Transposable Element Dysregulation in Hepatocellular Carcinoma: Epigenetic Mechanisms, Immune Remodeling, and Translational Opportunities

Abstract

Hepatocellular carcinoma (HCC) commonly develops in the context of chronic liver injury, viral hepatitis, metabolic dysfunction, alcohol-related liver disease and cirrhosis. Although immune checkpoint inhibitor-based combination therapies have improved the treatment of unresectable HCC, primary and acquired resistance and the lack of reliable predictive biomarkers continue to limit precision treatment. Transposable elements (TEs) and TE-derived sequences represent a regulatory layer linking epigenetic disruption, aberrant transcription and immune remodelling. In HCC, DNA hypomethylation, altered repressive histone modifications, dysfunction of TE-silencing machinery and dysregulated RNA-level control may promote the reactivation of LINE-1, HERV/ERV and other TE-derived sequences. Reactivated TEs may influence tumour-cell states and the immune microenvironment through cryptic promoter or enhancer activity, TE-derived transcripts, viral mimicry, innate immune sensing and potential tumour-associated antigens. HCC-specific evidence includes clinical associations of LINE-1 hypomethylation and mechanistic findings involving the TE/KDM1A/HNF4A axis and SETDB1-mediated HERV/ERV silencing and viral mimicry. Using a structured narrative literature search that emphasised studies published during the past five years while retaining relevant landmark studies, this review integrates the epigenetic, transcriptional, immune and translational dimensions of TE dysregulation in HCC. A five-level evidence framework is applied to distinguish HCC-specific mechanistic and in vivo evidence, HCC functional and cell-based findings, HCC clinical and omics associations, pan-cancer or non-HCC evidence, and hypothesis-generating candidates. This framework highlights the uneven maturity of the field and the need for locus-specific functional studies and independent clinical validation. TIGD family members are discussed as a hypothesis-generating example of TE-derived protein-coding candidates rather than as established HCC regulators, biomarkers or therapeutic targets.

Introduction

Hepatocellular carcinoma (HCC) is the most common histological subtype of primary liver cancer and remains a major cause of cancer-related mortality worldwide.¹ Most cases arise in the setting of chronic liver injury associated with viral hepatitis, metabolic dysfunction, alcohol-related liver disease, and cirrhosis.^2,3 HCC development and progression are not driven solely by genetic alterations, but result from the combined effects of persistent inflammation, repeated hepatocyte injury and regeneration, metabolic dysregulation, epigenetic reprogramming, and remodeling of the tumor immune microenvironment.^1–3

In recent years, immune checkpoint inhibitors combined with anti-angiogenic therapy have reshaped the treatment landscape for unresectable HCC,⁴ while dual-immunotherapy regimens have further expanded first-line treatment options.⁵ Nevertheless, primary and acquired resistance, together with the lack of robust predictive biomarkers, continue to limit precision treatment.^6,7 A better understanding of the epigenetic and immune regulatory mechanisms underlying HCC heterogeneity may therefore help clarify the biological basis of immune evasion and variable treatment response. Emerging evidence on PANoptosis further suggests that inflammatory programmed cell-death networks may influence HCC progression, tumor–immune interactions, and therapeutic responses, highlighting the broader importance of regulatory mechanisms connecting tumor-intrinsic stress with immune remodeling.⁸

Transposable elements (TEs) and TE-derived sequences provide a useful framework for investigating the links among epigenetic dysregulation, aberrant transcription, and immune remodeling in HCC. In addition to insertional mutagenesis, TEs may influence tumor biology by functioning as promoters, enhancers, transcription factor-binding sites, splicing regulatory elements, and sources of non-coding RNAs.^9,10 TE-derived transcripts, antigens, and innate immune-stimulatory nucleic acids have also emerged as potential contributors to tumor immunogenicity and candidate targets for cancer therapy.^11,12

HCC may provide a particularly permissive context for TE dysregulation. Chronic viral infection, metabolic inflammation, cirrhotic regeneration, and hepatic immune tolerance may weaken TE-silencing mechanisms and modify the biological consequences of TE activation. Recent HCC-specific studies have provided direct mechanistic evidence for this concept. Liver-accessible TEs can recruit KDM1A and epigenetically suppress HNF4A, thereby promoting HCC progression.¹³ In addition, SETDB1-suppressed HERV elements have been associated with HCC prognosis and viral mimicry-related immune programs.¹⁴ Together with findings on LINE-1 hypomethylation, these studies suggest that TEs may function not only as markers of epigenetic instability but also as active components of transcriptional and immune regulatory networks in HCC.

Beyond repetitive TE loci, domesticated TE-derived protein-coding genes represent an additional but less explored dimension of TE biology. Genes such as RAG1/2, SETMAR, PGBD5, and members of the PEG10/RTL family illustrate how transposon-derived sequences can be repurposed as host protein-coding or regulatory modules.^15,16 The Tigger transposable element-derived (TIGD) family, which originated from Tigger/pogo-like DNA transposons,^17,18 provides one representative example. Because TIGD genes have conventional gene annotations and are amenable to transcriptomic, single-cell, protein-level, and functional analyses,^19,20 they may serve as experimentally tractable candidates for investigating the protein-coding branch of TE biology. However, current evidence linking TIGD family members to HCC remains preliminary and largely correlative. They should therefore be considered hypothesis-generating candidates rather than established HCC drivers, biomarkers, or therapeutic targets.²¹

Despite growing interest in transposable elements in cancer, previous reviews have largely addressed TE biology from pan-cancer perspectives or have focused separately on epigenetic derepression, viral mimicry, and tumor immunogenicity. A dedicated HCC-focused synthesis integrating epigenetic TE dysregulation with transcriptional consequences, immune remodeling, and translational relevance, while explicitly distinguishing different levels of HCC-specific and extrapolated evidence, remains limited. Such an evidence-stratified perspective is particularly important in HCC because chronic viral infection, persistent inflammation, cirrhosis, repeated hepatocyte regeneration, and hepatic immune tolerance may substantially modify both TE regulation and the biological consequences of TE activation.

Against this background, this review examines TE-derived regulatory networks in HCC at two interconnected levels: repetitive TE-derived outputs and representative TE-derived protein-coding candidates. We distinguish among direct HCC-specific mechanistic or clinical evidence, findings extrapolated from pan-cancer or non-HCC studies, and emerging hypotheses that require further validation. The central premise is that TE reactivation may represent more than a passive consequence of epigenetic disruption. Instead, it may link DNA and chromatin abnormalities with aberrant transcription, viral mimicry, antigen presentation, immune remodeling, and heterogeneity in immunotherapy response. Within this framework, the TIGD family is discussed as a preliminary and experimentally tractable model for future mechanistic investigation.

Literature Search Strategy and Evidence Classification

A structured narrative literature search was conducted using PubMed and Web of Science. The search was last updated on 4 July 2026, with particular emphasis on studies published during the five years preceding the final search date, while earlier landmark studies were retained when necessary to establish the biological and mechanistic context. Search terms included combinations of “hepatocellular carcinoma” or “liver cancer” with “transposable element”, “retrotransposon”, “LINE-1”, “endogenous retrovirus”, “HERV”, “ERV”, “viral mimicry”, “SETDB1”, “TRIM28”, “KDM1A”, “transposon-derived gene” and “TIGD”.

Original studies directly investigating HCC were prioritized. Studies were included when they provided mechanistic, functional, clinical, genomic, epigenomic, transcriptomic, single-cell, or immune-related evidence relevant to TE biology in HCC. Pan-cancer and non-HCC studies were included when direct HCC-specific evidence was unavailable or when they provided important mechanistic context. Studies without clear relevance to TE regulation, TE-derived products, HCC biology, or cancer-associated immune remodeling were not included in the principal evidence synthesis.

To distinguish experimentally validated mechanisms from associative or extrapolated findings, the evidence discussed in this review was classified into five levels: Level 1, HCC-specific mechanistic and in vivo evidence; Level 2, HCC functional and cell-based evidence; Level 3, HCC clinical and omics-based associations; Level 4, pan-cancer or non-HCC evidence extrapolated to HCC; and Level 5, hypothesis-generating candidates lacking direct functional validation in HCC. This evidence hierarchy was applied throughout the review to distinguish relatively established findings from emerging hypotheses. The five-level evidence hierarchy and representative TE-related mechanisms in HCC are summarized in Figure 1.

Figure 1.

Evidence hierarchy of TE-related mechanisms in hepatocellular carcinoma.

Notes: Evidence discussed in this review is classified into five levels according to disease specificity and the strength of functional validation. Level 1 represents HCC-specific mechanistic and in vivo evidence, whereas Level 5 represents hypothesis-generating candidates lacking direct functional validation in HCC. The hierarchy reflects the current strength of evidence rather than the biological importance of individual mechanisms.

Transposable Elements and TE-Derived Genes

Major Classes of TEs and Regulatory Potential

TEs are generally classified into class I retrotransposons and class II DNA transposons according to their transposition mechanisms. Class I retrotransposons are amplified through RNA intermediates and reverse transcription, and include LINEs, SINEs, LTR retrotransposons, and ERvs Among these, LINE-1 is the most representative autonomous retrotransposon in the human genome.²² HERVs/ERVs originate from ancient retroviral integration events,²³ and their LTR regions may retain promoter, enhancer, or other transcriptional regulatory potential.²⁴

Class II DNA transposons primarily move through DNA intermediates. Although most DNA transposons in the human genome have lost autonomous mobility, their residual sequences can be repurposed by the host as regulatory elements, transcriptional units, or protein-coding genes.²⁵ Therefore, the biological significance of TEs should not be evaluated only by whether they remain mobile. Greater attention should be given to whether they participate in host transcriptional regulation, cellular state maintenance, or tumor-associated regulatory networks.

In cancer, TEs may contribute to tumorigenesis and progression by acting as sources of insertional mutagenesis, promoters, enhancers, splicing regulatory elements, non-coding RNAs, and tumor antigens.^9,10 TEs and TE-derived products are also being explored as potential therapeutic targets.¹¹ Rather than revisiting the general biology of TEs across cancer types, this review focuses on how TE reactivation in HCC intersects with chronic liver disease, epigenetic dysregulation, aberrant transcription, and immune remodeling.

From an HCC perspective, the significance of TE derepression is not limited to increased expression of repetitive sequences. LINE-1 hypomethylation may reflect genome-wide hypomethylation and genomic instability, and has been associated with HCC prognosis.²⁶ Specific liver-associated TEs may influence HCC progression through the KDM1A/HNF4A axis.¹³ In addition, derepression of SETDB1-suppressed HERV elements may be linked to viral mimicry-related immune programs.¹⁴

TE-Derived Transcripts, ncRNAs, and Regulatory Outputs

TE reactivation does not simply increase the expression of repetitive sequences; it can generate multiple layers of regulatory output. TE-derived regulatory elements that are normally silenced in tumor cells may become reactivated under conditions of DNA methylation loss, reduced repressive histone marks, or increased chromatin accessibility.²⁷ By acting as cryptic promoters or enhancers, these elements can drive tumor-specific transcription initiation events²⁸ and alter the expression of nearby genes or distal regulatory networks.²⁹

TE-derived RNAs represent another important output of TE reactivation. Transcripts derived from ERVs/HERVs, LINE-1, or SINEs can form virus-like nucleic acid structures and serve as molecular substrates for viral mimicry.³⁰ These TE-derived nucleic acids can also be detected by the innate immune system.³¹ This section focuses on their role as transcriptional outputs, whereas the specific nucleic acid sensing pathways and their immunological consequences in HCC are discussed in Viral Mimicry and Innate Immune Activation.

TE fragments also contribute substantially to the origin and diversification of lncRNAs and other regulatory transcripts.³² They may provide functional sequence elements for transcription initiation, splicing, polyadenylation, and RNA–protein interactions.³³ In HCC, re-annotating TE-derived ncRNAs may help identify regulatory outputs that are missed by conventional gene annotation, and is consistent with the broader effort to refine functional annotation of lncRNAs.³⁴

Some TE-derived transcripts may be translated into non-canonical peptides and presented by HLA/MHC molecules, thereby forming potential tumor-associated antigens.³⁵ Non-canonical splice junctions, TE-derived neoantigens, and TE-associated tumor antigens have been reported across cancer types.^36–38 However, detection of TE transcripts alone does not establish immunogenicity. Functionally relevant TE-derived antigens must undergo stable expression, translation, processing, HLA/MHC presentation, and recognition by T cells.³⁹

Therefore, discussions of TE reactivation in HCC should distinguish among TE-derived regulatory elements, TE-derived RNAs, TE-gene chimeric transcripts, TE-derived ncRNAs, and TE-derived antigens. This distinction is important to avoid inferring biological function solely from an overall increase or decrease in the expression of a given TE family.

TE-Derived Protein-Coding Candidates and the TIGD Family as a Representative Case

In addition to repetitive TE sequences and TE-derived transcripts, TE-derived protein-coding candidates represent a relatively underexplored but experimentally tractable area of TE biology. During evolution, some transposon-derived sequences have undergone molecular domestication and have been repurposed by the host as protein-coding genes or regulatory elements with potential cellular functions.^15,16 Representative domesticated genes, including RAG1/2, SETMAR, PGBD5, and members of the PEG10/RTL family, illustrate how TE-derived sequences can be converted into host protein-coding or regulatory modules during evolution. These genes, however, are not the focus of this review. Compared with highly repetitive TE loci that are difficult to quantify precisely, such genes usually have clearer gene annotations and detectable transcripts,¹⁹ making them more suitable for clinical cohort analysis, single-cell profiling, protein-level validation, and functional assays.

In this context, the TIGD family can be considered a representative example of TE-derived protein-coding candidates, rather than one of the strongest evidence lines in this review. Compared with repetitive TE loci, TIGD genes are more amenable to gene-level detection and functional intervention. However, compared with established HCC-specific evidence such as LINE-1 hypomethylation, the KDM1A/HNF4A axis, and SETDB1-HERV derepression, TIGD remains an emerging and incompletely characterized candidate family in HCC. The purpose of this section is therefore not to position TIGD as a central mechanism, but to illustrate how TE-derived protein-coding candidates may provide experimentally verifiable entry points for further studies of TE biology in HCC.

Incorporating the TIGD family into this framework complements conventional TE research from the perspective of protein-coding genes. Recent single-cell and transcriptomic analyses in HCC suggest that TIGD family members may be associated with tumor cell functional states, prognostic stratification, and immune-related features.²¹ However, these findings currently represent expression-level associations and hypothesis-generating evidence. They do not yet demonstrate that TIGD family members directly drive HCC progression or immune evasion. Accordingly, the discussion of TIGD in this review focuses on its role as a representative case and on the validation steps required for future mechanistic studies.

Epigenetic Dysregulation and TE Reactivation in HCC

Epigenetic dysregulation is a key molecular feature of HCC and involves multiple layers, including aberrant DNA methylation, altered histone modifications, chromatin remodeling, and dysregulated non-coding RNA control.⁴⁰ In normal cells, most TEs are repressed by DNA methylation, repressive histone marks such as H3K9me3, heterochromatin formation, and post-transcriptional regulatory mechanisms.⁴¹ During tumorigenesis, these silencing barriers may be weakened, leading to derepression of LINE-1, HERV/ERV, SINEs, and other TE-derived sequences.

In HCC, TE reactivation is not only a consequence of epigenetic dysregulation, but may also reshape tumor cell transcriptional states and the immune landscape. LINE-1 hypomethylation is associated with genome-wide methylation loss and poor prognosis in HCC.²⁶ SETDB1-dependent HERV repression further suggests that derepression of specific HERV elements may contribute to viral mimicry-related immune programs.¹⁴ The major mechanisms by which epigenetic dysregulation promotes TE reactivation in HCC are summarized in Figure 2.

Figure 2.

Epigenetic dysregulation-induced TE reactivation in HCC.

Notes: Epigenetic dysregulation in HCC, including DNA hypomethylation, loss of repressive histone marks, TE-silencing machinery dysfunction, KDM1A/HNF4A-related remodeling, and RNA editing or m6A dysregulation, may promote TE derepression and reactivation. Reactivated TE loci may contribute to aberrant transcription, genomic instability, TE-derived transcripts, and cytosolic TE-derived nucleic acids, while HCC-associated contexts may further shape these molecular consequences.

DNA Methylation and LINE-1 Hypomethylation

DNA methylation is one of the key mechanisms that maintain TE silencing.⁴² In normal cells, CpG methylation, together with heterochromatin formation, restricts aberrant transcription of LINE-1, HERV/ERV, and other repetitive elements. In HCC, global DNA hypomethylation often coexists with localized hypermethylation of CpG islands or promoters, forming a dual pattern of epigenetic dysregulation commonly observed in tumors.^43,44

LINE-1 methylation is one of the most frequently studied TE-related epigenetic markers in HCC. LINE-1 hypomethylation can serve as a surrogate marker for global DNA hypomethylation⁴⁵ and has been associated with the CIMP phenotype and poor prognosis in HCC.⁴⁶ At the mechanistic level, LINE-1 hypomethylation is therefore better understood as a composite readout of TE derepression and epigenetic instability, rather than as a standalone clinical biomarker.

Mechanistically, LINE-1 hypomethylation is not merely an epigenetic readout. LINE-1 derepression can lead to the expression of LINE-1 RNA and ORF1p/ORF2p, and may promote genomic instability, DNA damage responses, replication stress, and aberrant transcription initiation through retrotransposition-related processes.^47,48 However, whether LINE-1 actively drives HCC progression remains to be validated through locus-specific analyses and functional experiments.

Changes in TE methylation should therefore not be interpreted as a uniform biological event. Future HCC studies should further distinguish among different TE families, specific genomic loci, and cellular states, while integrating methylation status, locus-specific TE expression, chromatin features, immune phenotypes, and clinical outcomes.

HERV/ERV Reactivation and Viral Mimicry

Endogenous retroviruses (ERVs) and human endogenous retroviruses (HERVs) originate from ancient retroviral integration events.²³ Although most loci have lost full viral function, their LTR regions may retain cis-regulatory potential, including promoter, enhancer, polyadenylation, and splicing activities.⁴⁹

In tumor cells, DNA demethylation, altered histone modifications, and abnormalities in TE-silencing complexes such as TRIM28/KAP1–SETDB1 can relieve repression of HERVs/ERVs.^41,50,51 This may lead to re-expression of HERV/ERV-derived RNAs or LTR-driven transcripts. HERV/ERV reactivation can contribute to a viral mimicry response; however, this section focuses on the mechanisms underlying HERV/ERV derepression, whereas specific immune sensing pathways are discussed in TE Activity and Immune Remodeling in HCC.

Research on HERV/ERV reactivation in HCC remains at an early stage, but available findings suggest both mechanistic and clinical relevance. Recent studies have identified specific HERV elements repressed by SETDB1-dependent H3K9me3, and showed that loss or inhibition of SETDB1-mediated repression can upregulate viral mimicry-related interferon-stimulated genes in HCC cells. These findings suggest that HERV derepression may influence immune states and prognostic stratification in HCC. However, the consequences of HERV/ERV activation in HCC should not be categorized simply as anti-tumor or pro-tumor effects. They need to be interpreted in relation to the specific TE locus, the magnitude of activation, the duration of interferon signaling, immune-cell composition, and the underlying liver disease context. In murine HCC models, Setdb1 knockdown impaired in vivo tumour growth and increased CD8-positive T-cell infiltration, while both murine and human HCC cells showed increased ERV expression and interferon-stimulated gene activation.¹⁴

Histone Modifications and the TE-Silencing Machinery

In addition to DNA methylation, histone modifications and chromatin structure are central to the maintenance of TE silencing. TE loci are typically constrained by repressive chromatin marks such as H3K9me3 and H3K27me3, together with heterochromatin formation. SETDB1, TRIM28/KAP1, SUV39H1, KRAB zinc-finger proteins, HDACs, and related factors collectively constitute the TE-silencing machinery.⁵¹ Therefore, TE reactivation should not be viewed solely as a consequence of DNA hypomethylation, but may also reflect disruption of the broader chromatin-based silencing network.

Alterations in TE-silencing mechanisms may further influence the immune state of tumor cells. Pan-cancer studies have shown that SETDB1 can act as an epigenetic checkpoint of intrinsic tumor immunogenicity. Its inactivation may relieve repression of TE-derived regulatory elements, immunostimulatory genes, and TE-encoded retrovirus-like antigens.⁵² KDM5B can also promote immune evasion by recruiting SETDB1 to silence endogenous retroelements.⁵³

In HCC, the relationship between histone modifications and TE regulation is being gradually clarified. SETDB1-dependent H3K9me3 can repress specific HERV elements, whereas specific liver-associated TEs can mediate KDM1A recruitment, leading to epigenetic silencing of HNF4A and thereby promoting HCC cell proliferation and tumor progression.¹³

The TE/KDM1A/HNF4A axis suggests that TE function in HCC is not limited to passive derepression or increased expression of repetitive sequences. Certain TE sequences may act as epigenetic regulatory platforms that recruit chromatin-modifying factors and alter the expression of key hepatocyte identity genes. Thus, in HCC, TEs may be both targets of epigenetic dysregulation and active participants in chromatin remodeling and hepatocyte identity changes.

RNA-Level Regulation of TE-Derived Transcripts

The function of TE-derived transcripts depends not only on DNA methylation and chromatin status, but also on RNA-level regulation.⁵⁴ RNA editing, RNA modifications, alternative splicing, RNA stability and degradation, miRNA-mediated regulation, and interactions with RNA-binding proteins can all influence the structure, abundance, localization, and immune recognition of TE-derived transcripts.³³

A-to-I RNA editing has received considerable attention in the regulation of TE-derived RNAs. Repetitive sequences such as Alu elements can form double-stranded RNA structures and serve as important substrates for ADAR family enzymes. ADAR1-mediated A-to-I editing can alter the structure and immune recognition of endogenous dsRNAs, thereby limiting their misrecognition as non-self RNA by cytosolic nucleic acid sensors such as MDA5.^55,56

In HCC, dysregulated RNA editing has been associated with hepatocarcinogenesis, tumor progression, and adaptation to oxidative stress,⁵⁷ as well as with clinical outcomes and immune cell infiltration.⁵⁸ However, direct evidence for an ADAR–TE RNA axis remains limited. Future studies need to identify the specific edited TE-derived RNAs, their cellular origins, and their functional effects on interferon signaling and immune evasion.

RNA modifications, particularly N6-methyladenosine (m6A), may also regulate the fate of TE-derived RNAs. m6A can influence RNA splicing, nuclear export, stability, translation efficiency, and degradation.⁵⁹ Existing studies suggest that m6A RNA methylation can regulate ERV-derived RNAs and maintain cellular homeostasis by promoting the clearance of immunostimulatory ERV-derived RNAs.⁶⁰

In addition, TE fragments can be embedded within mRNAs, lncRNAs, or circRNAs, thereby affecting transcript splicing, secondary structure, RNA-binding protein recognition, and miRNA targeting. In HCC, the LTR retrotransposon-derived lncRNA LINC01446 promotes HCC progression and angiogenesis through the SRPK2/SRSF1/VEGF axis, supporting the direct functional relevance of TE-derived ncRNAs.⁶¹

TE Activity and Immune Remodeling in HCC

TE-derived effects are increasingly linked to immune remodeling in HCC. Much of the evidence connecting increased TE expression with immune infiltration, enhanced antigenicity, and immunotherapy response comes from pan-cancer studies. In HCC, however, these relationships are shaped by hepatic immune tolerance, antiviral immunity, chronic inflammation, and cirrhosis. This section therefore focuses on the immune consequences of TE activation, while distinguishing findings supported by direct HCC evidence from those that remain largely extrapolated from pan-cancer or non-HCC studies. The major mechanisms by which reactivated TEs may contribute to immune remodeling in HCC are summarized in Figure 3.

Figure 3.

TE-derived immune remodeling in HCC.

Notes: Reactivated TEs may generate nucleic acids, antigens, and regulatory transcripts that shape immune remodeling in HCC. TE-derived nucleic acids can activate viral mimicry-related innate immune sensing, whereas TE-derived antigens may be presented by MHC-I/HLA molecules and recognized by CD8⁺ T cells. These processes may influence checkpoint regulation and the HCC immune microenvironment.

Viral Mimicry and Innate Immune Activation

As discussed in TE-Derived Transcripts, ncRNAs, and Regulatory Outputs, some TE-derived RNAs can serve as molecular substrates for viral mimicry.^30,31 When TE-silencing mechanisms are compromised, RNAs derived from ERVs/HERVs, LINE-1, SINEs, and other TE sequences, as well as reverse-transcription intermediates, may form virus-like nucleic acid structures, including double-stranded RNA, RNA-DNA hybrids, and cytosolic DNA.³¹ These structures can activate innate immune sensing pathways such as MDA5, RIG-I, TLR3, and cGAS-STING, leading to the expression of type I interferons, chemokines, and antigen-presentation-related genes.^62–64

The focus of this subsection is therefore not epigenetic therapy itself, but how TE reactivation alters tumor immune states. TE-induced viral mimicry can enhance antiviral-like transcriptional programs in tumor cells, promoting the expression of interferon-stimulated genes, chemokines, and components of the antigen-processing machinery. These changes may influence dendritic cell recruitment, T-cell infiltration, and tumor immune visibility.

In HCC, this process must be interpreted within the liver’s unique immune environment. Short-term or moderate TE activation may enhance antitumor immune recognition. However, sustained type I interferon signaling may also promote immune adaptation, T-cell exhaustion, or treatment resistance.^65,66 Thus, the significance of TE-induced interferon signaling depends on signal intensity, duration, and the state of the tumor microenvironment.

Recent HCC studies provide direct support for this mechanism. Specific HERV elements suppressed by SETDB1 are associated, upon derepression, with changes in viral mimicry-related interferon-stimulated genes. This finding suggests that TE-silencing states in HCC may influence tumor immune visibility. However, the relationship between TE derepression and immunotherapy benefit still needs to be validated in treatment cohorts.

TE-Derived Antigens and Tumor Immunogenicity

In addition to inducing innate immune sensing, TE-derived effects may influence adaptive immunity by generating non-classical tumor antigens. Pan-cancer studies have shown that TE-gene chimeric transcripts can generate tumor-specific antigens, thereby expanding the repertoire of immune targets beyond conventional mutation-derived neoantigens.³⁵ Endogenous viral elements may also serve as complementary antigen sources for personalized tumor vaccines.⁶⁷

In HCC, TE-derived antigens have potential research value, but HCC-specific evidence remains largely indirect. Viral infection, epigenetic dysregulation, and chronic inflammation may provide a distinct context for the generation and recognition of TE-derived antigens. However, whether these antigens are stably presented in HCC, recognized by T cells, and linked to differences in immunotherapy response still requires validation through HCC immunopeptidomics, T-cell functional assays, and treatment cohorts.

Even when TE-derived peptides are translated, they must undergo protein processing, HLA/MHC loading, and T-cell recognition before they can function as immunologically relevant antigens. Tumor cells may also evade immune recognition through downregulation of HLA/MHC-I expression, defects in antigen processing, or upregulation of immune checkpoints. Therefore, the translational value of TE-derived antigens cannot be inferred from transcript-based predictions alone, but should be validated using immunopeptidomics and T-cell functional assays.³⁹

Future identification of immunogenic TE-derived antigens in HCC will require the integration of TE-aware RNA-seq, long-read sequencing, ribosome profiling, immunopeptidomics, mass spectrometry, HLA-binding prediction, and T-cell functional assays. These approaches should distinguish among simple expression, translatable transcripts, MHC-presented peptides, and truly immunogenic antigens.

Immune Checkpoints, Immune Infiltration, and Immunotherapy Response

TE-derived effects may provide a complementary perspective for understanding heterogeneity in immune infiltration and immunotherapy response in HCC. TE-associated interferon signaling may promote CD8⁺ T-cell infiltration and antigen presentation in some tumors, but it may also coincide with PD-L1 upregulation, T-cell exhaustion, infiltration of myeloid suppressor cells, or enrichment of immunosuppressive macrophages.⁶⁸ Thus, the relationship between TE activity and the tumor immune state is likely to be context dependent.

Immune checkpoint inhibitors have substantially reshaped the treatment landscape for HCC, but most patients with advanced disease still do not achieve durable benefit.⁷ Resistance to immune checkpoint-based therapies remains a major challenge.⁶⁹ Existing biomarkers cannot fully explain heterogeneity in treatment response.^70,71 Future studies should therefore evaluate whether TE-derived immune signatures can serve as complementary indicators of tumor antigenicity, innate immune activation, T-cell functional state, and the immunosuppressive microenvironment.

For clinical translation, TE-derived immune signatures require systematic validation in HCC cohorts receiving immunotherapy, including atezolizumab plus bevacizumab, durvalumab plus tremelimumab, tyrosine kinase inhibitor combinations with immune checkpoint inhibitors, or locoregional therapy combined with immunotherapy. Key endpoints should include objective response rate, progression-free survival, overall survival, acquired resistance, and immune-related adverse events.

Future research should also consider how etiological background shapes TE-mediated immune effects. HBV-associated, HCV-associated, metabolic dysfunction-associated, and alcohol-related HCC exhibit distinct antiviral immune responses, inflammatory states, liver functional reserve, and immunotherapy profiles.^68,72,73 These differences may influence IFN responses, antigen presentation, immune infiltration, and the therapeutic safety window following TE/ERV reactivation. Representative TE-derived outputs in HCC and their potential research relevance are summarized in Table 1.

Table 1.

Representative TE-Derived Outputs, Evidence Levels and Validation Needs in HCC

TE-Derived Output	Main Mechanism	HCC Relevance	Evidence Level and Validation Needs
LINE-1 hypomethylation	Global DNA hypomethylation and epigenetic instability	Prognostic and cfDNA biomarker research26,45,46	Level 3: HCC clinical and omics-based associations; assay standardisation and prospective validation are required
HERV/ERV reactivation	Loss of SETDB1-mediated epigenetic silencing and induction of viral mimicry	Selected HERV/ERV elements are linked to prognosis and immune activation in HCC14	Level 1 for the validated SETDB1-mediated mechanism; broader HERV signatures remain Level 3 and require locus-specific validation
TE-derived regulatory elements	Cryptic promoter or enhancer activity and chromatin regulation	Liver-associated TEs recruit KDM1A and suppress HNF4A13	Level 1: HCC-specific mechanistic and in vivo evidence; additional TE loci require independent validation
TE-derived transcripts and ncRNAs	Chimeric transcripts and regulatory RNAs	LTR-derived LINC01446 promotes HCC progression61	Level 2: HCC functional and cell-based evidence for a selected transcript; independent functional validation is required
TE-derived antigens	Translation and HLA/MHC presentation	Potential source of tumour-associated antigens35	Level 4: Primarily pan-cancer or non-HCC evidence; direct HCC immunopeptidomic and T-cell functional validation is lacking
TE-derived signatures	Integrated TE expression or methylation patterns	Potential research-use stratification markers14,26,45,46	Levels 3–4: HCC omics associations and extrapolated evidence; independent multicentre and treatment-cohort validation are required

Translational Implications of TE Dysregulation in HCC

The translational value of TE-derived effects in HCC is currently best framed in terms of research-use signatures, candidate biomarkers, and therapeutic hypotheses, rather than diagnostic or therapeutic strategies close to clinical application. Overall, TE methylation, HERV/ERV expression, TE-derived signatures, and TE-derived antigens all have potential research value, but most remain at the stage of discovery, retrospective validation, or methodological exploration.

Accordingly, the clinical value of TE-related markers cannot be inferred solely from differential expression or survival associations in public datasets. Nor should these markers be directly equated with established clinical tools such as AFP, BCLC staging, or treatment decision-making systems. Compared with conventional clinical variables, TE-derived signatures still need to demonstrate independent predictive value, assay reproducibility, and biological interpretability.⁷⁴

TE Methylation and TE-Derived Signatures as Research-Use Biomarkers

At the biomarker level, LINE-1/cfDNA methylation is mainly relevant to risk assessment and liquid biopsy research. Studies of plasma DNA methylation and cfDNA LINE-1 methylation suggest potential utility for non-invasive detection.^75,76 In HCC cohorts, LINE-1 hypomethylation has been associated with poor prognosis,⁴⁶ supporting its role as a candidate prognostic marker. In contrast to DNA Methylation and LINE-1 Hypomethylation, which focuses on mechanistic implications, this section emphasizes assay stability, external validation, and incremental clinical value.

Beyond LINE-1, HERV/ERV expression signatures may also have translational research value. Specific HERV elements repressed by SETDB1 have been associated with HCC prognosis and viral mimicry-related immune programs, providing direct support for HERV/ERV expression signatures as candidate biomarkers.

TE-derived expression signatures represent another area for further study. With the accumulation of transcriptomic data from TCGA, ICGC, GEO, and multicenter clinical cohorts, TE-aware pipelines can be used to reanalyze expression patterns of LINE-1, SINEs, LTR/HERV elements, DNA transposons, and TE-derived genes in HCC.^77–79 These signatures can then be evaluated in relation to prognosis, recurrence, vascular invasion, immune infiltration, and treatment response.

From the perspective of clinical biomarker development, TE-derived signatures should meet at least three criteria. First, they should be reproducible across sequencing platforms, algorithms, and sample types. Second, they should demonstrate additional predictive value beyond conventional clinical variables in independent external cohorts. Third, they should show plausible biological links with DNA methylation, chromatin status, viral mimicry, antigen presentation, or immune infiltration.

Epigenetic Therapy-Induced TE Reactivation as a Therapeutic Hypothesis

At the translational level, the key issue for TE-centered therapeutic strategies is not simply to restate the mechanism of viral mimicry, but to define the boundaries of potential clinical application. At present, immune sensitization based on TE reactivation in HCC should be regarded as a mechanistic rationale and research hypothesis rather than a mature therapeutic strategy. Evidence that epigenetic therapy can induce TE reactivation, expand the TE-related antigen repertoire, and enhance tumor immune visibility comes mainly from pan-cancer or non-HCC models.^80,81 Studies of DNMT/HDAC inhibition and epigenetic therapy-induced tumor-enriched antigens also provide mechanistic support for this strategy.^82,83 However, these findings cannot be directly translated into clinical feasibility in HCC. Key issues such as dose, treatment duration, timing, combination regimen, patient selection, and safety window still need to be addressed.

In HCC, immune-sensitizing strategies based on TE reactivation cannot simply be extrapolated from pan-cancer experience. Cirrhosis, chronic HBV/HCV infection, and impaired hepatic reserve may influence both the efficacy and safety of immunotherapy.^73,84,85 Future TE-related therapeutic strategies should therefore focus on low-dose, short-course, time-sequenced, and combination regimens, with patient selection guided by liver function, underlying etiology, TE-silencing status, the immune microenvironment, and antigen-presenting capacity.

The SETDB1-HERV axis provides a mechanistic clue for TE-related therapeutic strategies in HCC. SETDB1 inhibition can induce HERV expression and viral mimicry responses, suggesting that dependency on TE-silencing machinery may influence the immune visibility of HCC. However, epigenetic regulators such as SETDB1, DNMTs, and HDACs have broad biological functions, and non-selective intervention may affect immune homeostasis in normal liver tissue and cirrhotic liver. Therefore, TE-centered therapeutic strategies in HCC should balance immune activation, hepatic safety, and patient selection.

Technical Challenges in TE-Centered HCC Research

Technical challenges in TE-centered HCC research arise from both the repetitive nature of TE sequences and the complexity of HCC samples and clinical contexts. First, TE sequences are highly repetitive, with many similar copies within the same family or subfamily, making it difficult to uniquely map short-read RNA-seq or DNA-seq reads. Conventional workflows often discard multi-mapped reads or assign them inaccurately. TE-aware pipelines are therefore needed to improve TE expression quantification,^77–79 and long-read sequencing can be incorporated to improve locus-specific resolution.⁸⁶

Second, TE function is highly locus dependent. Even within the same TE family or subfamily, different copies may reside in distinct chromatin states and display different regulatory activities. Some TE loci may act as promoters or enhancers,^28,29 whereas others may generate chimeric transcripts or tumor-specific antigens. In contrast, many copies may remain silent remnants of repetitive sequences.

Third, HCC tissue has substantial compositional complexity. Changes in TE expression detected by bulk RNA-seq may originate from malignant hepatocytes, infiltrating immune cells, inflammatory liver tissue, or non-tumor hepatocytes.⁸⁷ Single-cell and spatial transcriptomics can help determine the cellular origin and spatial distribution of TE/TIGD expression.⁸⁸ Methods such as scTE, MATES, and CELLO-seq also provide a technical basis for quantifying TEs at the single-cell level.^89–91 However, conventional single-cell workflows remain limited in their ability to localize repetitive TE transcripts.

Finally, TE methylation, chromatin state, and TE expression are not always linearly correlated. Certain TE loci may remain transcriptionally silent despite demethylation, because TE activation also requires an appropriate chromatin accessibility state, promoter/enhancer activity, and transcription factor occupancy.²⁷ Conversely, some TE expression may be driven by local chromatin remodeling or changes in transcription factor binding rather than by DNA methylation changes alone.⁹²

The TIGD Family as a Representative TE-Derived Protein-Coding Candidate

Evolutionary Origin and Molecular Features

Members of the Tigger transposable element-derived (TIGD) family are protein-coding genes derived from sequences related to Tigger/pogo-like DNA transposons through transposon domestication.^17,18,25 Transposon domestication describes the evolutionary incorporation of transposon-derived sequences into the host genome, where they may subsequently acquire cellular functions.^15,16 Although the transposon-related evolutionary origin of TIGD genes is established, the functional consequences of this origin remain unclear.

Evolutionary origin alone does not demonstrate that TIGD proteins retain transposase-like biochemical activity, DNA-binding capacity, chromatin-interacting properties, or TE-regulatory functions. The molecular functions, genomic binding sites, interaction partners, and downstream targets of most TIGD family members remain largely unknown. Although the epigenetic instability and cellular heterogeneity of HCC provide a relevant context in which these possibilities can be investigated, they do not constitute evidence of a mechanistic role. Accordingly, any proposed chromatin- or TE-regulatory functions of TIGD proteins in HCC should currently be regarded as testable hypotheses rather than established mechanisms.

Evidence of Expression and Current Limitations

Evidence concerning TIGD family members in cancer remains limited and heterogeneous, with much of the available evidence derived from pan-cancer analyses or non-HCC tumor types. TIGD1, TIGD5, and TIGD6 have been associated with prognosis, immune-related features, or tumor-cell phenotypes in ovarian, lung, gastric, and other cancers; however, the reported directions and biological effects vary across family members and disease contexts.^93–96 These observations provide a rationale for further investigation but should not be extrapolated as evidence of TIGD function in HCC.

In HCC, a recent study integrating transcriptomic and single-cell analyses reported associations between several TIGD family members, particularly TIGD4, TIGD5, and TIGD6, and prognosis, malignant-cell functional states, stemness-related features, and immune infiltration.²¹ This study currently represents the most direct HCC-specific evidence for the TIGD family, but its findings remain primarily association-based. They do not establish protein-level expression, causal effects on HCC phenotypes, retained transposase-like activity, or direct chromatin- or TE-regulatory functions. Because the available HCC evidence is largely derived from a single study, independent validation is required.

As conventional protein-coding genes, TIGD family members can be assessed using RNA sequencing, quantitative PCR, immunohistochemistry, and proteomic approaches. However, analytical accessibility should not be equated with clinical utility. Before any TIGD-based prognostic model can be considered for clinical application, its performance must be validated in independent multicenter cohorts, compared with established clinicopathological variables, and evaluated at both the RNA and protein levels.^74,97 TIGD family members should therefore currently be regarded as research-use candidates rather than validated HCC biomarkers.

Mechanistic Hypotheses and Priorities for Validation

Current evidence does not establish a mechanistic role for TIGD family members in HCC. The reported associations with prognosis, tumour-cell states, stemness-related features and immune infiltration nominate TIGD genes for further investigation but do not demonstrate causality.²¹ Potential involvement in transcriptional or chromatin regulation, tumour-cell phenotypes or immune-related processes should therefore be regarded as testable hypotheses rather than conclusions. Moreover, individual TIGD members should be evaluated separately because their functions may differ across genes and disease contexts.

Validation should proceed through a staged, member-specific approach. Initial studies should confirm RNA and protein expression in independent HCC cohorts and determine the cellular and subcellular distribution of candidate TIGD proteins. Gain- and loss-of-function experiments, accompanied by rescue assays, should then assess effects on proliferation, apoptosis, migration, invasion and differentiation-related phenotypes in HCC models. Any proposed chromatin- or TE-regulatory function would require direct assessment of genomic binding, interacting proteins, chromatin accessibility, TE expression and downstream transcriptional changes. In vivo studies would subsequently be needed to establish whether effects observed in cultured cells are relevant to tumour growth and progression.

Associations between TIGD expression and immune-related features also require cautious interpretation because they may reflect tumour purity, cellular composition or broader transcriptional states rather than direct immune regulation. Single-cell and spatial analyses may help identify the cellular sources of TIGD expression, whereas functional models would be required to determine whether perturbing a specific TIGD member alters interferon signalling, antigen presentation, immune-cell interactions or therapeutic response. Until such evidence is available, it remains unresolved whether TIGD family members are functional regulators, context-dependent modifiers or bystander markers in HCC.

Future Perspectives

A major priority for future research on TE dysregulation in HCC is to move from correlation-based observations towards locus-specific mechanistic validation and clinically relevant assessment. The current evidence base remains uneven: LINE-1 hypomethylation, the TE/KDM1A/HNF4A axis and SETDB1-mediated HERV/ERV silencing have direct HCC-specific support, whereas TE-derived antigens, broad TE-induced immune sensitisation and TE-derived protein-coding candidates remain less well validated or hypothesis-generating. Future studies should therefore prioritise identifying functionally relevant TE loci, defining causal links between TE activity and immune remodelling, and determining whether TE-derived biomarkers or therapeutic strategies provide value beyond established clinical variables.

The first priority is locus-specific functional annotation of TEs. Because TE sequences are highly repetitive, short-read sequencing is often affected by multi-mapping reads, making it difficult to assign expression signals accurately to specific TE loci. TE-aware RNA-seq, long-read sequencing,⁸⁶ locus-specific TE expression analysis,⁹⁸ ATAC-seq, CUT&Tag/CUT&RUN, and chromatin interaction analyses should therefore be integrated to identify TE loci with genuine regulatory functions and their target genes.

The second priority is to clarify how TE activity relates to the epigenetic state of HCC and response to immunotherapy. This will require systematic analysis of interaction networks involving TEs, DNMTs, SETDB1, TRIM28, KDM1A, HDACs, KRAB-ZFPs, m6A regulators, and RNA editing enzymes. It will also be important to determine whether TE-derived immune signatures have independent predictive value in HCC cohorts receiving immunotherapy.

The third priority is functional validation of TE-derived immune mechanisms. Key questions include which TE/HERV loci can induce effective viral mimicry, whether they enhance HLA/MHC antigen presentation, and whether TE-derived antigens can be recognized by CD8⁺ T cells.³⁵ Addressing these questions will require immunopeptidomics, T-cell functional assays, and HCC clinical cohorts with well-defined etiological stratification.

Single-cell and spatial multi-omics approaches will be important for distinguishing TE signals originating from malignant hepatocytes from those arising from immune cells, stromal cells, endothelial cells or adjacent inflamed liver tissue. Integrating TE-aware single-cell transcriptomics with spatial transcriptomics and multiplex immunofluorescence may help determine whether locus-specific TE activity is associated with immune exclusion, T-cell exhaustion, macrophage enrichment, vascular invasion or invasive tumour regions.^88–90 However, such cell-state and spatial associations remain observational and require functional validation.

Finally, TE-derived research-use signatures, candidate biomarkers, and TE-centered therapeutic hypotheses require rigorous clinical validation. Future studies should not rely solely on public databases such as TCGA or GEO. Instead, the research value of TE methylation, TE expression, HERV/ERV signatures, TE-derived antigens, and representative TE-derived protein-coding candidates should be evaluated in multicenter HCC cohorts with well-defined etiology, comprehensive treatment information, and clear liver function stratification. At the therapeutic level, epigenetic therapy-induced TE reactivation remains worth exploring. However, because patients with HCC often have cirrhosis, chronic viral hepatitis, and impaired hepatic reserve, immune activation must be balanced against hepatic safety.

Conclusion

TE dysregulation provides a biologically relevant link between epigenetic disruption, aberrant transcription and immune remodelling in HCC. Current HCC-specific evidence is strongest for the clinical associations of LINE-1 hypomethylation and for mechanistic studies involving the TE/KDM1A/HNF4A axis and SETDB1-mediated HERV/ERV silencing and viral mimicry. These findings indicate that TE activity can have functional consequences in selected HCC contexts rather than representing only a passive marker of genomic or epigenetic instability. However, many proposed links between TEs, innate immune sensing, antigen presentation and treatment response remain based on associative, pan-cancer or non-HCC evidence.

Clinical translation has not yet been established. TE-derived signatures, antigens and therapeutic strategies should remain investigational until they are supported by locus-specific functional studies, independent multicentre cohorts and prospective treatment-response data. The potential benefits of therapeutically inducing TE activity must also be balanced against the risks associated with cirrhosis, chronic viral hepatitis and impaired hepatic reserve. TIGD family members currently represent a hypothesis-generating example of TE-derived protein-coding candidates: their transcriptomic associations in HCC warrant further study but do not establish direct chromatin-regulatory, TE-regulatory or therapeutic functions. The central priority is therefore to move from broad associations towards reproducible, mechanistically validated and clinically informative TE-related findings in HCC.

Funding Statement

This work was supported by the Ningxia Natural Science Foundation (2025AAC030449, 2025AAC020056, and 2026AAC030621).

Abbreviations

ADAR, Adenosine deaminase acting on RNA; ATAC‑seq, Assay for transposase‑accessible chromatin with sequencing; BCLC, Barcelona Clinic Liver Cancer; cfDNA, Cell‑free DNA; CUT&RUN, Cleavage under targets and release using nuclease; CUT&Tag, Cleavage under targets and tagmentation; ERV, Endogenous retrovirus; GEO, Gene Expression Omnibus; HBV, Hepatitis B virus; HCC, Hepatocellular carcinoma; HCV, Hepatitis C virus; HERV, Human endogenous retrovirus; HLA, Human leukocyte antigen; HNF4A, Hepatocyte nuclear factor 4 alpha; IHC, Immunohistochemistry; KDM1A, Lysine demethylase 1A; KDM5B, Lysine demethylase 5B; LINE-1, Long interspersed nuclear element-1; LTR, Long terminal repeat; m6A, N6-methyladenosine; MDA5, Melanoma differentiation-associated protein 5; MHC-I, Major histocompatibility complex class I; PD-L1, Programmed death-ligand 1; RIG-I, Retinoic acid-inducible gene I; RNA-seq, RNA sequencing; SETDB1, SET domain bifurcated histone lysine methyltransferase 1; SINE, Short interspersed nuclear element; TCGA, The Cancer Genome Atlas; TE, Transposable element; TIGD, Tigger transposable element-derived; TKI, Tyrosine kinase inhibitor; TLR3, Toll-like receptor 3; TRIM28, Tripartite motif-containing protein 28; VEGF, Vascular endothelial growth factor.

Data Sharing Statement

No new data were generated or analyzed in this review. All information discussed in this article was derived from previously published studies. Data sharing is therefore not applicable to this article.

Ethics Approval and Informed Consent

Not applicable. This review did not involve human participants, human samples, identifiable personal data, or animals.

Consent for Publication

Not applicable. This article does not contain any identifiable personal data, images, videos, or case details requiring consent for publication.

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors declare that they have no financial or non-financial competing interests relevant to this work.