in human cancer research, the potential necessity of genome instability for tumorigenesis in Drosophila melanogaster has, to our knowledge, never been determined at DNA sequence level. Therefore, we induced formation of tumors by depletion of the Drosophila tumor suppressor Polyhomeotic and subjected them to genome sequencing. To achieve a highly resolved delineation of the genome structure we developed the Deterministic Structural Variation Detection (DSVD) algorithm, which identifies structural variations (SVs) with high accuracy and at single base resolution. The employment of long overlapping paired-end reads enables DSVD to perform a deterministic, i.e. fragment size distribution independent, identification of a large size spectrum of SVs. Application of DSVD and other algorithms to our sequencing data reveals substantial genetic variation with respect to the reference genome reflecting temporal separation of the reference and laboratory strains. The majority of SVs, constituted by small insertions/deletions, is potentially caused by erroneous replication or transposition of mobile elements. Nevertheless, the tumor did not depict a loss of genome integrity compared to the control. Altogether, our results demonstrate that genome stability is not affected inevitably during sustained tumor growth in Drosophila implying that tumorigenesis, in this model organism, can occur irrespective of genome instability and the accumulation of specific genetic alterations.

DrosophilaLarval Brain Neoplasms Present Tumour-Type Dependent Genome Instability

“…Moreover, unlike Drosophila strains where CNVs affect more frequently regions that do not contain coding sequences ( Dopman and Hartl 2007 ; Emerson et al 2008 ), 97% of the CNVs found in our tumor cohort affect coding sequences. The range of CNVs length in our tumor cohort is also much larger than those found in a Drosophila epithelial tumor caused by the loss of polyhomeotic ( ph ) ( Sievers et al 2014 ) and similar to the 0.5 kb – 85 Mb range found in human cancer ( Beroukhim et al 2010 ).…”

“…In Drosophila, the sequencing of a single tumor caused by the loss of Polyhomeotic (Ph) revealed that neither single nucleotide polymorphisms (SNPs) nor copy number variations (CNVs) were significantly increased in comparison with non-tumoural control tissue, suggesting that genome instability (GI) may not be a pre-requisite for neoplastic epithelial growth in this model system. ( Sievers et al 2014 ). The question remains, however, as to the extent of GI in other samples of Ph tumors and, indeed, in different types of Drosophila malignant neoplasms.…”

Three-Dimensional Genome Organization and Function in Drosophila

“…Furthermore, homology of the two fly members of the PcG Psc and Su ( z ) 2 to a murine protooncogene named Bmi-1 strongly suggested that, in addition to its requirement during development, the appropriate regulation of PcG function is also required to prevent the emergence of cancer. Since then, countless reports have corroborated this hypothesis (Koppens and van Lohuizen 2016), extended the link with cancer to trxG proteins (Schuettengruber et al 2011) and, finally, the appropriate regulation of fly PcG components has also been demonstrated to prevent oncogenesis (Classen et al 2009; Martinez et al 2009; Sievers et al 2014). These findings have raised the interest of the scientific community for PcG and trxG proteins considerably.…”

A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila

“…Overall, these results show that the tumorigenic phenotype of ph 505 tissues is primarily due to the loss of ph since it can be rescued by the expression of the wild-type protein. We had shown previously that tumors with impaired ph do not accumulate genetic instabilities, even when cultivated for prolonged time in adult hosts ( Sievers et al, 2014 ). Hence, the observed neoplastic behavior can be solely restricted to the loss of the silencer ph and the ensuing deregulation of the transcriptional state described below.…”