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. 2021 Apr 23;16(4):e0250605. doi: 10.1371/journal.pone.0250605

Low efficacy of recombinant SV40 in Ugt1a1-/- mice with severe inherited hyperbilirubinemia

Xiaoxia Shi 1,*, Giulia Bortolussi 2, Lysbeth ten Bloemendaal 1, Suzanne Duijst 1, Andrés F Muro 2, Piter J Bosma 1
Editor: Chen Ling3
PMCID: PMC8064607  PMID: 33891666

Abstract

In contrast to AAV, Simian Virus 40 (rSV40) not inducing neutralizing antibodies (NAbs) allowing re-treatment seems a promising vector for neonatal treatment of inherited liver disorders. Several studies have reported efficacy of rSV40 in animal models for inherited liver diseases. In all studies the ubiquitous endogenous early promoter controlled transgene expression establishing expression in all transduced tissues. Restricting this expression to the target tissues reduces the risk of immune response to the therapeutic gene. In this study a liver specific rSV40 vector was generated by inserting a hepatocyte specific promoter. This increased the specificity of the expression of hUGT1A1 in vitro. However, in vivo the efficacy of rSV40 appeared too low to demonstrate tissue specificity while increasing the vector dose was not possible because of toxicity. In contrast to earlier studies, neutralizing antibodies were induced. Overall, the lack of a platform to produce high titered and pure rSV40 particles and the induction of NAbs, renders it a poor candidate for in vivo gene therapy.

Introduction

Crigler-Najjar syndrome (CNs), severe unconjugated hyperbilirubinemia, results from the deficiency of UGT1A1, the enzyme that catalyzes the conjugation of unconjugated bilirubin (UCB) with UDP-glucuronic-acid [1]. The conjugation of the hydrophobic UCB results in water soluble bilirubin glucuronides that can be excreted into bile [2]. If not treated effectively the severe form of CNs is lethal in childhood due to UCB accumulation to levels that cause irreversible brain damage [3]. Both lethality and brain damage can be prevented by intensive phototherapy, a cumbersome treatment that becomes less effective overtime [4, 5]. Most patients therefore do need a liver transplant at some point in their life, a highly invasive treatment with several challenges, like the need for re-transplantation, toxicities and adverse effects associated with long-term immunosuppression [6]. In addition, because of the limited availability of donor organs the patients are at risk to develop brain damage while on the waiting list. Novel therapies are therefore warranted, and recent clinical studies for other liver diseases, like hemophilia B show the potential of liver directed gene therapy [7].

The efficacy of several methods for liver directed gene therapy has been investigated for CNs in UGT1A1 deficient rodent models. Non-viral gene therapy approaches using lipophilic nanoparticles do show potential for delivery of mRNA resulting in effective but transient reduction of serum bilirubin levels in a Ugt1a1 deficient rat [8]. For delivery of DNA the efficiency of this non-viral method still is much lower compared to viral vectors. In addition, several viral vectors, such as rSV40 [9], Adenoviral [10], Lentiviral [11] and Adeno Associated Viral (AAV) [12] vectors and transposons [13] have been tested in the rat model, while only AAV vectors were tested in Ugt1a1 deficient mice [1416]. Of all these viral vectors, AAV vectors are the most advanced and are now tested in clinical trials (NCT03466463 and NCT03223194).

A major challenge for AAV mediated liver directed gene therapy is the presence of pre-existing Neutralizing Antibodies (NAbs) in a significant percentage of the CN patients [17]. These NAbs will block hepatocyte transduction hampering effective treatment efficacy. The induction of a high titer of NAbs upon the first AAV administration blocking re-treatment with this vector, is another important hurdle [18]. Re-treating a patient may be required upon loss of correction due to liver growth, when treating juveniles, or due to drug or alcohol induced liver damage, or in patients receiving a sub-optimal vector dose such as those participating in the safety and efficacy studies [19].

In this respect, rSV40 vectors with a low pre-existing immune prevalence seem a promising option [20, 21]. Also, the reported absence of a cellular response and absence of neutralizing antibodies upon repeated SV40 administration, render this vector a promising candidate for liver directed gene therapy [22, 23]. The recently developed novel production cell line ensures production of batches that are free of large T antigen, a prerequisite for clinical application of this vector [24].

A potential problem of clinical use of rSV40 vectors is the ubiquitous nature of the endogenous SV40 early promoter. This promoter has been used widely in expression studies and is suitable to provide expression of a transgene in many different cell types [25, 26]. For in vivo application, this ubiquitous nature is a disadvantage because expression of the therapeutic UGT1A1 protein, for instance in antigen presenting cells, could increase the risk of an adaptive immune response. Restricting the expression of UGT1A1 to the hepatocytes will reduce this risk significantly [12].

In this study an rSV40 vector with a liver specific promotor to drive the expression of a reporter gene and the therapeutic hUGT1A1 gene was developed and its specificity, efficacy and immunogenicity was tested in vitro and subsequently in vivo in a Ugt1a1 deficient mouse model.

Material and methods

Production of viral vectors

To generate liver specific rSV40 vectors a hybrid liver specific promoter (HLP) [27, 28] was inserted between the endogenous SV40 early promoter and the luciferase or hUGT1A1 cDNA, using the ClaI and SpeI sites present in Pam310 from AMARNA [24] and rSV-hUGT1A1 [29]. rSV-Luc and rSV-HLP-Luc vectors were produced in using co-transfection with a Cre-recombinase expressing plasmid as reported previously [29] or by removal of the bacteria backbone with Not-I, gel purification and re-ligation [24]. 3 and 6 days after transfection, the medium was collected and viral vector was concentrated using a spin filter (100 KD, Lot R9NA92290, Merck Millipore Ltd, Ireland). The rSV-hUGT1A1 and rSV-HLP-hUGT1A1 vectors used in vitro and in vivo studies were produced in Super-Vero cells by AMARNA Therapeutics (Leiden, The Netherlands) as described [24].

Transfection, transduction and Western blot analysis

104 cells per well were seeded in Costar white 96 well plates (ref 3610, corning incorporated Kennebunk, ME, USA). The next day cells were transfected using 40 ng of plasmid and 80 ng of PEI/well or transduced with rSV40 vector (400 vg/cell). Luciferase expression was determined 48 hours after transfection or 2–5 days after transduction by adding 100 μl lysis buffer with substrate (ONE-Glo™ Luciferase, Promega), and after a 15 minutes incubation at room temperature, luminescence was measured in the synergy HT, measurement time was 1 second/well. UGT1A1 expression was determined using western blotting at 2 days after transfection or 2–5 days after transduction. The cells were washed once with PBS and lysed with RIPA (50 mM Tris PH 8.0, 150 mM NaCl, 1% Triton X-100, 0.5% Na-deoxycholate, 0.1% SDS) buffer containing Protease-Inhibitor (1:100 dilution) (Roche, Germany) for 20 minutes. 30 μg of cell lysate was loaded on a 10% Acrylamide gel and blotted to PVDF membrane (semi-dry blotting, 1 hour, 0.05 mA per gel). A monoclonal antibody towards UGT1A1 (1:700 dilution) followed by a goat anti-mouse HRP labeled (Dakoplast, the Netherlands) (1: 5,000) was used to detect UGT1A1 as described previously [12]. An anti-UGT1 rabbit polyclonal antibody (Santa Cruz Biotechnology, Santa Cruz, CA) [28] was used to detect UGT1A1 expression in liver of Ugt1a1 deficient mice treated with rSV40 and for comparison, treated with rAAV8 and in wild type mice.

Animal study

FVB/NJ background Ugt1a -/- mice were treated with phototherapy (PT) until weaning and housed in a temperature-controlled environment with 12/12-hour light-dark cycle, with a standard diet and water ad libitum in the animal house unit [30]. The Ugt1a-/- mice have a one nt deletion in exon 4 of the Ugt1a locus causing a shift in the reading frame introducing a stop codon immediately after the deletion. Due to the absence of the co-substrate binding and transmembrane domains the truncated enzyme is inactive, as published previously [14]. All animal protocols were approved by the Animal Welfare and Ethics Committee of the International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy. At 60 days after birth, the mice were randomized and a single administration of rSV-hUGT1A1 (n = 7) or rSV-HLP-hUGT1A1 (n = 8) or a PBS injection control (n = 7) by tail vein injection, 3 mice with dose of 2x1011 vg/kg, and 4–5 mice with dose of 1.7x1012 vg/kg, respectively. Intravenous of rSV40 was performed under isoflurane anesthesia. No surgical or other procedures requiring anesthesia were performed. Animals were treated by researchers trained for animal care and monitored daily for general appearance. No signs of stress (lack of appetite, body weight loss, hair loss, stereotypic or aggressive behavior, etc.) or macroscopic alterations of vital functions were observed throughout the experimental phase. Blood was sampled at 1, 3, 5 and 8 weeks after vector administration by facial vein puncture and collected in EDTA-containing tubes. At the time of sacrifice mice were anesthetized with 5% isoflurane, cardiac puncture was performed to obtain blood samples, and sacrificed by cervical dislocation. Plasma was obtained by centrifuging at 400 g for 15 min at room temperature, and stored at -80°C for further analysis. Total bilirubin determination in plasma was performed following the instructions of the supplier (BQ KITS) as previously described [30]. Organs were directly frozen in liquid nitrogen and stored at -80°C for further analysis.

Determination of rSV40 neutralizing antibodies

SV40 NAbs titer in mice plasma were determined using the protocol reported for determination of the NAbs titer towards AAV, using serial dilution of plasma in FCS after complement inactivation by incubation at 56°C for 30 minutes [31]. Briefly, 104 COS-1 cells/well were seeded in costar white 96 well plates, in Dulbecco’s modified Eagle’s medium (DMEM) (Lonza/Westurg) containing 10% fetal calf serum (FCS), 100 U/ml penicillin/streptomycin (Invitrogen) and 20 mM L-Glutamine (Lonza/Westurg) and cultured overnight at 37°C in 5% CO2. The next day plasma samples were diluted in 7 steps on a half-log scale in FCS. Diluted samples were incubated with an equal volume of 2.5x109 vg/ml rSV-Luc at 37°C for one hour. The maximal transduction control, set to 100%, consisted of rSV-Luc incubated with FCS only, the negative control consisted of FCS diluted with medium; both were incubated under the same conditions. After this pre-incubation, 7.5 μl per well of each dilution was added to the COS-1 cells in triplicate. Positive and negative controls were performed in six-fold. The cells were incubated at 37°C, 5% CO2, and after two days the luciferase expression was determined using ONE-Glo™ Luciferase assay system (Promega), according to manufacturer’s protocol.

Anti-UGT1A1 antibody assay

An indirect ELISA approach was used to detect the anti-UGT1A1 IgG in the mice serum as previously described [32]. Per well of a 96 ELISA plate, 50 μl of recombinant human UGT1A1 protein (Bio Connect) (1 μg/ml) in coating buffer (15 mM Na2CO3, 35 mM NaHCO3) was added and incubated overnight at 4°C. The next day the UGT1A1 coating solution was replaced with 100 μl of blocking buffer, 1% gelatine in phosphate-buffered saline (PBS). After 1 hour, the blocking was removed and 50 μl serial dilutions of heparin plasma samples diluted in washing buffer were added to the wells and incubated for 1,5 hours at room temperature. After 3 washings with washing buffer 0.05% Tween-20 in PBS, UGT1A1 binding mouse immunoglobulins were detected with horseradish peroxidase (HRP) conjugated anti-mouse IgG 1:1000 dilution in conjugation buffer containing 4/5 blocking buffer and 1/5 washing buffer followed by o-phenylenediamine (Sigma) conversion.

Statistical analysis

Statistical significance was determined using GraphPad Prism 8.3.0 (GraphPad Software, La Jolla, CA).

Results

Insertion of a liver-specific promoter in rSV40 increases transcriptional activity in liver-derived cells

To restrict the expression provided by an SV40 vector to the liver, a liver specific promoter was inserted between the SV40 early promoter and the luciferase gene generating the rSV-HLP-Luc plasmid. In both human hepatoma cell lines, Huh7 and HepG2, transfection of the rSV-HLP-Luc plasmid provided a higher luciferase expression than the construct containing only the endogenous SV40 promoter, rSV-Luc (Fig 1A and 1B). In non-hepatoma cell lines, COS-1 and HEK293T, the latter was clearly more active (Fig 1C and 1D). This indicates that the liver-specific promoter is functional and significantly increases transcriptional activity in liver-derived cells. To investigate if the tissue-specific promoter remains functional in the viral vector, both plasmids were used to produce recombinant SV40 vector. The hepatoma and non-hepatoma cell lines were transduced using 400 vg/cell of rSV40, and luciferase expression was determined at 2–5 days after transduction. In both hepatoma cell lines transduced with the rSV-HLP-Luc vector, the luciferase intensity was significantly higher than in cells transduced with the rSV-Luc (Fig 2A and 2B). In contrast, in both non-hepatoma cell lines, the rSV-Luc vector provided a higher luciferase intensity (Fig 2C and 2D).

Fig 1. Insertion of a liver-specific promoter in rSV40-Luc plasmid enhances specific expression.

Fig 1

HepG2 (A), Huh7 (B), COS-1 (C), or HEK293T (D) cells were transfected with 40 ng plasmid/104 cells in a well of a 96 well plate, of rSV-Luc, rSV-HLP-Luc or rSV-GFP, respectively in 6 fold. 48 hours after transfection, luciferase expression was quantified by determining the luminescence intensity. * p <0.05, ** p <0.01, **** p<0.0001. Data represent the mean ± SD. Statistical significance was determined by One-way ANOVA test.

Fig 2. Insertion of a liver specific promoter in rSV40 vectors enhances specific expression of reporter gene.

Fig 2

400 vg/cell of rSV40-Luc or rSV40-HLP-Luc were added to 104 cells of HepG2 (A), Huh7 (B), COS-1 (C), or HEK293T (D) in a well of a 96 well plate (n = 3). After 2–5 days the luciferase expression was quantified by measuring the luminescence using the synergy HT machine. * p <0.05, ** p <0.01, *** p<0.001. Data represent the mean ± SD. Statistical significance was determined by Two-way ANOVA test.

To confirm that insertion of a liver-specific promoter in SV40 gene delivery vector also can improve expression of a therapeutic gene in hepatoma cells, rSV-hUGT1A1 and rSV-HLP-hUGT1A1 vectors were generated and used to transfect human hepatoma and non-hepatoma cell lines. The UGT1A1 expression was measured by western blot at 48 hours after transfection and demonstrated that presence of the HLP resulted in a significant increase in HepG2 cells (Fig 3A and 3B). In Huh7 cells, the difference in UGT1A1 expression between both vectors did not reach significance due to large variation. Again in non-hepatoma cell line HEK293T cells, the expression of HLP-driven UGT1A1 was significantly lower compared to the cells transfected with rSV-hUGT1A1. This increased transcriptional activity in liver-derived cells induced by presence of the HLP promoter was confirmed upon transduction of these cell lines with the rSV vector generated from these plasmids (Fig 3C and 3D).

Fig 3. Insertion of a liver specific promoter in rSV40 provides specific expression of a therapeutic gene.

Fig 3

(A) 105 cells of HepG2, Huh7, COS-1, or HEK293T cells were transfected with 1 μg of rSV-hUGT1A1 or, rSV-HLP-hUGT1A. 48 hours later, UGT1A1 expression was determined by western blotting and quantified normalizing to calnexin, a membrane protein (B). (C) 105 cells of Huh7 and COS-1 cells were transduced with 400 vg/cell of rSV-hUGT1A or rSV-HLP-hUGT1A1. After 2–5 days the cells were lysed and UGT1A1 expression was detected by western blotting and quantified by western blotting normalized to calnexin. All experiments were repeated 3–5 times. * p <0.05, ** p <0.01, *** p<0.001, **** p<0.0001. Data represent the mean ± SD. Statistical significance was determined by two-tailed Student t test.

In vivo, the poor efficacy of rSV vectors is not improved by the insertion of a liver specific promoter

Upon showing that a liver specific promoter enhances transgene expression in hepatocyte-derived cells, compared to other cell types, the efficacy of both vectors was studied in vivo. 2x1011 vg/kg rSV-hUGT1A1 or rSV-HLP-hUGT1A1 were injected in the tail vein of 60-day-old Ugt1a -/- mice. Upon injection the effect on serum bilirubin was monitored overtime. This resulted in at some time points significant, albeit a minor and far from therapeutic, decrease of serum bilirubin in mice injected with rSV-hUGT1A1 (Fig 4). In the mice treated with the liver specific rSV-HLP-hUGT1A1, the serum bilirubin levels were comparable to that in untreated controls, indicating that inserting the hepatocyte specific promoter does not improve in vivo efficacy of this vector. A possible explanation for the apparent lower in vivo efficacy of the rSV-HLP-hUGT1A1 compared to the rSV-hUGT1A1 vector could be a lack of liver tropism of the SV40 vectors, since the latter would result in transduction of many tissues upon injection into a peripheral vein. The bio-distribution of SV40, determined by the ratio between the human UGT1A1 gene carried by the vector and the mouse β-actin gene, showed presence of rSV vector genomes in several tissues. Although in several animals these levels were below detection, the bio-distribution results did not support a specific liver tropism for rSV40 upon injection into a peripheral vein (Table 1). Subsequently, in a higher dose of 1.7x1012 vg/kg rSV-hUGT1A1 and of rSV-HLP-hUGT1A1 was tested (Fig 4). At the time of injection, the serum bilirubin levels in this experiment were lower due to the natural variation occurring in this model. Administration of the higher vector dose did not result in therapeutic correction albeit that after one week the levels in the mice receiving rSV-HLP-hUGT1A1 did have lower serum level. The hUGT1A1 expression in liver was determined by western blot showing signals in mice treated with rSV-hUGT1A1 or rSV-HLP-hUGT1A1 comparable to that in PBS treated Ugt1a1 deficient mice (Fig 4D). In contrast administration of a 10 fold lower dose of AAV8 vector, containing hUGT1A1 behind the same liver specific promoter (AAV-L), did show presence of hUGT1A1 while treatment with a comparable dose of this vector (AAV-H), showed a very prominent presence of UGT1A1. Two of the mice injected with rSV-hUGT1A1 died within 24 hours after the injection.

Fig 4. Insertion of liver specific promoter does not improve the low efficacy of rSV40 vectors in vivo.

Fig 4

(A) 60-day-old Ugt1a -/- mice were treated with rSV-hUGT1A1, rSV-HLP-hUGT1A1, or PBS via tail vein injection. (B-C) Total serum bilirubin (mg/dL) was monitored overtime until week 8 after injection. (D) Presence of UGT1A1 in Ugt1a1 deficient mice treated with 1x1011 vg/kg of AAV8-hUGT1A1 (AAV L), PBS, 1.7x1012 vg/kg of rSV-hUGT1A1, 1.7x1012 vg/kg of rSV-HLP-hUGT1A1, or 1x1012 vg/kg of AAV8-hUGT1A1 (AAV H), and in a non-treated wild type mouse (WT). Calnexin was used as loading control on the same membrane. Data represent the mean ± SD. Statistical significance was determined by Two-way ANOVA with Dunnett’s multiple comparison test.

Table 1. Bio-distribution of rSV vector genomes.

Treatment Liver Spleen heart colon jejunum muscle brain
SV-hUGT1A1 mouse 1 UD 4.4E-03 UD 3.4E-03 UD UD UD
SV-hUGT1A1 mouse 2 UD UD UD 4.0E-03 UD 3.4E-03 8.3E-03
SV-hUGT1A1 mouse 3 UD 3.9E-03 7.0E-03 3.3E-03 UD 2.2E-03 UD
SV-HLP-hUGT1A1 mouse 4 3.3E-03 UD UD 4.2E-03 4.4E-03 UD UD
SV-HLP-hUGT1A1 mouse 5 3.7E-03 4.5E-03 UD UD UD 4.3E-03 6.6E-03
SV-HLP-hUGT1A1 mouse 6 UD UD UD 4.9E-03 2.9E-03 4.1E-03 UD

Note: the data represents the value of 2x(UGT1A1/B-actin), UD represents undetectable.

Intravenous injection of rSV40 does induce a neutralizing antibody response

Absence of a humoral response towards rSV40 would allow repeated administrations of this vector. Retreatment in case of loss of efficacy or upon sub-optimal dosing would be a major advance for rSV40 compared to AAV and Adenoviral vectors. To determine the presence of neutralizing antibodies COS-1 cells were transduced with rSV-Luc vector pre-incubated with serum from naïve mice or mice injected with rSV40. After 48 hours transduction efficiency was determined by measuring the luciferase expression in COS-1 cells. Pre-incubation with serum from mice injected with rSV40 did impair luciferase expression, indicating that intravenous administration of rSV40 does induce neutralizing antibodies towards this vector in vivo. Comparing to the mice before administration, the anti-SV40 neutralizing antibody titer increased in rSV40 treated mice but not in PBS treated ones (Fig 5). No humoral response towards the encoded hUGT1A1 was detectable irrespective of the presence of the hepatocyte-specific promoter restricting hUGT1A1 expression to the liver or to several tissues when its expression was controlled by the ubiquitous SV40 early promoter (S1 Fig).

Fig 5. Intravenous injection does induce neutralizing antibodies towards rSV40.

Fig 5

60-day-old Ugt1a -/- mice were treated with a lower dose of 2x1011 vg/kg of rSV-hUGT1A1 vector (n = 3), or rSV-HLP-hUGT1A1(n = 3), and a higher dose of 1.7x1012 vg/kg of rSV-hUGT1A1 vector (n = 4), or rSV-HLP-hUGT1A1(n = 5) via tail vein injection. Serum samples at 8 weeks after vector administration were tested for presence of NAbs towards rSV40 vectors using an in vitro transduction assay. NAbs titers are expressed as the highest serum dilution that inhibited AAV transduction by ≥ 50% compared with the control without serum. Pre represents before vector injection. Data represent the mean ± SD. Statistical significance was determined by Ordinary one-way ANOVA with Dunnett’s multiple comparison test.

Discussion

The data reported in this study show that insertion of a liver-specific promoter results in more specific expression of transgenes encoded by rSV40 vectors in vitro. The insertion of a hepatocyte specific promoter did not improve the efficacy of the rSV40 vector in vivo. A dose of 1.7x1012 vg/kg of these vectors did not result in a relevant reduction of serum bilirubin levels. Intravenous administration of both rSV40 vectors did result in the induction of neutralizing antibodies in all animals, rendering effective retreatment with this vector most unlikely.

In vivo gene therapy using rSV40 vector has been reported for unconjugated hyperbilirubinemia [9]. A replication-deficient rSV40 mediated a long-term amelioration of jaundice in Gunn rats. In that study, serum bilirubin levels were lowered by 35% upon a single injection, while in this study the reduction using a similar rSV40 vector in a UGT1A1 deficient mouse model is only about 10%. The different administration route, peripheral vein versus portal vein, may explain the difference in correction since upon peripheral vein injection no clear liver tropism for rSV40 was seen. The bio-distribution showed transduction of many tissues by rSV40 albeit all at a low level (Table 1). The lack of a liver tropism can also explain the better performance of the non-hepatocyte specific rSV40 vector since UGT1A1 expression in non-hepatic tissues also provides effective conjugation of UCB [15, 33, 34]. Administration into a peripheral vein of AAV8, a vector that does display a clear liver tropism, provides a much more efficient correction. A dose of 1x1011 vg/kg results in therapeutic correction of serum bilirubin levels [28] and in contrast to both rSV40 vectors, in clearly detectable levels of UGT1A1 in the liver (Fig 4D). In the Gunn rat, at least three repeated administrations of 3x109 I.U./ rat of 200–300 g, resulting in a total dose of 3x1010 I.U./kg of rSV40 were needed to provide a reduction of serum bilirubin by 70% [9]. In this animal model, AAV does provide therapeutic correction upon peripheral administration [28]. A dose of 5x1012 AAV8 vg/kg comparable to 2x108 Huh7 transducing AAV8 units, results in sustained and complete normalization of serum bilirubin [35]. These data indicate that the liver transduction efficacy of AAV vectors is higher than that of rSV40 vectors. This difference in liver transduction efficacy between AAV and SV40 vectors in rats has also been observed by others [36]. In that study a dose of 3.4x109 vg of AAV1-IGF1 provided a comparable expression of IGF-1 as 1x1011 vg of rSV40-IGF-1 per rat, which is a 30 fold higher dose. Although, comparing doses of different viral vectors is complicated by different titration methods, the higher efficacy seen with AAV vector renders that vector more suitable for in vivo gene therapy for inherited liver disorders. Another major hurdle for rSV40 vectors is the absence of a production and purification protocol to generate sufficiently high titered vector batches, which rendered testing the therapeutic efficacy of higher rSV40 vector doses in vivo is not possible because of toxicity. The cause of the toxicity seen in two out of four mice upon injection of the high dose of rSV-hUGT1A1 suggest the presence of impurities in our vector batch.

In the Gunn rat, repeated injections with rSV-hUGT1A1 did not inhibited liver transduction of rSV40-HBs antigen [9]. This indicated that rSV40 did not induce neutralizing antibodies. Others also reported the absence of NAbs upon injection of rSV40 [22]. Absence of a NAbs response would be a major advantage for rSV40 compared to AAV since it renders effective retreatment feasible upon loss of efficacy. Using an in vitro NAbs assay, comparable to that used to test for a response towards AAV, we observed the induction of an immune response that prevented transduction in vitro. At 8 weeks after rSV40 administration, serum from animals treated with rSV40 completely prevented the transduction of COS-1 cells. The observation that in Gunn rats re-administration was effective may be explained by the high dose of rSV40 administered locally to the liver via the portal vein. Presence of NAbs against AAV can, at least in part, be overcome by a high dose of vector or by co-administration of empty particles as a decoy [37]. Upon portal delivery the amount of NAbs present locally may not be sufficient to block the liver transduction completely. Although we cannot exclude that the presence of impurities in the vector batches used may have had an adjuvant effect resulting in a more prominent immune response seen in this study. However, the production system used in these studies is very similar to that used in those Gunn rat studies rendering such an explanation less probable.

Presence of pre-existing immunity towards viral gene therapy vectors is a challenge for AAV mediated in vivo gene therapy for liver disorders. The presence of NAbs renders about 30% of the Crigler-Najjar patients screened not eligible for the ongoing trial [17]. In this respect, the lower pre-existing immunity towards rSV40 is an advantage. In the general population seroconversion towards SV40 immunity is observed at a young age [38]. Most studies report about 10 to 25% of all subject have antibodies to this vector. The percentage of the population that has neutralizing antibodies towards SV40 is much lower [21, 39]. Although this shows that pre-existing immunity towards rSV40 is clearly lower than that reported for AAV, these studies do report presence of neutralizing antibodies in the normal healthy population. This presence supports our finding that injection of rSV40 vectors does induce neutralizing antibodies, which argues against the possibility of effective re-administration indicating this remains a hurdle for rSV40 vector also.

Conclusion

Our data indicate that a platform to generate high titered pure rSV40 vector batches is needed to support the potential use of rSV40 as an additional gene therapy vector to treat inherited liver diseases. The current vector batches have, compared to for instance AAV, a much lower transduction efficacy and lack the previously reported immune privilege could not be reproduced. Presently, the only advantage of rSV40 is the lower pre-existing immunity towards this vector in the general population.

Supporting information

S1 Fig. Absence of antibodies towards hUGT1A1 in serum of mice treated with rSV hUGT1A1 or rSV-HLP-hUGT1A1.

60-day-old Ugt1a-/- mice were treated with 2x1011 vg/kg of rSV-hUGT1A1 vector (n = 3), or rSV-HLP-hUGT1A1 (n = 3) via tail vein injection. At 8 weeks after vector administration the level of anti-hUGT1A1 IgG in serum was determined. Data represent the mean ± SD.

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S1 Raw images

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Acknowledgments

We thank AMARNA Therapeutics for the production of SV-hUGT1A1 and SV-HLP-hUGT1A1 viral vector batches used in vivo.

Data Availability

All relevant data are within the paper and its Supporting Information files.

Funding Statement

Xiaoxia Shi is recipient of a fellowship of the China Scholarship Council (CSC).

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Decision Letter 0

Chen Ling

22 Dec 2020

PONE-D-20-33243

Lack of purification method to produce pure high tittered batches, renders rSV40 a poor candidate for in vivo liver directed gene therapy

PLOS ONE

Dear Dr. Shi,

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PLOS ONE

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Reviewer #2: Yes

**********

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**********

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Reviewer #2: Yes

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Reviewer #1: This paper describes simian virus 40 (rSV40) is difficult to serve as candidate vector for in vivo gene therapy, due inefficient production and induction of immune neutralization. The study provides a novel sight that rSV40 triggered neutralizing antibody production, inconsistent with previous reports. Most of results are solid and convincing. However, some concerns and more experiments are need to further verify.

1. In vitro, authors used the human liver-derived cell lines (Huh7 and HepG2) to test the activation of hybrid liver specific promoter, they should use mouse liver-derived cell lines to test the promoter activity as well.

2. Authors are necessary to detect the expression of hUGT1A1 in mRNA and protein levels in liver from mice injected by rSV40 vectors.

3. In figure 4 and 5, statistical analysis methods should be included in figure legends.

4. There is no data description the “lack of purification method to produce pure high tittered batches” in title, hence the title needs to be amended.

5. Authors needs to present some data about the Ugt1a gene being knocked out in mice.

6. English/grammar should be improved for clarity, e.g. in 173-174 line, wass should be corrected to was.

Reviewer #2: This manuscript basically reported negative results. The reviewer appreciated the hard work and the authors’ scientific integrity. It is not clear whether the same viral vectors were used for in vitro and in vivo experiments. The expression of transgene in the liver should be detected by Western blot.

Minors,

Line 44, why there is only one sub-title for Introduction?

Line 204, rSV40 should be rSV.

**********

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Reviewer #1: No

Reviewer #2: Yes: Chen Ling

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Attachment

Submitted filename: Review-PONE-D-20-33243.docx

PLoS One. 2021 Apr 23;16(4):e0250605. doi: 10.1371/journal.pone.0250605.r002

Author response to Decision Letter 0


1 Feb 2021

Dr. P. J. Bosma

Amsterdam University Medical Centers

Tytgat Institute for Liver Research

Meibergdreef 69

1105 BK Amsterdam

The Netherlands

Dr. Joerg Heber

Editor-in-Chief

PLOS ONE

February 1st 2021

Dear dr. Joerg Heber,

We are grateful for your potential interest in our manuscript entitled manuscript “Lack of purification method to produce pure high tittered batches, renders rSV40 a poor candidate for in vivo liver directed gene therapy (ID: PONE-D-20-33243)”. We thank the reviewers for their comments and suggestions to improve our manuscript. A manuscript with the tracked changes in red and a clean version are submitted. Please find our point-by-point response below.

Yours sincerely,

Xiaoxia Shi

Dr. Piter Bosma

Journal Requirements:

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2. Thank you for including your ethics statement:  "Mice were maintained in the International Centre for Genetic Engineering and Biotechnology animal house unit. All animal studies were approved by the local ethical committee. ".   

Please amend your current ethics statement to include the full name of the ethics committee that approved your specific study.

For additional information about PLOS ONE submissions requirements for ethics oversight of animal work, please refer to http://journals.plos.org/plosone/s/submission-guidelines#loc-animal-research  

Once you have amended this/these statement(s) in the Methods section of the manuscript, please add the same text to the “Ethics Statement” field of the submission form (via “Edit Submission”).

Response: we have amended the ethics statement according to the requirement in the manuscript.

Line 122-124: All animal protocols were approved by the Animal Welfare and Ethics Committee of the International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.

3. In your Methods section, please provide additional information on the animal research and ensure you have included details on: (1) methods of sacrifice (2) methods of anesthesia and/or analgesia, and (2) efforts to alleviate suffering.

Response: According to the requirements, we have added the details in the manuscript.

Line 127-134: Intravenous of rSV40 was performed under isoflurane anesthesia. No surgical or other procedures requiring anesthesia were performed. Animals were treated by researchers trained for animal care and monitored daily for general appearance. No signs of stress (lack of appetite, body weight loss, hair loss, stereotypic or aggressive behavior, etc.) or macroscopic alterations of vital functions were observed throughout the experimental phase. Blood was sampled at 1, 3, 5 and 8 weeks after vector administration by facial vein puncture and collected in EDTA-containing tubes. At the time of sacrifice mice were anesthetized with 5% isoflurane, cardiac puncture was performed to obtain blood samples, and sacrificed by cervical dislocation.

4. PLOS ONE now requires that authors provide the original uncropped and unadjusted images underlying all blot or gel results reported in a submission’s figures or Supporting Information files. This policy and the journal’s other requirements for blot/gel reporting and figure preparation are described in detail at https://journals.plos.org/plosone/s/figures#loc-blot-and-gel-reporting-requirements and https://journals.plos.org/plosone/s/figures#loc-preparing-figures-from-image-files. When you submit your revised manuscript, please ensure that your figures adhere fully to these guidelines and provide the original underlying images for all blot or gel data reported in your submission. See the following link for instructions on providing the original image data: https://journals.plos.org/plosone/s/figures#loc-original-images-for-blots-and-gels.

In your cover letter, please note whether your blot/gel image data are in Supporting Information or posted at a public data repository, provide the repository URL if relevant, and provide specific details as to which raw blot/gel images, if any, are not available. Email us at plosone@plos.org if you have any questions.

Response: We have provided the original underlying images for all blot reported in our manuscript with the name of S1_raw_images.

5. Thank you for stating the following in the Acknowledgments Section of your manuscript:

"Xiaoxia Shi is recipient of a fellowship of the China Scholarship Council (CSC)."

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Response: We have deleted the sentence ‘Xiaoxia Shi is recipient of a fellowship of the China Scholarship Council (CSC)’ in the Acknowledgments section and want to include this in the Funding Statement.

6. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

Response: we have added the results as supplemental figure with the name of S1 Fig.


Reviewers' comments:


Reviewer #1: This paper describes simian virus 40 (rSV40) is difficult to serve as candidate vector for in vivo gene therapy, due inefficient production and induction of immune neutralization. The study provides a novel sight that rSV40 triggered neutralizing antibody production, inconsistent with previous reports. Most of results are solid and convincing. However, some concerns and more experiments are need to further verify.

1. In vitro, authors used the human liver-derived cell lines (Huh7 and HepG2) to test the activation of hybrid liver specific promoter, they should use mouse liver-derived cell lines to test the promoter activity as well.


Response: We agree that in view of the poor efficacy in vivo, showing that the promoter used is active in mouse hepatocytes is relevant. Although we have not tested this promoter in mouse hepatoma cells in vitro, we have used it activity of this promoter has been demonstrated in vivo in mouse liver. In AAV vectors this promoter provides the expression of UGT1A and human UGT1A1 in mouse liver upon systemic injection. Since this is indeed relevant we inserted the references to these previously published studies. The reference 27 and 28.


2. Authors are necessary to detect the expression of hUGT1A1 in mRNA and protein levels in liver from mice injected by rSV40 vectors.


Response: Showing mRNA expression is indeed a final prove of the expression from these constructs. We have determined mRNA expression using qPCR in the liver of the treated animals. In contrast to our studies using AAV, the mRNA levels in mice treated with the rSV40 vector were very low. Although a signal was detected in some of the treated mice, the levels were too low for reliable quantification using this very sensitive method, again confirming that rSV40 vectors appear very in-efficient for liver transduction in vivo.


3. In figure 4 and 5, statistical analysis methods should be included in figure legends.

Response: We do apologize for this omission and thank the reviewer, and have included the statistical analysis methods in figure 4 and 5.



4. There is no data description the “lack of purification method to produce pure high tittered batches” in title, hence the title needs to be amended.


Response: we thank the reviewer for this comment. As mentioned a good production system for rSV40 has been developed using the newly developed super Vero cell line. The generation of high titered vector needed for in vivo experiments depends on highspeed centrifugation. No methods have been developed to ensure the removal of cellular debris. Presence of this, consisting of cell membrane and DNA, can be toxic upon administration to the systemic circulation, explaining the toxicity seen in mice when increasing the dose. We do agree with the reviewer that we did not investigate the toxicity nor did we show presence of cell debris. Therefore we do agree with changing the title: Low efficacy of rSV40 in Ugt1a1-/- mice with severe inherited hyperbilirubinemia.


5. Authors needs to present some data about the Ugt1a gene being knocked out in mice.

Response: We thank the reviewer for this comment and have added additional describing the generation of this model and the data obtained in this model in our previous study (Bortolussi et al, 2012, FASEB J.)

Line 119-122: The Ugt1a-/- mice have a one nt deletion in exon 4 of the Ugt1a locus causing a shift in the reading frame introducing a stop codon immediately after the deletion. Due to the absence of the co-substrate binding and transmembrane domains the truncated enzyme is inactive, as published previously (14).


6. English/grammar should be improved for clarity, e.g. in 173-174 line, wass should be corrected to was.

Response: we thank the reviewer for helping us and have corrected this mistake.

Reviewer #2: This manuscript basically reported negative results. The reviewer appreciated the hard work and the authors’ scientific integrity. It is not clear whether the same viral vectors were used for in vitro and in vivo experiments. The expression of transgene in the liver should be detected by Western blot.

Response: we thank the reviewer for your recognition of our work. The viral vectors used in vitro and in vivo were identical. Both rSV-hUGT1A1 and rSV-HLP-hUGT1A1 were produced by AMARNA Therapeutics in Leiden, the Netherlands.

By treating the mutant mice with SV40 vectors, the expression of the transgene was too low to be detected by WB. We have seen in other gene therapy experiments using AAV vectors, that if the efficacy of the treatment is not enough to reduce plasma bilirubin levels below 3-4 mg/dL, the transgenic protein cannot be detected by WB analysis.


Minors,
Line 44, why there is only one sub-title for Introduction?

Response: We agree with the reviewer that this one sub-title is strange and have removed it.


Line 204, rSV40 should be rSV.

Response: we thank the reviewer’s point out that, and we change rSV40 to rSV in the manuscript.

Attachment

Submitted filename: Response to reviewers.docx

Decision Letter 1

Chen Ling

23 Feb 2021

PONE-D-20-33243R1

Low efficacy of recombinant SV40 in Ugt1a1-/- mice with severe inherited hyperbilirubinemia

PLOS ONE

Dear Dr. Shi,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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We look forward to receiving your revised manuscript.

Kind regards,

Chen Ling, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: (No Response)

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: Yes

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Reviewer #1: Authors have complemented the revision. I do not any other questions. If it is allowed,i hope these authors to provide a higher aesthetic picture!

Reviewer #2: The reviewer is disappointed that the authors decline to perform additional experiments. The reviewer understand that this manuscript basically reported negative results. But to make the story complete, some missing data should be provided. Only citing an almost ten-year old reference (Bortolussi et al, 2012, FASEB J.) is not enough. The reviewer recommends a Western Blot assay showing Ugt1a1 expression in the mice liver. The groups should include WT mice, Ugt1a1-/- mice, rSV40 treated mice, and probably rAAV treated mice from the previous reports. The authors should retain some tissues from the previous research. It is very hard to understand why the authors decline to perform a simple WB assay. The ratio of the rSV40- and rAAV-mediated transgene expression is very important for the reader to make a conclusion.

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PLoS One. 2021 Apr 23;16(4):e0250605. doi: 10.1371/journal.pone.0250605.r004

Author response to Decision Letter 1


7 Apr 2021

Reviewers' comments:


Reviewer #1: Authors have complemented the revision. I do not any other questions. If it is allowed,i hope these authors to provide a higher aesthetic picture!

Response: We thank the review’s suggestion, next time we will use a more professional tool to make figures and pictures.

Reviewer #2: The reviewer is disappointed that the authors decline to perform additional experiments. The reviewer understand that this manuscript basically reported negative results. But to make the story complete, some missing data should be provided. Only citing an almost ten-year old reference (Bortolussi et al, 2012, FASEB J.) is not enough. The reviewer recommends a Western Blot assay showing Ugt1a1 expression in the mice liver. The groups should include WT mice, Ugt1a1-/- mice, rSV40 treated mice, and probably rAAV treated mice from the previous reports. The authors should retain some tissues from the previous research. It is very hard to understand why the authors decline to perform a simple WB assay. The ratio of the rSV40- and rAAV-mediated transgene expression is very important for the reader to make a conclusion.

Response: Since using a very sensitive qPCR assay we did show the expression of hUGT1A1 mRNA in the rSV40 treated animals is close to background levels the presence of UGT1A1 protein in liver is expected to be undetectable. We do understand the point raised by the reviewer that a western will further strengthen our message that liver transduction by rSV40 vectors is very inefficient and have therefore performed this experiment. Using an anti-UGT1 rabbit polyclonal antibody (Santa Cruz Biotechnology, Santa Cruz, CA) to detect UGT1A1 expression in liver of Ugt1a1 deficient mice treated with rSV40 and for comparison, treated with rAAV8 and in wild type mice. This western has been added to the paper (Fig 4D) and indeed illustrates the major difference in efficacy of these two vectors in a very clear way. We therefore thank this reviewer for being persistent at this point.

The results of this western are presented as follows:

Line 223-228: The hUGT1A1 expression in liver was determined by western blot showing signals in mice treated with rSV-hUGT1A1 or rSV-HLP-hUGT1A1 comparable to that in PBS treated Ugt1a1 deficient mice (Fig 4D). In contrast administration of a 10 fold lower dose of AAV8 vector, containing hUGT1A1 behind the same liver specific promoter (AAV-L), did show presence of hUGT1A1 while treatment with a comparable dose of this vector (AAV-H), showed a very prominent presence of UGT1A1.

This result is also mentioned in the discussion as follows:

Line 268-270: A dose of 1x1011 vg/kg results in therapeutic correction of serum bilirubin levels (28) and in contrast to both rSV40 vectors, in clearly detectable levels of UGT1A1 in the liver (Fig 4D).

The legend of Fig 4D reads as follows:

Line 475-478: (D) Presence of UGT1A1 in Ugt1a1 deficient mice treated with 1x1011 vg/kg of AAV8-hUGT1A1 (AAV L), PBS, 1.7x1012 vg/kg of rSV-hUGT1A1, 1.7x1012 vg/kg of rSV-HLP-hUGT1A1, or 1x1012 vg/kg of AAV8-hUGT1A1 (AAV H), and in a non-treated wild type mouse (WT). Calnexin was used as loading control on the same membrane.

Attachment

Submitted filename: Response to reviewers.docx

Decision Letter 2

Chen Ling

12 Apr 2021

Low efficacy of recombinant SV40 in Ugt1a1-/- mice with severe inherited hyperbilirubinemia

PONE-D-20-33243R2

Dear Dr. Shi,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Chen Ling, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Acceptance letter

Chen Ling

15 Apr 2021

PONE-D-20-33243R2

Low efficacy of recombinant SV40 in Ugt1a1-/- mice with severe inherited hyperbilirubinemia

Dear Dr. Shi:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Chen Ling

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Fig. Absence of antibodies towards hUGT1A1 in serum of mice treated with rSV hUGT1A1 or rSV-HLP-hUGT1A1.

    60-day-old Ugt1a-/- mice were treated with 2x1011 vg/kg of rSV-hUGT1A1 vector (n = 3), or rSV-HLP-hUGT1A1 (n = 3) via tail vein injection. At 8 weeks after vector administration the level of anti-hUGT1A1 IgG in serum was determined. Data represent the mean ± SD.

    (PDF)

    S1 Raw images

    (PDF)

    Attachment

    Submitted filename: Review-PONE-D-20-33243.docx

    Attachment

    Submitted filename: Response to reviewers.docx

    Attachment

    Submitted filename: Response to reviewers.docx

    Data Availability Statement

    All relevant data are within the paper and its Supporting Information files.


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