LTR activation is involved in diseases, such as rheumatoid arthritis (29,30), type I diabetes (30), and schizophrenia (31). For example, the presence of LTR of the HERV-K family is associated with certain DQB alleles. Linkage disequilibrium with DQB1 alleles can contribute to susceptibility to rheumatoid arthritis (29). Expression of the GABBR1 gene is downregulated by HERV-W LTR in schizophrenia (31). Two members of the HERV-I family induce AZFa gene microdeletions in azoospermia patients (32). These abovementioned reports demonstrate that HERV LTR may be active in many diseases.

Previous studies (33–37) have described the detection of RNA transcripts from various HERV LTRs in various types of human tumors and cell lines. Elevated HERV-K 5′LTR mRNA is significantly associated with tested prostate cancer tissues (33). It is also reported that the transcripts of the HERV-H LTR-derived promoter are widely distributed in various human tissues and cancer cells (11). Based on the function of LTRs on their adjacent genes in physiology described above, the function of the adjacent gene was investigated in order to elaborate the role of the LTR in tumorigenesis. The cancer-related LTR adjacent genes include viral and cellular genes. Considerable cancer-associated genes regulated by HERV LTR in tumorigenesis are shown in Table II. For example, the transcriptional start sites of HERV-K Rec and Np9 oncoproteins are regulated by 5′LTR (Table II). HERV-K Np9 is preferentially expressed in various tumor tissues (34) and the expression of Np9 significantly promoted the growth of leukemia cells in vitro and in vivo (35). HERV-K Rec expression was involved in the process of melanoma and germ cell tumor (36,37). The GSDML gene with the alternative promoters from HERV-H LTR was able to promote cell proliferation and was correlated with carcinogenesis and the progression of uterine cervix cancer (Table II). DNAJC15 gene also possesses an alternative transcript provided by LTR33 and LTR7 elements. The LTR-related transcripts are only revealed in some cancer cells (HCT106, MCF-3, TE-1, HeLa and CCHM) compared to human tissues (38). Neuronal apoptosis inhibitory protein gene (NAIP), which contains LTR of endogenous retroviral elements as tissue-specific promoter, inhibits apoptosis in the neuron (39). Thus, HERV LTR is capable of regulating the expression of tumor-related genes in different tumor tissues or cells.

Genetic instability is one of the key features associated with cancer causation and progression (40,41). Instability exists at two distinct levels. In a small subset of tumors, instability is observed at the nucleotide level and results in base substitutions, deletions or insertions of a few nucleotides, such as polymorphisms. In the majority of other cancers, instability is observed at the chromosome level, resulting in losses and gains of whole chromosomes or large portions, for example insertion mutation and recombination. As a mobile element HERV LTR possesses the feature of genetic instability. Therefore, HERV LTR affects human genome instability involvement in tumorigenesis via three principal mechanisms: insertion, recombination and polymorphism (Fig. 2).

Retroviruses mediate malignant transformation via insertional mutagenesis or expression of viral genes. Similarly, HERV is also involved in human tumorigenesis via the mechanism of insertion (42). HERV LTR amplifies in the human genome by generating new integration events. The amplification of HERV integration in the human genome consists of three processes: replication, excision and transduction (Fig. 2). Insertions are therefore considered beneficial, negative or neutral. HERV LTR elements insert into genomic regions and contain crucial biological functions, resulting in insertional mutagenesis during evolution. Abnormal expression of novel gene and adjacent gene are also caused by the insertion of LTR. Among the examples of human cancers caused by LTR-mediated insertion mutagenesis, the expression of PTN gene contributes to the highly aggressive growth of human choriocarcinoma (42). LTR-associated insertional mutagenesis can contribute to cancer via germ-line and somatic mutations, either of which can directly lead to the onset of malignant transformation.

Solitary LTR is formed by homologous recombination between two full-length HERV families. A variety of different recombination products are shown in Fig. 2 (43), including recombination between the two LTRs of a single provirus, homologous recombination between two HERV on the same chromosome, recombination between the 3′ and 5′LTRs of one HERV and gene conversion between the non-homologous genes. Homologous recombination between two proviruses results in substantial deletion and rearrangements of cellular DNA. Gene conversion leads to non-homologous gene exchange with no proviral loss. This occurs predominantly through contributions to recombination, which is frequently detected in cancer (44). LTR33 and LTR7 are formed by recombination and can regulate DNAJC15 gene expression in cancer cells (38). Therefore, LTR recombination may be crucial for LTR to be involved in cancer progression.

The existence of polymorphism provides one explanation of how a ubiquitous gene causes disease in only a proportion of individuals. The polymorphism is subdivided into two broad categories: sequence and insertional polymorphisms. Only a few sequence polymorphisms have been described, partly due to the difficulty in identifying them against the background of closely similar proviruses. Using specific PCR primers spanning 5′LTRs of K115 and K113, Jha et al (45) reported the presence of three single nucleotide polymorphism sites in the K113 5′LTR and four in the K115 5′LTR that together constituted four haplotypes for K113. At present, there is little convincing evidence that any sequence polymorphism of a HERV provides susceptibility to human disease. For insertion polymorphisms, although most HERV families became integrated into the human genome millions of years ago, a new class of insertionally polymorphic HERV-K family members has recently been described (46,47). HERV-K113 and HER-K115 insertion has been reported to be involved in various types of cancer (48–51). New insertion polymorphism of HERVs could serve as novel genetic risk factors and thus provide new insight for research into HERV LTR and cancer.

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. The finding suggests that the hypomethylation context affects the expression of HERV-H elements in colon cancer cells (53). Increased HERV-K expression in melanomas may be due to increased promoter activity and demethylation of the 5′LTR (54). Thus, overexpression of the HERV sequence in cell lines is correlated with the demethylation of LTR.

HERV and LTR are usually oriented opposite to the transcription direction of corresponding host genes (55–57). Antisense transcripts affect the sense partner gene function by modifying the transcriptional and post-transcriptional regulation processes. Findings of a previous study (55) demonstrated that from 10 HERV-K LTRs which were localized in introns of unique human genes, nine exhibited opposite orientation to the transcription direction of the corresponding human genes. A hypothesis was propounded that LTR affects the gene expression by initiation of the antisense RNA synthesis (55). Subsequently, several reports supported the hypothesis (57–61). Antisense transcript of HERV-Ec1 affected the expression of cytosolic phospholipase A2 in urothelial carcinoma (57). A novel exon cassette is derived from the antisense transcript of the HERV-K element (58). Intronic RNAs arising from U3 of ERV-9 LTR are expressed as both sense and antisense transcripts, with the antisense transcript being expressed at higher levels compared to the sense expression in malignant cells (59). LTR from exogenous retrovirus HTLV can also generate antisense manuscripts such as the HTLV-1 basic leucine zipper factor (HBZ) (60). It has been reported that HBZ is consistently expressed and remains intact in all ATL cases and HTLV-1-infected individuals, where it promotes cell proliferation (61). Antisense transcripts are able to form double-stranded RNA and may recruit RNAi machinery. The abovementioned studies suggest that the abnormal expression of antisense transcripts of LTR retrotransposon may be a causative factor for tumorigenesis.

HERV LTR could also be reactivated by environmental factors including cytokines (62), radiation (63,64) and proteins of exogenous retroviruses (65,66). Radiation induced the epigenetic regulation of HERV-R 5′LTR and upregulated HERV-R env expression (63). HSV-1 activated the LTR activity of HERV-W to enhance their potential oligodendrotoxic and immunopathogenic effects (67). HSV-1 infection also induced the LTR-directed transcription of the HERV-K. HSV-1 immediate-early ICP0 protein was able to upregulate the activity of HERV-K LTR (66). Relative levels of transcripts encoding HERV-W elements and cellular genes are transactivated by viral infection in different cell lines by regulating the transcriptional activity (68). Several HERV LTRs could be activated by HTLV Tax and were involved in diseases (65). High-level expression of HERV-K has been demonstrated to be activated by the MITF-M gene in melanomas, breast cancers and teratocarcinomas (69). Of note, these factors can also target ERVs, for example, a HERV-K (HML-2) consensus element can be inhibited by APOBEC3F (70). Such LTR reactivation can enhance its impact on the surrounding genes in the pathological process of human cancer.