Custom human endogenous retroviruses dedicated microarray identifies self-induced HERV-W family elements reactivated in testicular cancer upon methylation control

Abstract

Endogenous retroviruses (ERVs) are an inherited part of the eukaryotic genomes, and represent ∼400 000 loci in the human genome. Human endogenous retroviruses (HERVs) can be divided into distinct families, composed of phylogenetically related but structurally heterogeneous elements. The majority of HERVs are silent in most physiological contexts, whereas a significant expression is observed in pathological contexts, such as cancers. Owing to their repetitive nature, few of the active HERV elements have been accurately identified. In addition, there are no criteria defining the active promoters among HERV long-terminal repeats (LTRs). Hence, it is difficult to understand the HERV (de)regulation mechanisms and their implication on the physiopathology of the host. We developed a microarray to specifically detect the LTR-containing transcripts from the HERV-H, HERV-E, HERV-W and HERV-K(HML-2) families. HERV transcriptome was analyzed in the placenta and seven normal/tumoral match-pair samples. We identified six HERV-W loci overexpressed in testicular cancer, including a usually placenta-restricted transcript of ERVWE1. For each locus, specific overexpression was confirmed by quantitative RT-PCR, and comparison of the activity of U3 versus U5 regions suggested a U3-promoted transcription coupled with 5′R initiation. The analysis of DNA from tumoral versus normal tissue revealed that hypomethylation of U3 promoters in tumors is a prerequisite for their activation.

Prostate Cancer Progression Correlates with Increased Humoral Immune Response to a Human Endogenous Retrovirus GAG Protein

“…In addition to the role of androgens on GAG-HERV-K expression, we explored the role of DNA methylation, a known mechanism for suppressing HERV expression (3)(4)(5)36). A recent article showed that HERV-K ch22q11.23 is preferentially expressed in hypomethylated prostate cancer cell lines and primary prostate tissue samples (37).…”

Microarray-based Identification of Individual HERV Loci Expression: Application to Biomarker Discovery in Prostate Cancer

“…First, a U3 negative signal in conjunction with a U5 positive one classifies the LTR as a promoter, and conversely U3 positive and U5 negative signals may reflect a polyadenylation role. We thus identified 326 promoter LTRs in a broad range of tissues 35 and, based on this U3-U5 dichotomous information provided by the array, we proposed and experimentally confirmed for some selected cases that such autonomous transcription was controlled by a methylation dependent epigenetic process 34 (Figure 8). Second, the detection of signals from e.g.…”

“…Also ending by cloning and sequencing steps, the genome repeat expression monitoring technique aiming to identify promoters among repeats identified active HML-2 specific human solitary LTRs 32,33 . We successively developed two generations of high-density microarrays dedicated to the analysis of the HERV transcriptome, introducing methodologies suitable for repeated element probe design in order to minimize cross reactions between paralogous elements within a family 34,35 . The HERV-V2 chip which targets 2,690 distinct proviruses and 2,883 solo LTRs of the HERV-W, HERV-H, HERV-E 4.1, HERV-FRD, HERV-K HML-2 and HERV-K HML-5 families, unveiled the expression of 1,718 HERV loci (Figures 7A and B) in a wide range of tissues 35 , illustrated in this paper by the identification of putative prostate cancer biomarkers.…”

“…Second, the detection of signals from e.g. LTR, gag and env independent probesets or issued from probes targeting specific splice junction is informative about the proviral splicing strategy, as illustrated by the ERVWE1/Syncytin1 expression profile in placenta or in tumoral testis 34 . This indicates that the process of HERV specific probe selection is robust enough to support the identification of tissue-associated splicing strategy, as efficiently as for conventional genes 36 ( Figure 8).…”

The role of human endogenous retroviral long terminal repeat sequences in human cancer (Review)

“…Genetic instability of LTR leads to the its wide distribution in the human genome, while the activation of LTR can be controlled by DNA methylation. For example, Gimenez et al (52) have recently reported that hypomethylation of the promoter domain of the HERV U3 element appears to be a prerequisite for the increased expression in tumor tissues compared to normal tissues. Colon cancer cells are treated with DNA methylation and histone deacetylase inhibitors, and RT-PCR results show that the expression patterns of HERV-H are significantly altered in several colon cancer cells.…”