PGBD5 promotes site-specific oncogenic mutations in human tumors

Abstract

Genomic rearrangements are a hallmark of human cancers. Here, we identify the piggyBac transposable element derived 5 (PGBD5) gene as an active DNA transposase expressed in the majority of childhood solid tumors, including lethal rhabdoid tumors. Using assembly-based whole-genome DNA sequencing, we found previously undefined genomic rearrangements in human rhabdoid tumors. These rearrangements involved PGBD5-specific signal (PSS) sequences at their breakpoints, recurrently inactivating tumor suppressor genes. PGBD5 was physically associated with genomic PSS sequences that were also sufficient to mediate PGBD5-induced DNA rearrangements in rhabdoid tumor cells. Ectopic expression of PGBD5 in primary immortalized human cells was sufficient to promote cell transformation in vivo. This activity required specific catalytic residues in the PGBD5 transposase domain, as well as end-joining DNA repair, and induced structural rearrangements with PSS breakpoints. This defines PGBD5 as an oncogenic mutator and provides a plausible mechanism for site-specific DNA rearrangements in childhood and adult solid tumors.

Therapeutic targeting of PGBD5-induced DNA repair dependency in pediatric solid tumors

“…Consistent with the genomic rearrangements promoted by PGBD5 in rhabdoid tumors (17), expression of PGBD5 induces DNA damage, which requires both DNA damage repair and DNA damage signaling, resulting in apoptosis if impaired by their selective inhibitors (Fig. 8).…”

“…We reasoned that specific PGBD5-dependent DNA damage response requirements may be identified by comparative analysis of growth and survival of RPE cells expressing GFP-PGBD5 , as compared to GFP control and its catalytically inactive GFP-PGBD5 D168A/D194A/D386A mutant. This mutant is expressed equally to wild-type PGBD5, as assessed by Western immunoblotting, and physically associates with chromatin, as assessed by chromatin immunoprecipitation and DNA sequencing (ChIP-seq), but does not support DNA transposition in reporter assays (17). To minimize the possible contribution of secondary effects of PGBD5 expression due to its induction of mutagenic DNA rearrangements and cell transformation, we used cells for experiments immediately after transgene transduction (17).…”

“…Previously, we observed that PGBD5 is expressed in the majority of childhood solid tumors, including neuroblastoma, medulloblastoma, Ewing sarcoma, and rhabdoid tumors (17). In particular, in rhabdoid tumors, we found that the DNA recombinase activity of PGBD5 was necessary and sufficient to induce genomic rearrangements in both rhabdoid tumor cell lines and patient tumors.…”

“…PGBD5-mediated DNA transposition requires the DDD catalytic triad in the PGBD5 transposase domain and specific DNA recognition sequences and target sites (16). In particular, PGBD5 was found to be expressed in the majority of childhood solid tumors, including refractory rhabdoid tumors, where it promotes site-specific genomic rearrangements and mutations of tumor suppressor genes at least in part due to the aberrant targeting of its DNA nuclease activity (17). This tumorigenic nuclease activity of PGBD5 raises the possibility that PGBD5-expressing cells may depend on active DNA damage repair and signaling.…”

Transposable Element Exprssion in Tumors is Associated with Immune Infiltration and Increased Antigenicity

“…piggyBac DNA transposons, in addition to being widely used as a genomic engineering tool to create insertional mutagenesis (44), are also ancestral to several domesticated host genes, such as PGBD5. PGBD5 was recently reported to encode an active DNA transposase expressed in the majority of childhood solid tumors and is responsible therein for site-specific oncogenic DNA rearrangements that require end-joining DNA repair (45). Together these findings suggest the possibility that activity of human DNA transposons may result in DNA damage, consistent with their known roles in chromosomal rearrangement and mutagenesis in other species (46,47).…”