Identification of Rtl1, a Retrotransposon-Derived Imprinted Gene, as a Novel Driver of Hepatocarcinogenesis

Abstract

We previously utilized a Sleeping Beauty (SB) transposon mutagenesis screen to discover novel drivers of HCC. This approach identified recurrent mutations within the Dlk1-Dio3 imprinted domain, indicating that alteration of one or more elements within the domain provides a selective advantage to cells during the process of hepatocarcinogenesis. For the current study, we performed transcriptome and small RNA sequencing to profile gene expression in SB–induced HCCs in an attempt to clarify the genetic element(s) contributing to tumorigenesis. We identified strong induction of Retrotransposon-like 1 (Rtl1) expression as the only consistent alteration detected in all SB–induced tumors with Dlk1-Dio3 integrations, suggesting that Rtl1 activation serves as a driver of HCC. While previous studies have identified correlations between disrupted expression of multiple Dlk1-Dio3 domain members and HCC, we show here that direct modulation of a single domain member, Rtl1, can promote hepatocarcinogenesis in vivo. Overexpression of Rtl1 in the livers of adult mice using a hydrodynamic gene delivery technique resulted in highly penetrant (86%) tumor formation. Additionally, we detected overexpression of RTL1 in 30% of analyzed human HCC samples, indicating the potential relevance of this locus as a therapeutic target for patients. The Rtl1 locus is evolutionarily derived from the domestication of a retrotransposon. In addition to identifying Rtl1 as a novel driver of HCC, our study represents one of the first direct in vivo demonstrations of a role for such a co-opted genetic element in promoting carcinogenesis.

Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression

“…In addition, in many cases, only a single transposon insertion was present at a CCG in tumor cells, suggesting that many CCGs are functioning as haploinsufficient TSGs. This is similar to what has been observed in other SB mutagenesis screens performed in solid tumors (18)(19)(20)(21)(22)(23)(24)(25)(26).…”

“…Identification of Trunk Driver Genes. Most CCGs identified by SB mutagenesis are thought to function during late stages of tumor progression (18)(19)(20)(21)(22)(23)(24)(25)(26). To identify the CCGs that function early in mammary tumor development, we selected transposon insertion sites represented by the highest number of sequencing reads (SB insertions in the CCG in ≥3 tumors with ≥9 reads per tumor), arguing that these insertions would be present in the largest number of tumor cells.…”

“…New technologies that would provide a more complete understanding of the genetics of TNBC are still needed to deconvolute the complexity of this deadly cancer. Our laboratory and others have pioneered the use of transposon mutagenesis in mice as a tool for cancer gene discovery (18)(19)(20)(21)(22)(23)(24)(25)(26). Transposons induce cancer by randomly inserting into the mouse genome, mutating, and disrupting potential cancer genes.…”

Domesticated transposable element gene products in human cancer

“…Recently, we described the identification of Retrotransposon-like 1 (Rtl1) as a gene involved in hepatocellular carcinoma (HCC) development through the use of a Sleeping Beauty transposon forward genetic mutagenesis screen in mice. 21 Subsequent in vivo validation of tumor-promoting activity and correlation to expression data from human liver tumors led us to conclude that activation of RTL1 may be a significant driving event in human HCC. In this mini-review, we discuss the functions of various domesticated TE gene products in cellular processes related to cancer, as well as summarize the results of studies correlating expression of this gene class with tumor status.…”

Sleeping Beautytransposon system for genetic etiological research and gene therapy of cancers

“…73 In SB transposon system-induced mouse models, retrotransposon-like 1 (Rtl1) and PDE4D have been identified as drivers of HCC and prostate cancer, respectively. 74,75 MYC is a dysregulated gene in human malignancies. Introduction of MYC through SB transposon system can generate liver cancer in a mouse model.…”