Interplay between Viruses and Endogenous Retroviruses in Immune Response and Diseases Affecting the Nervous System

Abstract

Endogenous retroviruses are integral part of the human genome. Endogenous retroviruses are integral parts of human genome that originate from waves of retroviral infections of human ancestors, insertion of the retroviral sequences into germ cell DNA and vertical transmission from parent to progeny. Over time the host has transformed these sequences to restrict the capacity of these to reinsert anywhere in the genome (jumping genes), to produce viral-like particles with limited effect or even proteins with distinct functions to the host. Moreover, the host controls the activity of endogenous retroviruses via epigenetic modulation, a mechanism that declines with age. Upon acute viral infection the equilibrium of human host and endogenous retroviruses can be disturbed. The interplay of viruses and endogenous retroviruses may lead to sustained dysregulation long after the infection (chronic inflammation). Recent findings have demonstrated many implications of a role of viruses and endogenous retroviruses in neurological diseases (in this chapter multiple sclerosis, amyotrophic lateral sclerosis, Alzheimer disease, HIV associated neurological disorder, SARS-CoV2 neurological symptoms, cancer and schizophrenia will be discussed).

1. Introduction

The origin of retroviruses dates back to the early Paleozoic Era 460 to 550 million years ago when first of them emerged under marine conditions, providing the oldest inferred estimate for any virus group [1].

Retroviruses are enveloped RNA viruses that depend on host for survival and reproduction. Upon infecting a host cell, retroviral RNA is reverse-transcribed into double-stranded DNA (dsDNA), typically between 6 and 11 kb long. This provirus is integrated permanently into the host cell genome and contains genes needed for new viral particle assembly (gag, pro, pol, env) flanked by regulatory long terminal repeats (LTRs) on both sides [2].

Retroviruses have evolved parallel to vertebrates and some of them have selected germ cells as their hosts and integrated their provirus into these cells. If retroviral insertions occurred at chromosomal sites that allowed birth of a viable offspring, the retrovirus had a chance of becoming endogenized in the host genome. These endogenized retroviruses in the germline have been vertically transmitted from parent to progeny and become fixated in a given population [3]. From the modern human genome, 8.29% is derived from human endogenous retroviruses (HERVs) [4].

Fixated HERVs adapted the life-style of transposable elements, copy-pasting themselves within the host genome. This activity carried potential for mutations and integrations at or into genes relevant for host cell homeostasis. Thus, HERV integrations have become mutated, (partially) deleted and epigenetically silenced as part of the host defense [5, 6]. In 85% of the cases even the long-terminal repeat (LTR) sequence alone have been kept in our genome [7]. In spite of their origin, HERVs function as human genome architects bringing species-specific features and being integrated into network regulating essential processes, for example by being dispersed at immune cells [8] and enabling placentation [9]. LTR sequences are powerful gene expression regulators, functioning as promoters [10] and as binding platforms for various transcription factors [11]. HERVs are involved in shaping cellular immune response against exogenous viruses [12, 13]. Aging, cancer, infections with exogenous viruses or inflammation can lift the epigenetic host control from HERVs causing their transcription [14]. This affects particularly the youngest and in humans polymorphic HERV-K family that can produce virions [15]. Some exogeneous viruses (HIV, HTLV-1, EBV, HHV-6) can activate HERVs directly. Continuously active HERVs can cause sustained neuroinflammation [14]. This chapter will introduce HERVs derived from exogenous retroviruses, enlighten the interplay between exogenous and endogenous retroviruses from the aspect on immune response and summarize evidence on HERV-derived mechanisms contributing to human nervous system pathogenesis.

2. Structure and function of retroviruses

Retroviruses are enveloped RNA viruses that use vertebrates as hosts on whom they depend on for survival and reproduction. For this to succeed, retroviral RNA is equipped with several features needed for viral replication: inverted repeat (IR) adjacent to LTR, LTR with unique 5 (U5), U3 and repeat (R) elements, primer binding site (PBS), polypurine tract (PPT) and poly(A) signal. IR serves as a recognition site for integrase. The main region on viral RNA that binds transcriptional promoters and enhancers is the LTR (U3). PBS (upstream of U5) binds viral transfer RNA (tRNA), a primer for reverse transcriptase, which will further bind host tRNA to initiate (−) strand DNA synthesis. In viral dsDNA (= provirus) that is integrated into the host genome, R element lies between U3 and U5 within the LTR. PPT (upstream of U3) is cleaved to produce primer for (+) strand DNA synthesis. In addition, more complex retroviruses have Rev or Rex response element (RRE) and constitutive transport element (CTE) to facilitate transport of retroviral RNA from nucleus to cytoplasm for viral protein translation. Provirus is typically 7–12 kb long and, in addition to the RNA regulatory elements described above, essentially includes gag, pro, pol and env genes, flanked by LTR on both sides.

Provirus is used to generate spliced and un-spliced viral RNA products using host machinery. Un-spliced RNA will form the genome of new viral particle. Spliced RNA products are generated using frameshift for translation of structural and regulatory viral proteins (gag, pro, pol, env) that build a mature viral particle. Gag encodes matrix, capsid and nucleocapsid proteins. These direct assembly of immature virus-like particles and budding from the cell. Pro encodes viral proteases that cleave immature virus-like particles into mature ones ready to infect the next host cell. Pol proteins include reverse-transcriptase, integrase and dUTPase, all of which are packed inside the viral capsid with the retroviral genome. Env encodes surface and transmembrane glycoproteins that mediate viral binding and entry to the host cell. Some more complex retroviruses (human immunodeficiency virus (HIV), human T-lymphotropic virus (HTLV), lentiviruses and spumaviruses) encode additional accessory proteins that fine-tune replication and infectivity of these retroviruses. For example, HIV encodes trans-activator of transcription (tat) protein which drastically enhances HIV transcription, viral infectivity factor (vif), viral protein R (vpr), viral protein U (vpu) and negative regulatory factor (nef) [2].

3. Endogenous retroviruses (ERVs)

In 1974, retroviral (HERV) particles were described in placental tissue [16]. Identification and cloning of the first HERV in human genome followed in 1981 [17]. More recent sequencing of human genome has revealed that 8.29% of the modern human genome is derived from ancient retroviral infections, with typical integration size between 6 and 11 kb [4, 18]. This encompasses about 40,000 HERV-derived sequences, including solitary LTR sequences, mostly on chromosomes 4, 20, X and Y [19].

HERVs are categorized to class I gamma- and epsilonretrovirus-like, class II betaretrovirus-like and class III spumavirus-like endogenous retroviruses. HERVs are further divided into at least 31 families/groups with each family presenting a single retroviral integration event in our ancestors [20]. This means that following a successful HERV endogenization into the germline, HERV has amplified itself within the human genome, behaving as transposable element, thereby generating copies of itself. Quite interestingly, some HERV insertions are present only in primates or are even human-specific [21]. Nomenclature of HERV families is based on the amino acid transported by tRNA that is complementary to the PBS of the particular HERV (lysine (K) for HERV-K, histidine (H) for HERV-H, tryptophan (W) for HERV-W etc.) [20]. Most of the different HERV sequences belong to class I and include HERV-H, HERV-F, HERV-W, HERV-R, HERV-P, HERV-E, HERV-T, HERV-I, HERV-FRD and HTLV-related endogenous sequence 1 (HRES-1). Class II HERVs are members of the HERV-K family and Class III includes HERV-L, HERV-S and HERV-U [22]. HERV-H and its LTR are the major components of the human-specific gene ESRG that drives human pluripotency [21, 23]. More recent HERV-K (with its LTR sequence) have expanded independently in the genomes of humans and great apes. These integrations potentially represent a source of genetic variation contributing to disease development, for example diabetes [15]. At present, no replication-competent HERV has been found and there is no evidence of novel HERV insertions in human genome, be it in germ cells or somatic cells [5, 24].

4. Host and ERV trade-off

Intriguingly, retroviral insertions in our genome have brought along a considerable degree of innovation and adaptivity [4]. They have become functional units that confer genomic fitness in our genome (exaptation) [25].

Throughout evolution, several ERVs have been repeatedly positively selected by different species to fulfill important functions in the cell. In particular the env ORF with full coding capacity belonging to various HERV insertions has been retained in the human genome [26]. Up to 85% of the HERV insertions in modern human genome, however, are the solo LTRs with internal retroviral sequence having been deleted through homologous recombination [7]. The LTR regulatory sequences of HERVs function as promoters in sense and anti-sense direction [10], contain binding sites for a variety of transcription factors, including the inflammatory ones [11], and RNA polymerase II regulatory sequences [27]. LTRs regulate transcription as enhancers and repressors. When located within a gene, LTRs can provide alternative splicing sites and poly-A signals [5]. Thus, LTRs of HERVs offer a variety of means for gene expression regulation. (Table 1) Together, HERVs regulate mammalian gene expression in cis and trans; [28] give rise to novel genes; [4] are transcribed at distinct stages of early human embryogenesis, e.g. HERV-H; [21, 23] mediate placentation (syncytins); [9] and shape the complexity of immune pathways [29]. Here, intriguingly, the phylogenetically younger and polymorphic HERV-K, which is still able to produce viral-like particles, has been integrated into the innate host defense against exogenous viral infections (during embryogenesis) [30].

Function	Examples	References
Gene expression regulation (cis/trans)	Transcription factor binding	[11]
	(Alternative) promoters	[5, 28]
	Enhancers	[5]
	Repressors	[5]
	(Alternative) splicing signals	[5, 28]
	Poly-A signals	[5]
	RNA polymerase II regulatory sequences	[27]
Giving rise to novel genes	ESRG	[21, 23, 28]
	Syncytins	[28]
Regulating early human embryogenesis	Pluripotency network	[21, 23]
	Morula	[28]
	Blastocyst	[21, 28]
Placentation, fetal-maternal tolerance	Syncytins	[9]
Evolution and complexity of immune pathways	Anti-viral immune response (innate and adaptive arms)	[12, 13, 29, 30, 51, 53]

Table 1.

Functions of LTRs and HERVs distributed within human genome.

5. Host regulation of ERVs

HERVs behaving as transposable elements and encoding transposition proteins, copy-and-pasted and cut-and-pasted themselves within the human genome. This means breaking, merging and degrading of nucleic acids, all of which are potentially dangerous activities for genomic integrity [5]. HERV mutations or insertions at or into relevant genes could also negatively impact host cell homeostasis. Thus, surviving with HERVs, bordering between own and foreign, demands a high-quality supervision from the host.

Mechanisms that host applies to manage these elements include mainly epigenetic silencing to repress transcription from HERVs and its LTRs, mutation and destruction of ORFs to avoid composition of infection-capable viral particles. As retroviral infections and HERV integrations occurred before the host was ready to combat these, host defense mechanisms are always one step behind the HERVs. This applies also for other pathogens. So is the rapid (co-)evolution of apolipoprotein B mRNA editing enzyme catalytic polypeptide 3 (APOBEC3) genes driven by HERVs and exogenous retroviruses, such as HIV via its vif protein. APOBEC3 encodes antiviral proteins that mutate viral genomes [31]. Thus, in general, phylogenetically older HERV insertions (such as majority of the HERV-H family) are tamed more efficiently than the younger HERV insertions (such as the polymorphic and still intact ORFs containing HERV-K (HML-2) family) [32].

Epigenetic silencing is a powerful tool for the host to control ERVs. Especially the LTR sequences of ERVs that regulate the expression of ERVs but also that of several host genes, need to be addressed in host defense [33]. DNA methylation is maintained during DNA replication and is thus a relatively stable way to repress ERVs [34]. Harsher means of epigenetic silencing are applied to protect the germline cells from overwhelming transposition leading to mutagenesis and potentially cancerous transformation [35] and in the initial stages of embryogenesis [36]. These involve histone-lysine N-methyltransferase (SETDB1) methylation of histones that bind ERV-containing DNA into repressive chromatin (nucleosomes). One of the most effective repressive modifications is trimethylation of histone H3 at lysine 9 (H3K9me3) at the LTR sequences of ERVs, followed by recruitment of chromodomain proteins to support heterochromatin [34, 35]. Although other silencing mechanisms are preferred in somatic cells, in some fully differentiated cells, namely B lymphocytes [37] and T lymphocytes [38] ERV suppression is also critically mediated by repressive histone methylation catalyzed by SETDB1. At the same time, permissive transcription of ERVs requires a set of cell-type specific transcription factors binding to ERV and initiating its transcription [37].

DNA hypermethylation is the dominant control method to restrict ERVs in differentiated cells [36]. The key mechanism of ERV silencing in adult brain and neuronal progenitor cells is mediated by krüppel-associated box domain (KRAB) associated protein-1 (KAP1), also known as tripartite motif-containing protein 28 (TRIM28) [39]. To control ERVs, KAP1 forms a complex with KRAB zinc-finger proteins (KRAB-ZNFs) and binds to ERV sequences at LTRs where it initiates cytosine methylation. KAP1 also prevents interferon (IFN) and RNA-sensing response through mitochondrial antiviral signaling protein (MAVS) [40]. Host-derived KAP1 can thus regulate gene expression in neuronal progenitor cells and in the brain where ERVs have been shown to provide transcriptional start sites for several nearby genes [39]. The importance of such host defense is further demonstrated by lethality when KAP1 is deleted during brain development and that heterozygous deletion of KAP1 causes behavioral changes resembling those observed in human psychiatric conditions involving ERV upregulation [41].

Despite the host defense mechanisms, HERVs can still behave as viruses, producing viral RNA, reverse transcribing it into dsDNA, encoding proteins and even forming (normally gutless) viral particles. All this can affect normal host cell function [42, 43]. Different HERV sequences within a particular HERV family expressed in the same host cell are actually able to form viral particles from partial proviruses. Namely, they can combine their proteins and genomes with each other in phenotypic mixing. So can polymorphic HERV-K (HML-2) produce viral particles [44] that package and transmit viral RNA from members of the HERV-K family. Viral genome within these particles (retroviral RNA) can even become reverse-transcribed, however, not (re-)integrated into the host genome [45]. With the potential to behave as viruses, ERVs can be immunogenic and may alarm the host immune system, making these elements semi-tolerated by the host [42].

Thus, the host aims at protecting itself from damaging effects of ERVs, yet maintaining the enrichment these bring as genome architects up to domesticating several HERV sequences.

6. Interaction between exogenous viruses and endogenous retroviruses

6.1 Immune response to retroviral infection

Recognition of PAMPs (viral proteins and nucleic acids) and danger-associated molecular patterns (DAMPs) (molecules released from damaged cells) is the function of innate immune system. It creates a general inflammatory milieu to stimulate virus/antigen specific adaptive immune response. Different PAMPs are recognized by specialized receptors. Viral DNA (dsDNA and ssDNA), mitochondrial DNA (mtDNA) and RNA-DNA hybrids are recognized by cytoplasmic DNA sensors, such as cyclic GMP-AMP synthase (cGAS), Z-DNA binding protein 1 (ZBP1) and toll-like receptor 9 (TLR9) [46, 47, 48]. Viral ssRNA is recognized and bound by TLR8 in humans [49], viral dsRNA by TLR3 and TLR9, melanoma differentiated associated gene 5 (MDA5) and ZBP-1 [46, 50], while retinoic acid inducible gene I (RIG-I) can sense both, viral ssRNA and dsRNA [50]. Also MAVS and STING are adaptor proteins activated as part of the innate immune response. Through this recognition of viral pathogen, innate immune system triggers the pro-inflammatory cytokine, such as tumor necrosis factor α (TNF-α), nuclear factor κβ (NF-κβ), chemokine and type I IFN (IFN-α and IFN-β) release. This activates absent in melanoma protein 2 (AIM2) inflammasome pathways [51], polyclonal T lymphocytes [52] and alarms adaptive immune system that is trained to combat the particular viral infection.

Adaptive immune response to viral infection is mediated by antibody-producing B lymphocytes (humoral immunity) and viral antigen specific T cell receptor (TCR) carrying T lymphocytes (cellular immunity). Self-derived peptide specific T lymphocytes are typically deleted already during development to avoid autoimmunity. Nevertheless, endogenous peptides can also mediate positive selection of developing thymocytes with specific TCR repertoire as well as augment activation and maintenance of peripheral CD4+ helper T lymphocytes [53]. Such thymic positive selection of HERV-specific T lymphocytes and presence of replication-defective HERV-derived proteins can shape the exogenous virus specific TCR repertoire and determine the avidity of the T lymphocyte response to retroviral infection. This involves a multitude of HERV proteins, including the polymorphic HERV-K, presented by cell surface molecules of highly polymorphic major histocompatibility complex (MHC) alleles. Further, this might explain the inter-individual heterogeneity regarding immune response to retroviral infections [12, 13].

6.2 Exogenous virus and HERV as allies

Retrovirus is built to establish a persistent infection by finding a suitable host cell repertoire thereby evading the innate (general) and adaptive (specific) immune system of the host. Retroviruses use different strategies for this, such as extensive glycosylation of the env protein that helps them hide from neutralizing antibodies produced by B lymphocytes or increasing mutation rate through re-infecting new host cells and through repeated rounds of replication [2].

Yet another way to evade the host immune surveillance, at least initially, is the advantageous similarity some exogenous retroviruses share with their endogenous counterparts in the host genome [42]. Exogenous viruses entering the host can have a strong effect on ERV transcription. First, they seem to lift the epigenetic suppression on ERVs in a cell-intrinsic fashion. In particular, this affects the ERV integrations near or embedded within similarly modulated host genes [54]. Further, sufficient similarity between ERV and exogenous retrovirus epitopes can weaken immune response against the exogenous counterpart [55], repair defects in this exogenous retrovirus [56], and facilitate chronic viral replication [57]. Not less relevant is that ERVs provide a rich pool for recombinational events with exogenous retroviruses. When a host cell is infected by two viruses, heterologous trans-activation can take place where transcription of one virus is initiated by factors produced by the other virus. Using mimicry, HIV rev which mediates nuclear export of HIV messenger RNA (mRNA) can also export HERV-K mRNA and through this promote HERV-K translation, leading to elevated HERV-K viral proteins in HIV patients [58]. Also, when HERVs provide env glycoproteins to exogenous retroviruses, these can develop a new host cell repertoire and circumvent immune system response [59]. Of note, in addition to exogenous retroviruses, other exogenous viruses have been shown to interact with HERVs, modulating their virulence and immune response. Activation of ERV transcription can directly be achieved by several exogenous viruses, such as Epstein-Barr virus (EBV), cytomegalovirus (CMV), influenza, herpesviruses and rabies virus. Some of these can even induce a self-sustained HERV activation [54, 60, 61, 62, 63, 64].

6.3 Exogenous virus and HERV as opponents

On the other hand, one of the functions that the inherent HERVs have been set in for by the host, is protection against viral infections mainly via regulation of the innate immune response under certain conditions, such as, for example, the early developmental phase. Thus, exogenous viruses and HERVs can act as opponents.

Starting with the initial stages of viral infection cycle, when exogenous (retro)virus attempts to enter a host cell, it might encounter blockage of necessary cellular receptors. This is triggered by an HERV already present in the host cell genome, providing thereby protection from the particular exogenous (retro)virus [65]. A pre-requisite for this, however, is shared specificity of the env surface and transmembrane glycoproteins [66] which mediate viral binding and entry to the host cell. Once the retrovirus has reverse transcribed its RNA into dsDNA and provirus becomes integrated into the host genome, substantial similarity between exogenous retrovirus and HERV could lead to fusion of viral proteins and production of defective viral particles. This may happen between HERVK(HML-2) gag and HIV gag [67]. If HERV antisense transcripts are complementary to the exogenous retrovirus RNA transcripts, interaction between the two can block viral replication and dsRNA is recognized as a PAMP by host immune system [68].

7. Virus dysregulation of HERVs in disease development and maintenance

Mechanisms of virus dysregulation of HERVs in disease development and maintenance discussed in this chapter are summarized in Figure 1.

Figure 1.

Summary of the five mechanisms, discussed in chapters 7.1. Through 7.5., mediated by human endogenous retroviruses (HERVs) that can contribute to neurological disease development. Font size of HERVs represents the importance of a particular HERV in a given mechanism. Created with BioRender.com.

7.1 Exogenous virus and HERV interplay in the nervous system pathogenesis

Exogenous viruses can activate HERVs directly and/or indirectly. Also, host reaction to viral infection can differ based on a background of higher HERV activity due to prior sensitization with the virus [69], already aberrant cellular gene expression resulting from changed epigenome or due to increased amounts of HERV products. In particular, the phylogenetically youngest and polymorphic HERV-K, which the host has not yet managed to control this strictly, seems to be sensitive to external activation. Interplay between exogenous and endogenous viruses is often seen to contribute to various human pathologies and affect the outcome of these.

Infection with HIV causes acquired immunodeficiency syndrome (AIDS). HERV-K plays an important role in the HIV-associated neurodegenerative disorder (HAND), a complication of AIDS [70] that can lead to dementia in young adults [71]. HAND might be further aggravated by opportunistic infections, such as CMV, EBV, VZV and human herpes virus type 6 (HHV-6) [72]. HIV tat protein can directly facilitate HERV-K expression and viral particle production. Through activating HERV-K, HIV also stimulates production of HERV-K (HML-2) env oncogenic splice products Rec and Np9 in lymphocytes and monocytes [73]. HERV-K Rec shares functional similarity with HIV Rev. which is involved in nuclear import and export signals [74]. HIV can further activate CD8+ T lymphocyte mediated immunity towards such HERV peptides that share with it at least a four-amino-acid sequence similarity. Turning this around, HERV-specific T lymphocytes can recognize and react to HIV, opening a new avenue in HIV pathogenesis and vaccine design.

Whole exome sequencing of cohorts of Alzheimer disease (AD) patients have pointed to the causative role of herpesviruses HHV-6A but also HHV-7 in clinical dementia and neuropathology traits in AD patients [75]. Infection with another herpesvirus, herpes simplex virus type 1 (HSV-1), is sufficient to mimic neuropathology observed in AD in a 3D human brain-like tissue model [76]. HHV-6A and HSV-1 with neuronal tropism both activate transcription of HERVs and their reverse transcriptase in lymphocytes, neuronal and endothelial cells of the brain [77, 78, 79]. HERV-K and HERV-W transcription in AD is associated with neuroinflammation and neuronal death [80, 81].

More abundant evidence exists for the interplay between exogenous and endogenous viruses in multiple sclerosis (MS) pathogenesis. MS is strongly associated with HERV activation (mainly HERV-W but also HERV-K and HERV-H) through herpesviruses (most prominently the EBV [78, 82, 83, 84] but also HHV-6, HHV-3 (additionally known as varizella zoster virus (VZV)) and HSV-1) [85]. In addition to herpesviruses, coronaviruses are detected in the brains of MS patients [86, 87]. That severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) increases HERV-W env expression in the leucocytes of COVID-19 patients [88], causative virus for the coronavirus disease 2019 (COVID-19) pandemic, raises the possibility of MS-like demyelinating disease as a long-term complication of COVID-19.

7.2 ERV activation leading to sustained inflammation

If normally the immune reaction caused by viral infection resolves after the external intruder has been combated, it can become more complicated when HERVs get involved, either through the external virus or via the subsequent immune response [14].

Certain HERVs are distributed within the genome to function as response elements to IFN type I [51] which is the key product of innate immune system in response to viral infection. Dispersed at relevant immune genes, the polymorphic HERV-K (HML-2) loci form an additional layer of immune response regulation [8]. In an attempt to clear up the immune response triggered by HERVs, TLR stimulation can activate HERV instead by [89], for example, recruiting transcription factors to the LTR sequence of the HERV [90]. The same happens when exogenous virus stimulates TLR on the background of already present pro-inflammatory milieu. In this feedback loop, HERV activity is upregulated by anti-viral immune response through inflammatory mediators but also through epigenetic dysregulation [11, 33, 91], giving rise to chronic stimulation of the immune system and ultimately to chronic inflammation [11, 22, 91, 92].

HERV, such as HERV-K [58, 93], but also HERV-W [94], dynamic activation by HIV, resulting TLR4 stimulation and pro-inflammatory cytokines (interleukin 6 (IL-6), IL-1β, TNF-α, IFN-γ) augments neurodegeneration and neuroinflammation accompanying HAND. Such boosted HERV-K transcription in the brain, intriguingly precedes clinical symptoms and cognitive impairment [95]. Sustained HERV-K expression in neurons leads to neurite retraction, neuronal death [80] and motor deficits [96], which might contribute to the ALS-like syndrome observed in HIV patients [97].

HERV involvement in the pathogenesis of ALS, a neurodegenerative disease characterized by progressive loss of cortical and spinal motor neurons [98] was first suspected when retroviral reverse transcriptase was found in the CSF of HIV-negative ALS patients [99] and in the serum of their first-degree relatives, suggesting inheritance of the retrovirus [100]. Transcription of HERV-K, in particular the one from the 7q36.1 cytogenic locus with ORF for reverse transcriptase [101], triggered by neuroinflammation and neuronal injury, is one of the hallmarks of ALS [102] and is associated with retracting neurons [96, 103]. HERV-K activation in the brain of an ALS patient is regulated by the functional IFN-stimulated response elements in HERV-K promoter region [102] and possibly involves nuclear translocation of IFN regulatory factor 1 and NF-κβ isoforms p50 and p65 [102]. Increased HERV-K and HERV-W env and gag expression in muscular tissue from the ALS patients is, in turn, linked with neurogenic atrophy of the muscle and macrophage activation [104].

AD is a progressive neurodegenerative disorder characterized by gradual cognitive decline. The disease starts subtly and likely decades before the appearance of clinical symptoms [105]. Initial inflammation in AD brain aims to clear up the emerging amyloid-beta plaques, one of the hallmarks of AD. As the disease progresses, the neuroinflammation becomes too overwhelming to handle [106]. Injured neurons release HERV-K (HML-2) transcripts, the 5’-GUUGUGU-3′ sequence in their env region activates neuronal and microglial TLR8, mediating neurodegeneration and further microglia accumulation [80]. Progressing inflammation stimulates also regional HERV-W transcription [81]. Thus, chronic neuroinflammation in the brain stimulates local HERV transcription [81, 102, 107] which, in combination with higher age, can be particularly detrimental [81, 108].

MS is a neurodegenerative and neuroinflammatory disease caused by immune system activity against the central nervous system (CNS) myelin antigens (myelin basic protein, proteolipid protein, myelin oligodendrocyte glycoprotein (MOG)). Disease is characterized by multifocal demyelinating lesions in the white matter of the brain and the spinal cord and gradual decline in physical and cognitive function. Progression of MS lesions and maintenance of the inflammatory state are associated with increased HERV-W and HERV-K expression accompanied by elevated TNF-α levels, monocyte activation and differentiation [81]. In particular, HERV-W env is highly expressed in the brain, cerebrospinal fluid (CSF), blood and serum of MS patients [109, 110] and plays a central role in MS pathology. Higher HERV-W transcription predicts faster disease progression and worse prognosis [111]. Several HERV-W genomic loci are actively transcribed in the disease. HERV-W sequence on 14q11.2 chromosome locus lies within the TCR αδ gene [83]. The expression of HERV-W (env) from 7q21.2 chromosome locus gives rise to syncytin-1 glycoprotein and is in MS transcribed in tandem with HERV-H sequence 1 kb apart [83, 109]. The expression of syncytin-1 is toxic for oligodendrocytes but not to neurons and boosts neuroinflammation associated with pro-inflammatory astrocytes, IL-1β production, release of redox reagents (nitric oxide, peroxynitrite) and protein oxidation. Further, syncytin-1 expression is linked with inhibition of oligodendrocyte maturation, myelin damage and antagonization of remyelination, causing neurobehavioral deficits, such as weakness, gait unsteadiness and altered executive functions, in mice [109].

Collectively, viral infection induced immune system activation and inflammatory stimuli often activates transcription of different HERV families residing within the genome. Enhanced HERV transcription can be further boosted by virus at hand, external and internal factors, which mainly affect the epigenome [54, 112], together leading to sustained inflammation.

7.3 Changes in epigenome and de-repression of HERVs

Changes in the epigenome (methylation and acetylation level) affect chromatin accessibility and have an impact on both, transcription of HERVs as well as host gene expression. LTR sequences of HERVs can activate gene expression in cis and trans [10, 11, 28] and function over longer genomic distances (topologically associated domains) [113]. In addition, LTR-HERVs can provide splicing and polyadenylation signals and [5, 28, 114], located within a gene, give rise to chimeric gene products [4].

As we age, global DNA methylation will slowly decrease while regions involved in regulation of cell differentiation and DNA-dependent transcription regulation can become hypermethylated [115]. This might be facilitated by the increasingly destabilized Polycomb repressive complex [116]. Our genome gradually loses its stability and formerly repressive chromatin will become more accessible, also at the widely spread ERVs [117, 118]. Increased ERV activity due to aging has been reported in humans (HERV-K, HERV-W) [119], mice [120] and drosophila (LTR element gypsy) [121]. This has been associated with shorter lifespan, neurodegeneration and memory deficits in drosophila [121]. In antibody-deficient muMT mouse, elevated expression of ERV-K family member intracisternal A-particle (IAP) in hippocampi leads to down-regulation of genes involved in synaptic function and contributes to cognitive impairments in contextual fear memory and spatial learning [108].

Global hypomethylation is characteristic also to cancer. Here, this is associated with oncogene activation (expression of certain aberrant alternatively spliced proteins) initiated via the HERV LTR sequence (ERV promoter exaptation = onco-exaptation) for example through expression of truncated proteins when HERV is located in an intron downstream the canonical translation site [122]. HERV-K and HERV-H LTR sequences can additionally become available for transcription factors favoring oncogenesis such as the core pluripotency factors needed for somatic cell reprogramming into a pluripotent one [123]. Intriguingly, more than one third of tumor suppressor p53 binding sites in the human genome have been dispersed by class I HERV sequences, which have become major components of the p53 regulatory network [124].

One of the genes, associated with familial ALS is the TDP-43. TDP-43 and HERV-K expression in ALS correlate positively with each other [101] and disruption of HERV-K (HML-2) env by Staphylococcus aureus Cas9 endonuclease could down-regulate the expression of TDP-43 [125]. Further, TDP-43 has five binding sites on the LTR sequence of HERV-K dsDNA via which it is able to transactivate HERV-K [96].

Schizophrenia is a neuropsychiatric disorder characterized by episodes of psychosis, hallucinations, delusions, apathy and disorganized thinking. The disease development is believed to combine genetic background, environmental factors, pre- and postnatal infections [126], subclinical inflammation [127] and variation within brain-associated and immune genes [128]. Early stages of schizophrenia are characterized by reduced DNA methylation levels at HERV-K sequences in peripheral blood when compared to age- and gender-matched controls [129].

Epigenome could be also targeted for the purpose of treating the disease, such as cancer. One such approach is viral mimicry that uses HERV-mediated inflammation to sensitize cancer for immunotherapy [130]. Briefly, chromatin modifier enzymes, such as DNA methyltransferase inhibitors, lysine methyltransferase inhibitor, lysin-specific demethylase 1 inhibitor or cyclin-dependent kinase 9 inhibitor are used to reactivate HERV in a cancer cell. This stimulates immune response as upon viral infection. Released dsRNA molecules are detected by TLR3 and MDA5 which binds MAVS, stimulating IFN response and HERV-derived tumor associated antigen presentation, making cancer cells visible to cytotoxic T lymphocytes [130, 131]. However, caution is required when targeting HERVs that border between self and non-self, especially at genomic and epigenetic levels, as it will be difficult to predict the outcome involving individual copies spilled within the genome.

7.4 HERV sensing by immune system, HERV proteins and molecular mimicry

Although low amounts of HERV-specific antibodies have been reported in the host (incomplete central tolerance) [42], enhanced HERV transcription stimulates further HERV-specific B and T lymphocyte responses [132, 133]. Circulating lymphocytes with low affinity for self- antigens may be stimulated by infection. Infection is accompanied by inflammation and dendritic cells expressing high levels of co-stimulatory signals together with a self-antigen, can activate naïve T lymphocytes with low affinity for this self-antigen. Extensive cell-death can cause chromatin-fragments and CpG sequences within the DNA (normally associated with bacteria) and ssRNA to become available. Cell-internal TLR9 recognizes unmethylated CpG sequences. Uridine-rich ssRNA complexes are sensed by TLR8. Both provide the necessary co-stimulatory signal to activate chromatin- or RNA-specific B lymphocytes which can now act as antigen-presenting cells to stimulate autoreactive T lymphocytes. Normally ignorant self-reactive B and T lymphocytes may also be activated by unusual location or availability of this (self-)antigen that can happen as a consequence of inflammation or massive tissue damage [134].

HERV-K expression is one of the hallmarks of the ALS disease in humans [96, 103]. HERV-K pol,gag and env are all transcriptionally active in certain brain regions (prefrontal, sensory, motor, occipital cortex) of ALS patients [95, 96] and HERV-K env additionally in cortical and spinal neurons of sporadic ALS patients [96]. The importance of HERV-K env in ALS pathogenesis is demonstrated by mice where HERV-K env expression leads to a progressive motor neuron disease affecting upper and lower motor neurons, characterized by advancing motor dysfunction, impaired synaptic function and selective loss of motor cortex volume [96].

HERV-K env protein plays a role also in the CNS cancer, where it promotes malignant phenotype in Merlin-deficient meningioma, schwannoma and ependymoma tumors [135]. Expression of ERVK3–1, a small HERV-K (HML-6) env protein encoded from 19q13.43b chromosome locus predicts poor outcome in glioblastoma, the most aggressive brain tumor in adults [136]. Also HERV-K env splice products Rec and Np9 elicit oncogenic function [137] by regulating cancer viability, migration and invasion [135].

While HERV ORFs have been heavily mutated as part of the host defense, the env ORF has been often retained with full coding capacity [26]. HERV env proteins can activate the immune system and antibodies raised against env glycoprotein of HERVs, such as HERV-K and HERV-R, HERV-W, have been linked autoimmune diseases in humans [138, 139, 140]. Also, ERV-specific antibody response can be stimulated by exogenous viral infections [141]. Such molecular mimicry happens when a pathogen and self-protein share a significant part of the amino acid sequence or, alternatively, an important functional domain. Activated ERV-specific B lymphocytes can cross-react also with other self-proteins via molecular mimicry, and cause autoimmune diseases, such as Sjögren’s syndrome, mixed connective tissue diseases, inflammatory neurological disease and MS [138, 142].

HERV-W, HERV-K, and HERV-H transcripts and proteins are more abundant in MS patients compared with controls [138, 143, 144]. The key role of HERV-W in MS pathology might be explained by the five regions of HERV-W env protein resembling the Ig-like domain of MOG, thus creating molecular mimicry between the two. In line with this, HERV-W env is found to be expressed in myeloid cells associated with axons [138, 145] in acute and chronic MS demyelinating lesions [109]. There, HERV-W acts as a PAMP boosting inflammation by stimulating dendritic cells and CD4+ T lymphocytes associated with demyelination in MS pathology [146]. Given the central role of HERV-W in MS pathology, HERV-W env antagonist GNbAC1, temelimab, has shown promise via significant neuroprotective effect for MS treatment in PhaseIIb clinical trial (ClinicalTrials.gov identifier: NCT02782858, 138].

SARS-CoV-2, the causative virus for the COVID-19 pandemic, shares molecular mimicry with HERVs via its several retroelement-like sequences and some of these sequences could be linked with the severity of the COVID-19 infection [147]. A recent study found higher expression of the pathogenic HERV-W env protein in the leukocytes of COVID-19 patients, correlating to T lymphocyte differentiation and exhaustion as well as blood cytokine levels [88].

7.5 HERV superantigens

Superantigens are molecules that stimulate unusually large numbers of CD4+, CD8+ and γδ + T lymphocytes by cross-linking the Vβ variable domain of the TCR with MHC class II molecules on target cells, leading to a robust immune system activation and massive inflammatory cytokine release [148]. Retroviruses [148] and proteins generated by HERVs, such as the env glycoprotein, can be sensed by host as superantigens [141]. Expression of endogenous superantigens is enhanced by different exogenous viruses [149]. For example, EBV can transactivate the HERV-K18 superantigen. EBV latent membrane protein 2A (LMP-2A) namely stimulates B lymphocytes that will activate HERV-K18 env gene present in the first intron of the CD48 gene, from which CD21 subfamily of immunoglobulin-like receptors are produced [82, 150]. HERV-K18 superantigen is also induced by HHV-6A [79]. As another example, rabies virus induces the HERV-W superantigen [64]. HIV takes advantage of the HERV-superantigen stimulated robust T lymphocyte activation, further aggravated by chronic infections with EBV or CMV [151]. This points to a relevance of combined viral infections and HERV activation. In addition to HIV, HERV-derived superantigens are suspected to contribute to type I diabetes, lymphomas and human autoimmune disease, such as rheumatoid arthritis and MS [152].

8. Conclusion

Retroviral infections have occurred throughout the human evolution causing a considerable portion of our genome to be of retroviral origin. HERVs with their LTRs are enrolled into fulfilling different functions by the host, including shaping the innate immunity and T lymphocyte response to exogenous viruses. As distant relatives, HERVs interact with exogenous viruses (EBV, HHV-6, HHV-3, HIV, HTLV, SARS-CoV2) and this might lead to, most commonly, autoimmune, neurodegenerative and neuroinflammatory diseases as well as cancer. A particular HERV might play a key role in certain diseases, such as HERV-W in multiple sclerosis or HERV-K in Alzheimer’s disease and in amyotrophic lateral sclerosis, whereas others, such as cancer, could rather result from global hypomethylation and de-repression of LTRs and HERVs. Looking at the combination of HERVs and their triggering viral components present in a given disease might open new aspects in understanding the pathology as well as offer novel therapeutic targets.