Mechanisms of HERV-K (HML-2) Transcription during Human Mammary Epithelial Cell Transformation

Abstract

Increasing evidence suggests that repetitive elements may play a role in host gene regulation, particularly through the donation of alternative promoters, enhancers, splice sites, and termination signals. Elevated transcript expression of the endogenous retrovirus group HERV-K (HML-2) is seen in many human cancers, although the identities of the individual proviral loci contributing to this expression as well as their mechanisms of activation have been unclear. Using high-throughput next-generation sequencing techniques optimized for the capture of HML-2 expression, we characterized the HML-2 transcriptome and means of activation in an model of human mammary epithelial cell transformation. Our analysis showed significant expression originating from 15 HML-2 full-length proviruses, through four modes of transcription. The majority of expression was in the antisense orientation and from proviruses integrated within introns. We found two instances of long terminal repeat (LTR)-driven provirus transcription but no evidence to suggest that these active 5' LTRs were influencing nearby host gene expression. Importantly, LTR-driven transcription was restricted to tumorigenic cells, suggesting that LTR promoter activity is dependent upon the transcriptional environment of a malignant cell. Here, we use an model of human mammary epithelial cell transformation to assess how malignancy-associated shifts in the transcriptional milieu of a cell may impact HML-2 activity. We found 15 proviruses to be significantly expressed through four different mechanisms, with the majority of transcripts being antisense copies of proviruses located within introns. We saw active 5' LTR use in tumorigenic cells only, suggesting that the cellular environment of a cancer cell is a critical component for induction of LTR promoter activity. These findings have implications for future studies investigating HML-2 as a target for immunotherapy or as a biomarker for disease.

Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites

“…1 c), a tumorigenic breast cancer cell line known to produce RVLPs under hormonally-stimulated conditions [ 3 , 38 , 39 ]. However, this activity level was only about half that seen in the Tera-1 cells, consistent with our previous report that Tera-1 cells produce markedly higher numbers of HML-2 transcripts than breast cancer cell lines [ 32 ].…”

“…The association between LTR sequence and cell line-specific expression suggests that certain sequence-specific elements, such as transcription factor binding sites, play a large role in determining differential promoter activity. Increased HML-2 expression is largely seen during tumorigenesis and our recent results indicate that LTR-driven transcription does not occur until post-transformation [ 32 ]. The following experiments were performed to further investigate the relationship between malignant transformation and expression and to elucidate the specific LTR sequences required.…”

“…Expression from HERV-K (HML-2), the most recently integrated and biologically active HERV group, is upregulated in up to 85% of breast cancer samples, although the mechanism of activation is still unclear [ 28 – 31 ]. RNA sequence analysis of cells in an in vitro mammary carcinogenesis model shows that LTR-driven transcription of HML-2 proviruses is restricted to tumorigenic human mammary epithelial cells (HMECs), suggesting that stage-specific transcription factors appearing during malignant transformation play a role in LTR activation [ 32 ]. The goal of this study was to investigate how LTR sequence variation among the various HML-2 proviruses affects activation of its promoter during HMEC transformation.…”

Human endogenous retrovirus HERV-K(HML-2) RNA causes neurodegeneration through Toll-like receptors

“…Although HERV-K(HML-2) encodes various former retroviral proteins and even retrovirus-like particles, no replication-competent HML-2 alleles have been identified as yet (11,12). While HERV-K(HML-2) RNA is detected in various human tissue and cell types, transcription patterns of specific HERV-K(HML-2) proviruses differ considerably between tissue and cell types and also inter-individually, the latter due to presence/absence of alleles of HERV-K(HML-2) elements (9,(13)(14)(15)(16)(17)(18). Deregulated HERV-K(HML-2) transcription has been reported for various diseases, including inflammatory and neurological disorders (19)(20)(21).…”

Human Endogenous Retrovirus-K HML-2 integration within RASGRF2 is associated with intravenous drug abuse and modulates transcription in a cell-line model

“…transcription of the surrounding genes (14,15). Moreover, some evidence suggests that intronic integrations of transposable elements could reshape the transcriptome upon reactivation during cancer development (16), although there is no evidence that HK2 reactivation could result in gene modulation in cancer development (17).…”