Heterologous expression cassette, DNA construct and vaccine composition to immunize against flavivirus and/or other pathogens
11230574 · 2022-01-25
Assignee
Inventors
Cpc classification
C12N2770/24122
CHEMISTRY; METALLURGY
C12N2770/24134
CHEMISTRY; METALLURGY
C12N2770/24121
CHEMISTRY; METALLURGY
Y02A50/30
GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
C12N15/86
CHEMISTRY; METALLURGY
C12N15/66
CHEMISTRY; METALLURGY
International classification
C12N15/66
CHEMISTRY; METALLURGY
C12N15/86
CHEMISTRY; METALLURGY
Abstract
A heterologous expression cassette, DNA construct and vaccine composition for immunization against flavivirus and/or other pathogens. DNA constructs, recombinant viruses and vaccine compositions containing the recombinant viruses were obtained. This invention also concerns and provide an improved expression vector of the live-attenuated yellow fever 17D virus. Modifications in the expression cassette of heterologous proteins in the intergenic E/NS1 region of the yellow fever 17D vaccine virus, were made. The two new functional domains inserted in the expression cassette were (1) a coding sequence for the N-glycosylation motif, located between the NS1 N-terminal motif and the heterologous protein and (2) a sequence which promoted the proteolytic cleavage, or not, of the recombinant protein in such a way as to release it from its C-terminal containing the transmembrane domains and, consequently, from its association with the membrane of the endoplasmatic reticulum—ER.
Claims
1. An expression cassette for heterologous proteins in an intergenic E protein/NS1 protein (E/NS1) region of a yellow fever 17D vaccine virus, wherein said expression cassette comprises: an insertion sequence comprising: a first functional domain, and a second functional domain, wherein said first functional domain comprises a) a spacer sequence coding for a furin cellular protease cleavage motif, or b) a spacer sequence coding for a Picornaviridae 2A factor, wherein said second functional domain comprises a spacer sequence coding for a N-glycosylation motif, and wherein the spacer sequence coding for a N-glycosylation motif is inserted into the expression cassette between a sequence coding for a NS1 N-terminal motif and a sequence coding for the heterologous protein.
2. The expression cassette of claim 1, wherein said Picornaviridae 2A factor sequence is inserted into the expression cassette before a sequence encoding a stem and an anchor domain of the E protein.
3. The expression cassette of claim 2 wherein, said Picornaviridae 2A factor sequence comprises an auto-cleavage motif, wherein the motif comprises SEQ ID 61, SEQ ID 62, SEQ ID 63, SEQ ID 64, SEQ ID 65, SEQ ID 66, SEQ ID 67, or SEQ ID 68.
4. The expression cassette of claim 1, wherein the spacer sequence coding for the N-glycosylation motif is selected from target sequences of the E protein of a Dengue type 2 virus and a G glycoprotein of a rabies virus.
5. The expression cassette of claim 1, wherein the first coding sequence for the furin cellular protease cleavage motif is at least one of, a von Willebrand human coagulation factor (vWF), or a furin cleavage motif of the prM protein of the encephalitis virus transmitted by ticks.
6. The expression cassette of claim 1, wherein said second coding sequence for the N-glycosylation motif is a glycan acceptor motif.
7. The expression cassette of claim 6, wherein the glycan acceptor motif comprises N-X-S/T, wherein N is an asparagine amino acid, and wherein -X comprises any amino acid, with the exception of proline, and -S/T comprises serine or threonine.
8. The expression cassette of claim 7, wherein said N-glycosylation motif allows for any heterologous protein expressed by the yellow fever virus to comprise an N-glycosylation motif not present in its native amino acid sequence, but present in said expression cassette.
9. A DNA construct of a modified recombinant vector virus, said construct comprising: a nucleotide sequence, wherein the nucleotide sequence comprises: a first sequence coding for at least one heterologous protein or a fragment thereof; wherein the first sequence is inserted into an intergenic E/NS1 region; a second sequence coding for an NS1 protein; and a third sequence coding for an E protein of a flavivirus, wherein the nucleotides present in the 5′-terminal of the NS1 protein and all or part of the E protein stem and anchor domains are present at both ends of the heterologous protein sequence; and wherein the expressed and processed heterologous protein induces an immune response in a host cell, and wherein a Picornaviridae 2A factor sequence motif is inserted into the intergenic E/NS1 region and before a sequence encoding a stem and an anchor domain of the E protein.
10. The DNA construct of claim 9, where a glycan acceptor motif is inserted after the domain in the 5′-terminal of the NS1 gene.
11. The DNA construct of claim 9, wherein the glycan acceptor motif comprises N-X-S/T, wherein N is an asparagine amino acid, and wherein -X comprises any amino acid, with the exception of proline, and -S/T comprises serine or threonine.
12. The DNA construct of claim 9, wherein the construct comprises SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, or SEQ ID NO:12.
13. A vaccine composition for immunization against Flavivirus and/or other pathogens comprising the DNA construct of claim 9.
14. The expression cassette of claim 2, wherein said Picornaviridae 2A factor sequence produces said heterologous protein by interruption of the viral RNA translation of ribosomes in the anterior region of the carboxy terminus of a fragment of the heterologous protein.
15. The expression cassette of claim 1, wherein said furin cellular protease cleavage motif produces said heterologous protein through cleavage by a furin cellular protease.
16. The expression cassette of claim 1, wherein the E protein comprises transmembrane segments, wherein said first functional domain comprising a spacer sequence is inserted into the expression cassette before a sequence encoding for a transmembrane segments domain of the E protein; and wherein said first functional domain comprising a spacer sequence provides for proteolytic cleavage of said heterologous protein from said transmembrane segments, thereby providing for releasing said heterologous protein from said transmembrane segments.
17. A DNA construct of a modified recombinant vector virus, said construct comprising: a nucleotide sequence, wherein the nucleotide sequence comprises: a first sequence coding for at least one heterologous protein or a fragment thereof; wherein the first sequence is inserted into an intergenic E/NS1 region; a second sequence coding for an NS1 protein; and a third sequence coding for an E protein of a flavivirus, wherein the nucleotides present in the 5′-terminal of the NS1 protein and all or part of the E protein stem and anchor domains are present at both ends of the heterologous protein sequence; and wherein the expressed and processed heterologous protein induces an immune response in a host cell, and wherein a spacer sequence coding for a Furin cellular protease cleavage motif is inserted into the intergenic E/NS1 region before a sequence encoding a stem and an anchor domain of the E protein.
18. A vaccine composition for immunization against Flavivirus and/or other pathogens comprising the DNA construct of claim 17.
19. A vaccine composition for immunization against Flavivirus and/or other pathogens according to claim 18, wherein said construct comprises a sequence, and wherein the sequence is selected from the group consisting of SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO:12.
Description
BRIEF DESCRIPTION OF THE FIGURES
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DETAILED DESCRIPTION
(8) Thus, in the present disclosure, it can be demonstrated that the retention of the recombinant protein in the ER produces greater disturbance of the viral processes associated with this cell compartment.
(9) Two modifications were made in this disclosure. In the first, motifs were fused between the heterologous protein (SEQ ID NO:25, SEQ ID NO:26) and the stem-anchor domain of the E protein of DEN4 (SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71 and SEQ ID NO:72) for the removal of the transmembrane anchors. Two kinds of motifs were used:
(10) Option (1)—target sequences of the cell furin proprotein convertase, represented by SEQ ID NO:45 to SEQ ID NO:60; and,
(11) Option (2) the autocleavage motif of the 2A peptide of the picornavirus represented by SEQ ID NO:61 to SEQ ID NO:68.
(12) In the first option (Option 1), two different cleavage motifs of the furin proprotein convertase were used. Furin is a member of the family of secretory proprotein convertases, which possesses a proteolytic domain of the subtilisin type. This is a type I transmembrane protein and occurs in vertebrates and invertebrates. Furin cleaves proprotein sequences to liberate mature proteins, preferably by the cleavage motif R-X-(R/K)R↓, where R means the amino acid arginine, K represents lysin, X can be any amino acid and the symbol indicates the proteolytic cleavage site [60]. The furin is mainly located in the Golgi and Trans-Golgi network (TGN). However, its circulation also occurs from the endocytic system to the cell membrane, with its return to the Trans-Golgi network or release to the extracellular medium in truncated form.
(13) The proteolytic activity of furin is essential to the activation of proproteins, such as hormones, zymogenes and proteins of the cell surface [61]. Examples of proteins which are processed by furin are albumin, the component of the complement C3, the von Willebrand (vWF) coagulation factor. Elsewhere this enzyme performs a function of great importance in viral infectivity, such as in HIV [62] and in the flu virus [63].
(14) In flaviviruses, the furin protein performs an important role in the maturation of the viral particle. This process begins during the assembly of the viral particle, when the budding of the nucleocapsid occurs (C protein associated with viral genomic RNA) for the lumen of the ER, becoming enveloped by a lipidic membrane surrounded by the envelope proteins (E) and the membrane (prM). The prM protein is associated in such a way as to protect the region of the E protein which contains the peptide motif for fusion to the membrane, in order to prevent the fusion of E to the internal membranes of the cell during the intracellular transportation of the immature viral particles. In the TGN, at pH 6.0, this association of prM and E undergoes a rearrangement which exposes the cleavage motive to furin, allowing for its proteolysis. However, the viral particle originated, despite possessing a form similar to the infective particle, also has a pr fragment associated with the E protein. As the process is dependent on the pH, the dissociation of the pr fragment only occurs after the release of the virion of the cell, thus forming the infective viral particle [64, 65].
(15) The second motif (Option 2) which was used to remove the two transmembrane alpha-helices (TM1 and TM2) of the expression cassette in substitution of the cleavage motif by furin, was the 2A peptide of the aphthous fever virus, a picornavirus. The principal functional characteristic of this 2A peptide is to promote the decoupling of the ribosome from the nascent chain of a polypeptide during the process of protein synthesis. In this event, the translation may conclude at the end of the 2A peptide or continue onwards. The interruption in the protein elongation occurs following a proline and glycine sequence. The 2A motif of the aphthous fever virus consists of a sequence of around 18 amino acids SEQ ID NO:73 (LLNFDLLKLAGDVESNPG↓P), where the carboxy-terminal asparagine, proline and glycine motif (underlined), on being followed by a sequence with proline (bold) causes a pause in the translation and its decoupling. This autoprocessing motif is present in several picornaviruses, and in some insect viruses and type C rotaviruses. Several types of 2A motifs are used in the expression of recombinant proteins [66]. It is important to highlight that the sequence represented by SEQ ID NO: 63 and SEQ ID NO:64 (QLLNFDLLKLAGDVESNPGP) corresponds to the sequence of amino acids of the 2A peptide of the aphthous virus. As can be observed, there is a glutamine (Q) at the start of the sequence SEQ ID NO:64, which forms part of the viral sequence, but is not decisive in the motif's being functional. This motif was included to reduce the hydrophobicity of the start of the sequence.
(16) The second modification of the present disclosure was the introduction of a glycan acceptor motif (SEQ ID NO: 29 to SEQ ID NO: 44) in the anterior region to the amino terminus of the recombinant protein fragment in the heterologous expression cassette. This allows any heterologous protein to be expressed by the YF virus to carry an N-glycosylation motif not necessarily present in its amino acid sequence, but present in the heterologous expression cassette. This post-translational modification is the most common occurring in the ER. Thus, most nascent proteins destined for this cell compartment, for the plasmatic membrane, for secretion or other endocytic compartments, are N-glycosylated. In addition to increasing protein solubility, in an environment with a high concentration of proteins, the addition of glycans assists in the correct process of protein folding, which occurs in the ER, since the processing of protein-bound oligosaccharides provides signals for the recruitment of lectin chaperones resident in the ER and which modulate the protein folding [67, 68]. Initially, to the NXS/T acceptor motif—which corresponds to the asparagine amino acids—any amino acid with the exception of proline—serine or threonine; present in the protein—a block of preformed oligosaccharides is added covalently to the asparagine residue of this arrangement. This precast oligosaccharide precursor is originally bound to a lipid (dolichol phosphate) and is translocated to the protein to be modified by the enzyme oligosaccharyltransferase (OST). The oligosaccharide precursor in eukaryotes consists of three glucoses, nine mannoses, and two N-acetylglucosamines (Glc3Man9GlcNAc2) [67, 69]. Most nascent polypeptides emergent in the ER lumen are glycosylated, receiving from 1 to 14 glycan residues [70]. The glycosylation of proteins post-translationally directed by the specialized catalytic subunit of oligosaccharyltransferase, STT3B, may also occur at a lower rate, with the assistance of accessory proteins [71]. An important aspect in the quality control of recently synthesized and glycosylated proteins is provided by the differential processing of the precursor oligosaccharides associated with these. This creates an identification that is recognized by the quality control system, for the correct protein folding, and by the machinery of the ERAD (degradation associated with ER, in English: “ER-associated degradation”), which directs the nascent glycoprotein to the different compartments of the ER and the secretory pathway. Thus, in this system the structure of the oligosaccharide in the polyprotein indicates the state of its folding allowing it to differentiate between correctly folded, unfolded and incorrectly folded forms [69].
(17) Thus, a new methodology and expression of heterologous proteins by the YF 17D virus in the E/NS 1 was developed. Basically, two new functional domains were introduced into the expression cassette; the first was a coding sequence for the N-glycosylation motif, located between the N-terminal NS1 motif and the heterologous protein (
(18) Further illustration is provided with reference to the following examples, but it should be understood that the present invention should not be limited thereto.
(19) The Examples below provide representative methods. A person skilled in the art will know how to substitute the appropriate reagents, raw materials and purification methods known.
EXAMPLES
Example 1. Design and Obtention of New Viral Expression Platforms in the Intergenic E/NS1 Region
(20) Two important modifications were made to the original expression platform of the yellow fever 17D vaccine virus, known as I [43, 72], in which heterologous genes could be inserted and expressed in the intergenic E/NS1 region (
(21) Subsequently, to promote the greater genetic stability of the construct, the HA elements of the C-terminus of the expression cassette, originating from the E protein of the YF virus, were replaced by the equivalent sequences of the dengue 4 virus (SEQ ID NO:69, SEQ ID NO: 70) and truncated versions were derived from this domain (SEQ ID NO: 71 and SEQ ID NO: 72) in which the H1 and CS elements were removed from the stem portion [43, 73].
(22) The introduction of an N-glycosylation site in a flanking region of the recombinant protein ensures that, independently of the presence of added glycan motifs in a given heterologous sequence of interest, this will have greater stability of expression, and this modification will also facilitate the exodus thereof from the ER. In the case of the chosen protein, green fluorescent protein, this does not possess N-glycan acceptor motifs and, moreover, it has two cysteine residues, but which do not naturally form disulfide bridges. In the present disclosure, it has been shown that the GFP expressed by this new version of the yellow fever viral vector acquires greater stability in this expression strategy.
(23) Two alternative versions of this new viral vector were designed, which versions used an N-glycosylation motif of the G protein of the rabies virus and another of the E protein of the dengue 2 virus, shown here in Table 1.
(24) TABLE-US-00001 TABLE 1 Platform II Modification: (variant) Origin N-glycosylation GeneBank Sequence Modification: II-1 G Glycoprotein 267- NP056796.1 RKGSQTSNTTKWAPPGQGSPG and of the rabies QTSNETKWCPPGQ- (SEQ ID NO: 29 until II-1 HAc virus 275 SEQ ID NO: 36 II-2 E Protein- SGEEHAVGNDTGS Q9WDA6 RKSGEEHAVGNTTGS Den 2 virus (SEQ ID NO: 37 until SEQ ID NO: 44) II-3 G Glycoprotein 267- NP056796.1 RKGSQTSNTTKWAPPGQGSPG of the rabies QTSNETKWCPPGQ- (SEQ ID NO: 29 until virus 275 SEQ ID NO: 36) Modification: Release of Platform II transmembrane (variant) Origin anchoring GeneBank Sequence Modification II-1 Furin cleavage 754- NP 000543 SGSSPLSHRSKR↓SLSCRPPM motif of the von SSPLSHRSKR↓SLSCR VKEGSSIG Willebrand PPMVK-773 (SEQ ID NO: 45 until (vWF) human SEQ ID NO: 52) coagulation factor 11-2 Furin cleavage 84- NP775501.1 SGGKQEGSRTRR↓SVLIPSHA motif of the prM GKQEGSRTRR↓SVLIP QGKEGSSIG protein - TBE SHAQG-103 (SEQ ID NO: 53 until virus SEQ ID NO: 60) II-3 2A cleavage QLLNFDLLKLAGDVES SGSSPQLLNFDLLKLAGDV site of the NPGP ESNPGPKEGSSIG aphthous fever (SEQ ID NO: 61 until virus SEQ ID NO: 68) HAc-means complete stem-anchor II-1 is represented by the sequences SEQ ID NO: 5 and SEQ ID NO: 6 II-1 HAc is represented by SEQ ID NO: 7 and SEQ ID NO: 8. II-2 is represented by the sequences SEQ ID NO: 9 and SEQ ID NO: 10 II-3 is represented by the sequences SEQ ID NO: 11 and SEQ ID NO: 12
(25) The five N-glycosylation acceptor sites of the G protein of the rabies virus had been described previously [74] [75]. The third site of this protein was chosen, with the sequence SEQ ID NO:74 QTSNETKWCPPGQ (position 263-275, as shown in Table 1. However, this underwent a change whereby the C residue, position 274, was altered to A (SEQ ID NO: 31 and SEQ ID NO: 32). This was done to avoid undesirable effects such as the formation of a disulfide bridge with another cysteine of the cassette, which could lead to an altered conformational structure. Finally, amino acid spacer sequences were associated with this glycan addition motif, at its N-terminus, RKGS amino acids (SEQ ID NO: 33 and SEQ ID NO: 34), and, at the C-terminus, GSPG (SEQ ID NO: 35 and SEQ ID NO: 36) in order to confer flexibility on this section of the expression cassette for GFP.
(26) The other motif used consisted of one of the sugar acceptor sequences of the E protein of the dengue virus 2, as shown in Table 1. The sequence corresponds to the acceptor asparagine of position 154 of the E protein, comprised within the chosen region SEQ ID NO:75 SGEEHAVGNDTGS. However, the acceptor motif of N-glycans NDT was changed to the NTT equivalent (SEQ ID NO: 39 and SEQ ID NO: 40). The glycosylation motif, in both the sugar acceptor sequences, was placed in the expression cassette between the amino terminal portion of a similar motif to the first nine amino acids of the NS1 protein (SEQ ID NO: 27 and SEQ ID NO: 28) of the YF virus and the start of the heterologous protein. The RK spacer amino acids (SEQ ID NO: 41 and SEQ ID NO: 42) and GS (SEQ ID NO: 43 and SEQ ID NO: 44) are located flanking this motif.
(27) In the present disclosure, the expression cassette was further modified in order to increase the stability of the recombinant protein and release it from the anchoring in the membrane of the endoplasmic reticulum (ER). The first motif which was fused to the cassette consisted of adding an N-glycosylation motif in the region close to the amino terminus of the recombinant protein. In this methodology, it was considered that the N-glycosylation motif would be located in the amino portion of the exposed recombinant protein in the lumen of the ER so that there would be no structural disruption of the N-terminal domains of the NSL motif (of the amino terminus of the recombinant protein) and the GFP. Flanking the N-glycosylation motif of the G glycoprotein of the rabies virus, in the amino terminal, the RKGS motif (SEQ ID NO: 33 and SEQ ID NO: 34) and, in the carboxy-terminal, the GSPG motif (SEQ ID NO: 35 and SEQ ID NO: 36) were placed. In the N-glycosylation motif of the E protein of the dengue 2 virus, in the amino-terminal, the RK motif (SEQ ID NO: 41 and SEQ ID NO: 42) and, in the carboxy-terminal, the GS motif (SEQ ID NO: 43 and 44) were used. Spacer sequences were used to provide greater flexibility between the different functional domains of this carboxy-terminal region.
(28) The second functional motif was added before the stem-anchor region of the E protein of dengue 4 virus, located in the carboxy terminus of the expression cassette, which promotes anchoring of the heterologous protein to the ER membrane. This motif promotes the separation of the heterologous protein from these domains for anchoring the recombinant protein to the membrane (Table 1). Thus, one of the motifs used, the furin cleavage motif of the von Willebrand coagulation factor (vWF), represented by the amino acid sequence SSPLSHRSKRSLSCRPPMVK (SEQ ID NO: 47 and 48) was placed in the expression cassette between the GFP and the stem-anchor portion. This functional domain was flanked by the SG amino acids (SEQ ID NO: 49 and SEQ ID NO: 50) and KEGSSIG (SEQ ID NO: 51 and SEQ ID NO: 52) to promote greater flexibility of the region and, consequently, greater exposure to proteolytic cleavage by furin. The final motif was then SGSSPLSHRSKRSLSCRPPMVKEGSSIG (SEQ ID NO: 45 and SEQ ID NO: 46). In another version of this approach, the furin cleavage motif, GKQEGSRTRRSVLIPSHAQG (SEQ ID NO: 55 and SEQ ID NO: 56) present in the prM protein of the virus transmitted by ticks, the TBE virus (“Tick-borne encephalitis virus”) was used and received the SG flanking amino acids (SEQ ID NO: 57 and SEQ ID NO: 58) and KEGSSIG (SEQ ID NO: 59 and SEQ ID NO. 60). The final motif resulted in SIV Gag the sequence SGGKQEGSRTRRSVLIPSHAQGKEGSSIG (SEQ ID NO: 53 and SEQ ID NO: 54).
(29) By way of an alternative, the present invention provides the option of testing, in the carboxy-terminal region of the expression cassette preceding the HA domain of the recombinant protein, another option that does not involve proteolytic cleavage. As such, the 2A motif of the aphthous fever virus (shown in Table 1), the QLLNFDLLKLAGDVESNPGP motif, was chosen (SEQ ID NO: 63 and SEQ ID NO: 64), which promotes the decoupling of the nascent viral polyprotein from the ribosomal translation complex. Although this strategy is different from proteolytic cleavage by furin, the same result is produced, i.e., the recombinant protein without its carboxy-terminal (stem and anchor domain) and, consequently, without association with the ER membrane. To this motif were fused the flanking amino acids SGSSP (SEQ ID NO: 65 and 66) and KEGSSIG (SEQ ID NO: 67 and 68). The final motif resulted in the sequence SGSSPQLLNFDLLKLAGDVESNPGPKEGSSIG (SEQ ID NO: 61 and SEQ ID NO: 62).
(30) The new constructs derived from this methodology present different combinations of the carboxy-terminal region of the expression cassette, which are the complete region of the stem-anchor of the E protein of the dengue 4 virus or its truncated version, without the H1 alpha-helix or the SC motif, and are presented, regarding this aspect, in Table 1A.
(31) TABLE-US-00002 TABLE 1A Variant fragment of the stem and anchor of the E Platform II protein of the dengue 4 virus II-1 and 11-2 TSLGKAVHQVFGSVYTTMFGGVSWM1RILIGFLVL WIGTNSRNTSMAMTCIAVGGITLFLGFTVGA (SEQ ID NO: 69 and SEQ ID NO: 70) II-1 Hac and KMFESTYRGAKRMAILGETAWDFGSVGGLFTSLGK II-3 AVHQVFGSVYTTMFGGVSWMIRILIGFLVLWIGTN SRNTSMAMTCIAVGGITLFLGFTVGA (SEQ ID NO: 71 and SEQ ID NO: 72) HAc - means complete stem-anchor
(32) Table 1A shows the amino acid sequence of the carboxy-terminal domain of the expression cassette of the different constructs of expression platform II. Viral variants containing the complete (96 amino acids) and partial (66 amino acids) domain of the stem-anchor domain of the E protein of the dengue virus 4 were created.
(33) The table below shows a description of the sizes of the expression cassettes and the predicted size of the recombinant proteins expressed in comparison with those foreseen for the viruses of platform I. The molecular weights of the recombinant proteins were calculated using the ProtParam program (available on the ExPASy web page of the Swiss Institute of Bioinformatics) and refer to the molecular weights of the recombinant proteins without any desired post-translational modification, such as glycosylation or the removal of the transmembrane anchors from the carboxy terminus. It would be expected that the glycosylation of the recombinant protein would lead to an increase of 2 to 3 kDa in the molecular weight. On the other hand, the removal of the stem-anchor domains would lead to a reduction of about 7 kDa in the truncated version and 10 kDa, in its complete version.
(34) TABLE-US-00003 TABLE 2 Size of the expression cassettes codified by the different viruses Predicted Molecular Weight Construct Virus Size (nt) Size (aa) (kDa) Platform I I-1 939 313 34.7 SEQ ID SEQ ID NO: 13 NO: 14 I-1 HAc 1029 343 37.9 SEQ ID SEQ ID NO: 15 NO: 16 Platform II II-1 1083 361 39.6 SEQ ID SEQ ID NO: 17 NO: 18 II-1 HAc 1173 391 42.9 SEQ ID SEQ ID NO: 19 NO: 20 II-2 1068 356 39.1 SEQ ID SEQ ID NO: 21 NO: 22 II-3 1185 395 43.2 SEQ ID SEQ ID NO: 23 NO: 24 HAc - Haste means complete stem-anchor
(35) The construction of the recombinant viruses was realized through molecular cloning of synthetic genes in the plasmid pT3. The synthetic genes (GenScript) were designed with codon optimization for the frequency of use of the YF virus. The binding of the synthetic genes of the constructions was realized in the plasmid pT3 EagI/NarI in directional form, which is to say, both the plasmid and the synthetic genes presented sites of cleavage by the restriction enzymes EagI (C/GGCCG) and NarI (GG/CGCC). This procedure allowed the insertion of the cassette in the correct orientation into the plasmid pT3 Eag IWar I, as the site for Eag I is present in the N-terminal of the cassette while Nar I is found in the C-terminus of the expression cassette. In a step prior to the binding, 1 ug of each plasmid or insert was digested with 5U of the respective restriction enzymes at 37° C. for 2 h, in a final volume of 100 μE. The binding of the insert to the vector was realized with the enzyme T4 DNA ligase (Invitrogen) using 100 ng of the plasmid pT3 to 50 ng of the insert, in the equimolar proportion of 5:1 respectively. Recombinant clones were selected and sequenced to confirm the integrity of the construct.
(36) The plasmids cloned from the pT3, or the pT3 without insert (viral control without insertion), and the plasmid pG1/2, which contains the complementary DNA of the genome of the YF virus, were digested by the enzymes Nsi I and Sal I (Promega) with 20U of each enzyme to 2 ug of plasmid DNA. The completely digested plasmids were purified using the system “QIAquick PCR Purification Kit” (Qiagen).
(37) Each binding reaction was realized with 200 ng of the PGI/2 and 300 ng of the pT3 or derivative, with 1U of the enzyme T4 DNA ligase (Invitrogen) under the conditions established by the manufacturer. The samples were then treated with 30 U of the enzyme Xho I (Promega), by incubation at 37° C. for 3 h, followed by inactivation of the enzyme by heating at 65° C. for 15 minutes. The DNA molds generated were concentrated by precipitation with 10% 3M ammonium acetate and ethanol and, the DNA resuspended in 10 mM Tris pH 7.5.
(38) The cDNA mold preparations were transcribed using the mMessage mMACHINE Kit (SP6) (Ambion) in accordance with the manufacturer's instructions. 2 ug of total RNA transcribed in vitro was used for transfection of Vero cells by electroporation. The RNA sample was added to the Vero cells in PBS suspension (free of endonucleases) and the cell suspension was then subjected to a controlled electric pulse (200 V, 850 mF, resistance ∞ in 4 mm cuvette) in Gene PulserXcell equipment (Bio Rad). The cell suspension was seeded in 25 cm.sup.2 bottles with a density of 40,000 cells/cm2 with 12 ml of complete medium 199 with Earle's salts. The bottles containing the transfected cells were incubated at 37° C. in an oven containing 5% CO.sub.2, and monitored until the appearance of the cytopathic effect (CPE). The supernatant of this culture (known as IP, first cell passage) was collected in aliquots and stored at −80° C. All the recombinant viruses generated were submitted to RNA extraction, followed by RT-PCR and nucleotide sequencing to verify the integrity of the insert.
(39) All the new constructs were viable and presented CPE after 4 to 5 days post-transfection.
(40) For the characterization studies of the new recombinant viruses, second cell passage viral stocks (2P) were obtained after infection of an aliquot (IP) in a T-175 flask containing 62,500 cells/cm.sup.2 and a Medium 199 w/Earle's 5% NaHCO.sub.3 and 5% fetal bovine serum. The viral inoculum was incubated in a CO.sub.2 oven at 37° C. until the appearance of CPE, when the supernatant (2P) was collected and stored in aliquots which were conserved at −80° C.
Example 2. Biological Characterization of the Viruses of Expression Platform II
(41) The growth rate of the new viral variant platforms was evaluated in relation to the original viruses of expression platform I and the control viruses. The control viruses used were the 17DD YF vaccine virus strain and the G1/2T3 virus, with a similar genome to the recombinant viruses, but without heterologous insertion. Vero cells cultured at a density of 62,500 cells/cm.sup.2 in 25 cm.sup.2 bottles containing 12.5 ml of Medium 199, w/Earle's 5% NaHCO.sub.3 and 5% fetal bovine serum were infected in a multiplicity of infection (MOI Multiplicity of Infection) of 0.02. Aliquots of the supernatant of the infected culture were collected at 24h intervals until 96h, of which 100 μl were titrated in cell monolayers. The analyses were performed at least in triplicate. From these data growth kinetic profiles were obtained, whose statistical analysis was performed using the One Way ANOVA test, Dunnett's post-test, using the GraphPadPrism 5.03 program (GraphPad, Inc.). The differences were only considered significant when P<0.05.
(42)
(43) Regarding the determination of the viral proliferation during the course of the infection in Vero cells,
Example 3. Expression of the Heterologous Protein by the YA Viruses of Platform II
(44) Recombinant viruses of platform II were also characterized in relation to the expression of the heterologous protein through three different analyses: fluorescence microscopy, flow cytometry and Western blotting. For these analyses, Vero cells were infected for 72h in MOI (multiplicity of infection) of 0.02 (
(45) Cells infected with the new recombinant viruses of platform II presented, on analysis by fluorescence optical microscopy, much more intense autofluorescence than observed in cells infected with the I-1 YF virus under the same conditions of infection and image capture. These data indicate a greater capacity for expression of the heterologous protein, in the case of EGFP, by the YF II viruses. This was confirmed by the analysis of different samples of infected Vero cells using flow cytometry. The cell infection was realized in MOI of 0.02 for 72h, and the samples were subjected to staining with the antibody VFA in order to compare GFP fluorescence with the staining for viral antigens in infected cells. At least 10,000 events per sample were obtained.
(46) The conditions used are described in Bonaldo, M C, et al., Construction and characterization of recombinant flaviviruses bearing insertions between E and NS1 genes. Virol J, 2007. 4: p. 115. Briefly, Vero cells were cultured and infected in 6-well plates with 62,500 cells/cm.sup.2. At 72 hours of incubation, the culture medium was removed and cells were subjected to treatment with trypsin and centrifuged at 400 g for 7 min, followed by two washes with sterile PBS and then fixed in 2% paraformaldehyde. The cells were permeabilized with PBS supplemented with 1% BSA containing 0.15% saponin for 15 min at 4° C., centrifuged at 400 g for 7 min, and then stained with mouse monoclonal antibody directed at the YF virus (Biogenesis), diluted 1:200 in PBS with 1% BSA and 0.15% saponin for 1h in an ice bath. The cell suspensions were washed with 1 ml of PBS supplemented with 1% BSA also containing 0.15% saponin and centrifuged at 400 g for 7 min and resuspended in the presence of the secondary antibody Alexa Fluor 647 goat anti mouse IgG (Molecular Probes) at a dilution of 1:400 as described above. Finally, the cells were resuspended in 0.3 ml of 2% paraformaldehyde and analyzed in C6 Flow Cytometer System equipment using the program C-Flow Plus (Accuri cytometers). The data were analyzed using the program Flow J (TreeStar Inc.).
(47) The data presented in
(48) This difference in the pattern of expression of the heterologous protein in platforms I and II was also confirmed by the analysis of extracts of Vero cells infected by Western blotting, obtained as previously described in Bonaldo, M. C., et al., Construction and characterization of recombinant flaviviruses bearing insertions between E and NS1 genes. Virol J, 2007. 4: p. 115. [76] (
(49) TABLE-US-00004 TABLE 3 Antibodies used for the detection of proteins by Western-blotting DILUTION ORIGIN PRIMARY ANTIBODY GFP (JL-8) - mouse IgG 1:8000 Living Colors A.v. Monoclonal Antibody - Clontech β-tubulin - mouse IgG 1:1000 Invitrogen Yellow Fever NS3 - 1:500 LABMOF rabbit IgG SECONDARY ANTIBODY (CONJUGATED TO PEROXIDASE) Mouse IgG 1:2000 KPL Rabbit IgG 1:4000 Amersham Biosciences
(50) Thus, the profiles obtained in the Western blotting show that the mass of the recombinant protein detected in infected cells is much greater in those that were infected by the recombinant virus of platform II (II-1) than evidenced for those of platform I (I-1) and, again, that these differences are not due to lower rates of translation in platform I, since the non-structural protein NS3 is detected at the same intensity in both conditions. These profiles associated with the intensity of fluorescence emitted by the recombinant protein in infected cells in the flow cytometry analysis, allow us to estimate a difference of around twenty times greater than the fluorescence and mass detected for GFP in cells infected with the virus of the original platform I.
(51) These differences were also proven through the determination by RT-PCR in real time of the number of copies of viral RNA present in these samples of infected Vero cells. For the PCR assay in real time the target region selected was the fragment of the NS5 region (nt 10188-10264) of the YF genome with a size of 77 pb, amplified with the oligonucleotides sense YF 17D 10188 (5-GCG GAT CAC TGA TTG GAA TGA C-3) and reverse YF 17D 10264 (5-CGT TGG GAT ACG ATG GAT GAC TA-3), and TaqMan probe (5-6FAM-AAT AGG GCC ACC TGG GCC TCC C-TAMRA-3). For absolute quantification of the viral RNA present in the samples, a standard curve was included in the assay composed of synthetic RNA containing the region to be amplified in the concentrations equivalent to 10.sup.3 to 10.sup.9 copies of the YF genome. The synthetic RNA was obtained in our laboratory by cloning the cDNA of 673 bp of the NS5 region of the 17D virus (10055-10728) in the plasmid vector pGEM-T Easy Vector (Promega), followed by purification, in vitro transcription and treatment with DNase. The calculation of the number of RNA molecules was realized through verifying the mass by optical density. For amplification, 3 μM of both oligonucleotides (sense and reverse) were applied, 2.5 μM of probe, MultiScribe/RNase Inhibitor mix 40×, TaqMan One-Step RT-PCR Master Mix 2×, 10 to 100 ng of RNA and free water of nucleases to complete the total volume of 20 μl per reaction. The cycling conditions were: 1 cycle of 48° C. for 30 minutes and 95° C. for 10 minutes followed by 40 cycles of 95° C. for 15 seconds and 60° C. for 1 minute, in StepOnePlus Real-Time PCR System equipment (Applied Biosystems).
(52) The values obtained in the quantitative RT-PCR were 8.4 Log 10 copies/reaction for the parental virus G1/2T3; 8.6 Log 10 copies/reaction for the virus I-1, 8.4 Log 10 copies/reaction for the virus II-1 and 8.3 log 10 copies/reaction for the virus II-2, and indicate that there was no significant difference between the number of RNA copies present in the infected cell extract for all the viruses analyzed, demonstrating that the viral infection was homogeneous in the cell density established for the viruses studied, as had been observed by flow cytometry and fluorescence microscopy with the staining of AF antigens. It was also confirmed that the differences in the fluorescence of the GFP observed are not due to variations in viral proliferation.
Example 4. Secretion of the Heterologous Protein by the YF Viruses of Platform II
(53) In order to better characterize heterologous expression in the viral variants of Platform II, an analysis was undertaken of extracts and the extracellular medium of Vero cell monolayers infected by the recombinant viruses II-1, II-1 HAc and II-3.
(54)
(55) The recombinant protein exhibits a similar band profile in Vero cell extracts (
(56) Another important property of expression platform II is that it has the capacity to allow the secretion of the recombinant protein by the infected cell. This characteristic has been confirmed through the detection of this protein by Western blotting of protein extracts from an extracellular medium of cell cultures infected with the viruses II-1, II-1 HAc and II-3 (
(57) In this patent application, significant modifications were introduced into the expression cassette of heterologous proteins in the intergenic E/NS1 region of the yellow fever vaccine virus 17D, whose original strategy was the object of patent application P10504945 (WO2007/051267).
(58) The modifications introduced into the present invention, the N-glycosylation motifs and the dissociation of the recombinant protein from its carboxy end containing transmembrane alpha-helices, by furin cleavage or by the presence of the picornaviruses 2A motif, caused a significant impact on the expression of the recombinant GFP, principally in the quality of its folding and its trafficking to the secretory pathway.
(59) In addition to this, the present invention provides the option of testing in the carboxy-terminal region of the expression cassette, antecedent to the HA domain of the recombinant protein, without involving proteolytic cleavage, through the use of the 2A motif of the aphthous fever virus (QLLNFDLLKLAGDVESNPGP—SEQ ID NO: 63 and SEQ ID NO: 64), which promotes the decoupling of the nascent viral polyprotein from the ribosomal translation complex. Although this strategy is different from proteolytic cleavage by furin, the same result is produced, which is to say, the recombinant protein without its carboxy-terminal (stem and anchor domains) and, consequently, without association with the ER membrane.
(60) The composition of the present invention is intended to immunize against the viral vector or virulent forms homologous thereto and/or other pathogens, from which the gene of the heterologous protein expressed by the recombinant virus originated. The composition uses pharmaceutically acceptable carriers.
(61) As used herein, a pharmaceutically acceptable carrier is understood to be a compound that does not adversely affect the health of the organism to be vaccinated. Various pharmaceutically acceptable solutions for use in the preparation of the vaccine composition of the present invention are well known and can be readily adapted by those skilled in this art (see, for example, Remington's Pharmaceutical Sciences (18th edition), ed. A. Gennaro, 1990, Mack Publishing Co., Easton, Pa.).
(62) Table 4 is presented below with a description of the sequences cited and used in the present invention.
(63) TABLE-US-00005 TABLE 4 Numbering of the sequence and description Organism Full sequences of the viruses 1. Virus I - cDNA viral Yellow Fever Virus 2. Virus I - Protein Yellow Fever Virus 3. Virus I HAc - cDNA viral Yellow Fever Virus 4. Virus I HAc - Protein Yellow Fever Virus 5. Virus II-1 - cDNA viral Yellow Fever Virus 6. Virus II-1 - Polyprotein Yellow Fever Virus 7. Virus II-1 HAc - cDNA viral Yellow Fever Virus 8. Virus II-1 HAc - Polyprotein Yellow Fever Virus 9. Virus II-2 - cDNA viral Yellow Fever Virus 10. Virus II-2 - Polyprotein Yellow Fever Virus 11. Virus II-3 - cDNA viral Yellow Fever Virus 12. Virus II-3 - Polyprotein Yellow Fever Virus Sequences of the inserts 13. Insert I - DNA Yellow Fever Virus 14. Insert I - Protein Yellow Fever Virus 15. Insert I HAc - DNA Yellow Fever Virus 16. Insert I HAc - Protein Yellow Fever Virus 17. Insert II-1 - DNA Yellow Fever Virus 18. Insert II-1 - Protein Yellow Fever Virus 19. Insert II-1 HAc - DNA Yellow Fever Virus 20. Insert II-1 HAc - Protein Yellow Fever Virus 21. Insert II-2 - DNA Yellow Fever Virus 22. Insert II-2 - Protein Yellow Fever Virus 23. Insert II-3 - DNA Yellow Fever Virus 24. Insert II-3 - Protein Yellow Fever Virus Sequences of the motifs 25. EGFP - DNA Aequorea victoria 26. EGFP - Protein Aequorea victoria 27. N-terminal NS1 - DNA Yellow fever virus 28. N-terminal NS1 - Protein Yellow fever virus 29. motif containing the N-glycosylation site of the Rabies virus G protein of the rabies virus 30. motif containing the N-glycosylation site of the Rabies virus G protein of the rabies virus - Protein 31. segment corresponding to the N-glycosylation Rabies virus site of the G protein of the rabies virus 32. segment corresponding to the N-glycosylation Rabies virus site of the G protein of the rabies virus - protein 33. spacer 5′ of the motif containing the N- Artificial sequence glycosylation site of the G protein of the rabies virus 34. N-terminal spacer of the motif containing the N- Artificial sequence glycosylation site of the G protein of the rabies virus - protein 35. spacer 3′ of the motif containing the N- Artificial sequence glycosylation site of the G protein of the rabies virus 36. C-terminal spacer of the motif containing the N- Artificial sequence glycosylation site of the G protein of the rabies virus - protein - protein 37. motif containing the N-glycosylation site of the Dengue virus type 2 E protein of the dengue virus type 2 - DNA 38. motif containing the N-glycosylation site of the Dengue virus type 2 E protein of the dengue virus type 2 - Protein 39. segment corresponding to the N-glycosylation Dengue virus type 2 site of the E protein of the dengue virus type 2 40. segment corresponding to the N-glycosylation Dengue virus type 2 site of the E protein of the dengue virus type 2 - Protein 41. spacer 5′ of the motif containing the N- Artificial sequence glycosylation site of the E protein of the dengue virus type 2 - DNA 42. N-terminal spacer of the motif containing the N- Artificial sequence glycosylation site of the E protein of the dengue virus type 2 - Protein 43. spacer 3′ of the motif containing the N- Artificial sequence glycosylation site of the E protein of the dengue virus type 2 - DNA 44. C-terminal spacer of the motif containing the N- Artificial sequence glycosylation site of the E protein of the dengue virus type 2 - Protein 45. Motif containing the furin cleavage site of the Homo sapiens von Willebrand human factor - DNA 46. Motif containing the furin cleavage site of the Homo sapiens von Willebrand human factor - Protein 47. segment corresponding to the furin cleavage Homo sapiens site of the von Willebrand human factor - DNA 48. segment corresponding to the furin cleavage Homo sapiens site of the von Willebrand human factor - Protein 49. spacer 5′ of the motif containing the furin Artificial sequence cleavage site of the von Willebrand human factor - DNA 50. N-terminal spacer of the motif containing the Artificial sequence furin cleavage site of the von Willebrand human factor - Protein 51. spacer 3′ of the motif containing the furin Artificial sequence cleavage site of the von Willebrand human factor - DNA 52. C-terminal spacer of the motif containing the Artificial sequence furin cleavage site of the von Willebrand human factor - Protein 53. Motif containing the furin cleavage site of the Tick-Borne prM Protein - TBE virus - DNA Encephalitis Virus 54. Motif containing the furin cleavage site of the Tick-Borne prM Protein - TBE virus - Protein Encephalitis Virus 55. segment corresponding to the furin cleavage site Tick-Borne of the prM Protein - TBE virus - DNA Encephalitis Virus 56. segment corresponding to the furin cleavage site Tick-Borne of the prM Protein - TBE virus - Protein Encephalitis Virus 57. spacer 5′ of the motif containing the furin Artificial sequence cleavage site of the prM Protein - TBE virus - DNA 58. N-terminal of the motif containing the furin Artificial sequence cleavage site of the prM Protein - TBE virus - Protein 59. Spacer 3′ of the motif containing the furin Artificial sequence cleavage site of the prM Protein - TBE virus 60. C-terminal spacer of the motif containing the Artificial sequence furin cleavage site of the prM Protein - TBE virus 61. C-terminal spacer of the motif containing the Artificial sequence furin cleavage site of the prM Protein - TBE virus 62. Motif containing the 2A peptide of the aphthous Foot-and-mouth fever virus disease virus 63. Motif containing the 2A peptide of the aphthous Foot-and-mouth fever virus disease virus 64. segment corresponding to the 2A peptide of the Foot-and-mouth aphthous fever virus disease virus 65. segment corresponding to the 2A peptide of the Foot-and-mouth aphthous fever virus disease virus 66. spacer 5′ of the motif containing the 2A peptide Artificial sequence of the aphthous fever virus 67. N-terminal spacer of the motif containing the 2A Artificial sequence peptide of the aphthous fever virus 68. spacer 3′ of the motif containing the 2A peptide Artificial sequence of the aphthous fever virus - DNA 69. C-terminal spacer of the motif containing the 2A Dengue virus type 4 peptide of the aphthous fever virus 70. Truncated stem-anchor domain of the E protein Dengue virus type 4 of the dengue virus type 4 71. Truncated stem-anchor domain of the E protein Dengue virus type 4 of the dengue virus type 4 72. Truncated stem-anchor domain of the E protein Dengue virus type 4 of the dengue virus type 4
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