1. Introduction
Hepatitis С virus (HCV) is responsible for 9% of chronic liver disease cases worldwide [
1]. Currently the World Health Organization estimates 58 million people to be chronically infected with this virus [
2]. Chronic hepatitis C (CHC) is often accompanied by persistent liver inflammation and gradual development of fibrosis [
3]. As result, one in 3-10 patients will develop liver cirrhosis within a 20-30 year period [
2,
3,
4]. Patients with liver cirrhosis have substantial risks of hepatic decompensation and hepatocellular carcinoma. HCV infection is the cause of death of almost 400 000 patients with end-stage liver disease each year [
1]. Combinations of direct acting antivirals (DAAs) can clear the infection in almost every patient, though some CHC carriers with genotype 3 of the virus or with decompensated cirrhosis may not achieve sustained virological responses (SVR) [
5,
6]. While the high price of anti-HCV drugs still limits access to therapy in some parts of the world, insufficient screening allows between 68-94% of chronic hepatitis C cases to remain undiagnosed [
7]. Moreover, SVR upon DAA treatment does not reduce the risk of liver cirrhosis and cancer to the level in the uninfected population [
8]. Therefore, more insight into HCV pathogenesis is needed in order to develop drugs that may suppress or prevent liver dysfunction. One of the directions in this area is investigation of virus-induced changes in metabolism of infected cells.
HCV infection drives fibrogenesis and hepatocarcinogenesis by multiple mechanisms. These include chronic inflammation [
9], production of profibrotic cytokines (i.e. TGFβ1) [
10], interference of viral proteins with multiple signalling pathways in infected hepatocytes and concomitant inhibition of apoptosis and increased cell survival [
11], overproduction of reactive oxygen species (ROS), dysregulation of antioxidant defence systems [
12,
13], and alteration of metabolic pathways [
14]. HCV was reported to perturb multiple metabolic pathways including glycolysis, glutaminolysis, and amino acid metabolism. Specifically, this virus increases rates of glycolysis and lactate production [
15,
16,
17] and enhances consumption of glutamine and its conversion into α-ketoglutarate to drive tricarbonic acid (TCA) cycle in a tumour-like fashion [
18]. HCV also increases levels of nucleos(t)ides, some amino acids and fatty acids and decreases intracellular concentration of AcCoA [
15,
17,
19]. Replication of the virus also relies on metabolites such as sphingomyelin that is critical for formation of double membrane vesicles where the virus replicase is localized [
20]. However, the status of many other important metabolic pathways in HCV-infected hepatocytes remains unknown.
Biogenic polyamines are low molecular weight compounds that carry several positively charged amino groups and thus can interact electrostatically with negatively charged nucleic acids and proteins. Spermine and spermidine are found in all types of eukaryotic cells at high concentrations, with their levels generally correlating with cell proliferation rates [
21]. Polyamines are synthesized from ornithine, a metabolite of the urea cycle that is also linked to proline and glutamine/glutamate metabolic pathways (
Scheme 1) [
22,
23]. The rate-limiting step of polyamine biosynthesis is the conversion of ornithine into diamine putrescine (1,4-diaminobutane) catalysed by ornithine decarboxylase (ODC). Putrescine is then converted into spermidine and spermine by spermidine and spermine synthases (SRM, SMS), respectively with decarboxylated S-adenosyl methionine (dcSAM) being provided by S-adenosylmethionine decarboxylase (AMD). Polyamine degradation is achieved by two alternative pathways. The first one is a two-step process of acetylation by spermidine/spermine-N
1-acetyl transferase (SSAT) with oxidation of acetylated spermine and spermidine by acetylpolyamine oxidase (PAOX) into spermidine and putrescine, respectively. An alternative pathway is a direct oxidation of spermine into spermidine by spermine oxidase (SMOX). Cells maintain levels of spermine and spermidine by multi-level control of expression of ODC, SSAT, SMOX, and, to some extent, AMD. Increased polyamine concentrations are a hallmark of hyperproliferative disorders such as cancer and autoimmune diseases [
24]. At the same time, increased expression of SMOX that produces hydrogen peroxide and toxic acrolein is a feature of stroke, acute pancreatitis, or is the key factor of carcinogenesis during
Helicobacter pylori or
Bacteroides fragilis infections [
25,
26]. Thus, targeting polyamine-metabolizing enzymes with pharmacologic inhibitors/activators is considered as a promising strategy for treatment of cancer. An example is the considerable progress that was achieved in treatment of neuroblastoma by addition of ODC inhibitor difluoromethylornithine (DFMO) to the standard combination of drugs [
27,
28].
However, much less is known about the interplay between polyamines with viral infections [
22]. Previously we reported that transient expression of HCV core and NS5A proteins affects expression of the key polyamine-metabolizing enzymes via enhanced ROS production [
29]. Moreover, a stable Huh7 cell line harbouring a full-length HCV replicon exhibited suppressed expression of ODC and SSAT, up-regulated expression of SMOX, and diminished levels of spermine and spermidine. However, all this was shown in a non-infectious system, and warrants investigation in a model that ensures all steps of the viral life cycle. So far, nothing is known on whether polyamines are important for HCV replication, although other viruses have been shown to rely on spermine and spermidine at various stages of their life cycles [
30]. The primary goal of this project was to investigate if hepatitis C virus interferes with metabolism of biogenic polyamines and related metabolites, and if compounds that target polyamine-metabolizing enzymes affect HCV replication.
4. Discussion
Polyamines are ubiquitous compounds critical for cell growth and differentiation. Changes in their metabolism are associated with development of proliferative and metabolic disorders such as tumorigenesis and autoimmune pathologies (i.e. psoriasis) [
45,
46]. However, significance of spermine and spermidine for viral infections until recently was studied less extensively. Several viruses including Kaposi’s sarcoma-associated virus (KSAV) [
47], Epstein-Barr virus (EBV) [
48], Dengue virus [
49], were shown to suppress expression of SSAT at transcriptional or translational levels. KSAV also induces expression of ODC, although only at latent stages of replication in 2D culture [
50] or in 3D models [
47]. A similar, although transient, increase in ODC was described in 3D organoids infected with KSAV [
47]. As a result, at least some of these infections increase polyamine content in infected cells. In contrast, SARS-CoV-2 [
51], porcine reproductive and respiratory syndrome virus (PRRSV) [
52], and porcine endemic diarrhoea virus (PEDV) [
53] upregulate expression of SSAT and thus decrease polyamine levels in infected cells. Exhaustion of spermine and spermidine levels due to lowered expression of ODC is also a feature of lytic KSAV [
50] and Coxsackie virus B3 (CVB3) [
54] infections. So, our data expand the list of viral pathogens that deregulate expression of polyamine-metabolising enzymes and decrease polyamine content.
Polyamines are important for replication of various viruses. In recent years the Mounce group demonstrated that polyamines ensure infectivity of virions either by direct incorporation into the virus particle [
55] or by incorporation of cholesterol [
56] thus conferring binding of virions to the cell surface and concomitant virus entry [
55,
57,
58]. During polyamine exhaustion, non-infectious viral particles can be formed, as shown for Bunyaviruses [
59]. So, it is not surprising that polyamine biosynthesis inhibitors such as DFMO or SAM486A exhibit activity towards members of the Filo- [
60], Herpes- [
50], Entero- [
61], Picorna- [
61], Alpha- [
62], Corona- [
57,
61], Flavi- [
61], Bunya- [
61], Rhabdo- [
61], and Hepadnaviridae [
63] families. However, in all these cases their mechanism of antiviral action involved exhaustion of polyamine level in cells. In this study, to our great surprise inhibitory activity of the compounds was accompanied by increase in polyamine pool. The mechanism by which polyamines suppress HCV replication are not fully understood. On one hand, spermine and spermidine stimulate RNA polymerase activity of the HCV NS5B protein, however at the same time they inhibit RNA unwinding by the viral helicase [
64].
Suppression of enteroviruses was earlier also shown for DENSpm [
65]. Again, our study shows that these inhibitors also demonstrate anti-HCV activity and add APA to the list of antiviral agents. Moreover, we show that HCV replication can be inhibited by the inhibitor of polyamine oxidases MDL72.527 that was previously studied only for Ebola virus [
66].
Polyamines also support replication of viruses by ensuring the hypusination of eIF5A. KSAV [
47,
50], Coxsackie virus B3 [
67], vesicular stomatitis (VSV), influenza A, Zika and Chikungunya viruses [
68] increase levels of hypusinated eIF5A. This factor enhances translation of the Ebola genome [
69] and HIV transcription [
70]. Inhibitors of deoxyhypusine synthase and deoxyhypusine hydrolase also exhibit a wide spectrum of antiviral activity [
50,
57,
60,
68,
70]. Interestingly, neither of them had an anti-viral effect on HCV in our study.
One of most unexpected results of the study is the nonstandard response of Huh7.5 cells and especially the cells harbouring HCV replicon to the treatment with compounds that target polyamine-metabolizing enzymes such as DENSpm and especially DFMO. First, Huh7.5 cells demonstrated high resistance to DENSpm: this compound caused only moderate reduction of spermine and spermidine levels upon treatment, and the cells remained viable even upon treatment with 300 µM of the drug (
Figure S1). Second, the cells also demonstrated resistance to DFMO which is an irreversible inhibitor of ODC: at subtoxic concentrations this drug decreased intracellular ODC activity by two-fold only. Third, a treatment of cells containing the HCV replicon led to an unprecedented elevation of the levels of both spermine and spermidine. It could be speculated that the effect can be due either to enhanced polyamine derived from serum import from culture medium or by some nonstandard feedback mechanism by which the cells counteract polyamine depletion. Such an effect was previously described by J. Janne’s group that raised DFMO-resistant human and murine leukaemia cell lines by maintaining cells in the presence of subtoxic drug concentrations and then observed either multiplication of the ODC1 gene or its enhanced transcription [
71]. In the presence of DFMO this cell line enhanced ODC expression to counteract inactivation of the enzyme by the drug. Although we have not quantified ODC1 copy numbers in Huh7.5 cells with the HCV replicon, it cannot be excluded that ODC1 multiplication occurs during selection of the cells possibly mediated via HCV-enhanced ROS production [
29,
66].
Here we show that HCV decreases expression of ARGI and thus causes accumulation of its substrate arginine in the infected Huh7.5 cells. So far, the data on expression of Arginase 1 in the context of HCV infection have been discrepant. Several groups did not find any changes in Arg1 expression in liver samples of chronic hepatitis C virus patients without signs of steatosis [
72,
73], while the others observed increased staining of the enzyme in biopsy sections [
74]. However, Arg1 downregulation was also reported for Huh7.5 cells harbouring the full-length HCV replicon [
75]. Decreased expression of Arg1 and concomitant accumulation of arginine could be the feature of hepatocarcinoma cells during non-alcoholic steatohepatitis and metabolic syndrome [
76]. So, we cannot rule out that down-regulation of Arg1 during HCV expression can contribute to viral pathogenesis.
Cell metabolism is affected not only by the virus but by the culture medium. Almost all studies are performed in cell lines maintained in classical media (such as MEM, DMEM, RPMI, F12 etc) formulated in 1950s or early 1960s [
42]. Their recipes were to ensure rapid growth of cell biomass and longer period between replacement of conditioned medium with a fresh one. However, several lines of evidence have appeared during last decade that metabolism of cells maintained in classical medium sometimes does not mimic the processes
in vivo (summarised in [
42]). One of the most pronounced differences is addiction of various tumour cell lines on glutaminolysis when grown in DMEM or other “old” medium with no noticeable effect of antitumor/antiproliferative activity of a glutaminase 1 inhibitors
in vivo or in 3D cell cultures [
77,
78]. The other example is an inverted urea cycle in cells maintained in DMEM-F12 medium like the one used in our study: arginine is converted not into ornithine or citrulline but into argininosuccinate, albeit with different efficiency in different cell lines [
33]. Therefore, several groups recently developed media (HPLM, Plasmax) that resemble human blood plasma and showed “normalization” of the urea cycle [
79,
80]. So, we used Plasmax medium to verify the changes in cell metabolism in HCV-infected cells. Indeed, the key event, i.e. the suppressed expression of arginase 1, was consistent in case of both media.
Proline biosynthesis and catabolism may be not only the independent processes that regulate steady-state proline concentrations but also form a proline cycle [
81]. It is formed by conversion of the amino acid into Δ
1-pyrrolidine-5-caboxylate (P5C) in mitochondria by PRODH, export of this metabolite into cytoplasm with subsequent reverse transformation into Pro by Δ
1-pyrrolidine-5-carboxylate reductase 3 (P5CR3, P5CRL). This cycle both feeds oxidative phosphorylation in mitochondria by providing electrons from the PRODH-reduced flavin (FADH2) and supports nucleotide biosynthesis via oxidation of NADPH into NADP
+ by P5CRL. So, enhanced metabolic flux of proline and P5C may be a mechanism of activation of other metabolic pathways. However, upregulation of PRODH in the HCV-infected cells is not accompanied by changes in expression of proline biosynthetic enzymes, and of P5CRL in particular, thus excluding importance of proline cycle in regulation of the pentose phosphate pathway during HCV infection. Of note, PRODH expression is positively regulated by AMPK, p53, and PPARγ, and negatively by cMyc transcription factors. Since HCV is known to activate cMyc [
18,
82] and suppress p53 [
83] and AMPK signalling [
79], they are unlikely to mediate upregulation of PRODH during the infection. This points to PPARγ as the likely regulator of PRODH expression in HCV-infected cells.
Polyamines are synthesized from a non-proteinogenic amino acid ornithine which in turn can be produced either from arginine in the urea cycle or from glutamic semialdehyde (GSA) by ornithine aminotransferase (OAT). The latter is formed either via a non-enzymatic isomerization of P5C (i.e. from proline catabolism) or from glutamate by Δ
1-pyrrolidine-5-carboxylate synthase (encoded by the ALDH18A1 gene) (i.e. from glutaminolysis). Few papers suggest that neoplastic transformation may switch an origin of ornithine from arginine to GSA, although these data were obtained from non-liver cells [
84]. Since HCV activates both glutaminolysis [
18] and proline catabolism and suppresses conversion of arginine into ornithine (this study), it is tempting to speculate that this virus also reprograms routes of ornithine production. Although origins of ornithine were not accessed using flux analysis by mass-spectrometry using
13C-labelled ornithine and glutamate/proline, we used an inhibitor of OAT – L-canaline. However, this compound only slightly affected viability of HCV-infected cells (
Figure S1) and did not affect HCV replication levels thus not supporting our assumption.
Arginine:glycine amidinotransferase (GATM, AGAT) is an enzyme that catalyses an alternative arginine-to-ornithine conversion pathway. Its second product, guanidinoacetate is a precursor for the biosynthesis of creatine and creatinine by GAMT. It is generally accepted that the first reaction takes place in kidney, whereas the second – in the liver. However, GATM mRNA levels in the liver in hepatocarcinoma Huh7.5 cells as well as in nontumor hepatocyte-like HepaRG cells are at least six-fold higher than those of arginase 1 [
85]. So, we cannot exclude that in HCV-infected cells ornithine is synthesized via a GATM-mediated reaction.
Agmatinase is the least studied enzyme of polyamine biosynthesis in mammalian cells. In prokaryotic and plant and fungi cells agmatinase produces ornithine from agmatine generated from arginine by arginine decarboxylase (ADC). Since mammals were thought not to encode ADC in its genome, almost no attempts to identify arginase in mammalian cells were made. In 2002 this gene was identified in HepG2 cells and upregulation of its transcription in the context of HBV infection was reported [
86]. Later, ADC was also discovered in mammalian brain cells [
87]. However, biological significance of agmatinase in mammals remains obscure, since the its substrate agmatine can originate either from gut biota or from food, as ADC has very low expression levels in a majority of tissues. Nevertheless, we included this gene into our analysis and demonstrated absence of its regulation in HCV-infected cells.
Author Contributions
Conceptualization, A.K., S.K, B.B. and A.I.; methodology, C.B., A.K., S.K, B.B. and A.I.; formal analysis, B.B. and A.I.; investigation, N.Z., O.K., O.S., J.M., S.D., D.Y., V.V.-E., L.M., B.G., O.I., I.K., M.G., B.R. and A.I.; resources, C.B., A.K., S.K., B.B. and A.I.; data curation, N.Z., O.K., O.S., J.M., D.Y., L.M., B.G., O.I., I.K., C.B., B.R., B.B. and A.I., ; writing—original draft preparation, O.S., B.B. and A.I.; writing—review and editing, N.Z., O.K., O.S., J.M., S.D., D.Y., V.V.-E., L.M., B.G., O.I., I.K., M.G., C.B., B.R., A.K., S.K., B.B. and A.I.; visualization, A.I.; supervision, B.B. and A.I.; project administration, B.B. and A.I..; funding acquisition, S.K., B.B. and A.I. All authors have read and agreed to the published version of the manuscript.