Patent Application
20230145894
The present invention relates to a method for detecting an immunoglobulin in a sample, the fusion protein to be used in this method as well as mutant luciferases with improved properties that notably can be used in this method.
To test for evidence of past or present adaptive immune response to infection in a subject, serological assay against the infectious agent or allergen using either rapid diagnosis test or laboratory-based immunoassay formats must be performed.
There is wide range of serological tests on the market. For example, laboratory-based immunoassay may be enzyme immunoassay (EIA), radio-immunoassay (RIA), fluorescence immunoassay (FIA), chemoluminescence immunoassay (CLIA) or electroluminescence assay (ECL).
However, whatever the protocol used for the serological test, it has to meet safety, quality and performance standards (with regard to both analytical and clinical sensitivity and specificity).
Most standard serological tests on the market for detecting and/or quantifying an immunoglobulin indicative of a past or present infection are sensitive but they require relatively large amount of plasma (which can be problematic when testing young children), and are also limited by their cost and the need for a specific instrument to analyze the test's results. Therefore, further developments are needed to improve the sensitivity of serological test, while markedly reducing the volume of sample required and the cost, without sacrificing assay robustness, reproducibility and accuracy.
Now, the applicant has found that by fusing a variable domain of a camelid heavy-chain antibody (VHH) to a luciferase derived from the catalytic domain of Oplophorus gracilirostris luciferase, it can be performed the detection of specific immunoglobulin in reduced sample volume while keeping the required specificity and sensitivity with an increased dynamic range and a shorter time of assay. The serological assay designs by the application may be used in rapid diagnosis test. It is thus possible to design assays for detecting and/quantifying immunoglobulins specific for any infectious disease of interest but also allergy or autoimmune diseases.
A subject of the present invention is therefore a fusion protein comprising:
The applicant has also found that the results of its serological test are ever improved using specific mutants of the NanoKAZ luciferase.
Thus, the present invention also relates to a luciferase having at least 80% amino acid sequence identity to the amino acid sequence SEQ ID NO: 1 and comprising at least one amino acid substitution selected from the group consisting of:
Luciferase Mutants
“Luciferase” as used herein refers to a class of oxidative enzymes that produce bioluminescence. Bioluminescence is the emission of light produced in a biochemical reaction involving the oxidation of a substrate via an enzyme.
Luciferases encompass are commonly found in lower organisms such as bacteria, fungi, insects, dinoflagellates, radiolarians, cnidarians, crustaceans, jelly fishes and cephalopods. Among these various luciferases, the one from the deep sea shrimp Oplophorus had promising properties (Shimomura O, Masugi T, Johnson F H, Haneda Y., Properties and reaction mechanism of the bioluminescence system of the deep-sea shrimp Oplophorus gracilirostris. Biochemistry. 1978 Mar. 21; 17(6):994-8.). However, the 19 kDa subunit (KAZ) having the luciferase activity of this heterodimeric structure does not retain many of the desirable features of the native enzyme as it is unstable and poorly expressed in the absence of the regulatory subunit. The activity has been increased seven fold with the natural substrate coelenterazine by the three amino-acid substitutions V44I, A54I and Y138I (eKAZ) in the sequence of KAZ (Inouye S, Sato J, Sahara-Miura Y, Yoshida S, Hosoya T. Luminescence enhancement of the catalytic 19 kDa protein (KAZ) of Oplophorus luciferase by three amino acid substitutions. Biochem Biophys Res Commun. 2014; 445(1):157-162.).
The folding of the enzyme has been optimized by the mutations of hydrophobic amino acids by hydrophilic residues at the protein surface: A4E, F68D, L72Q, M75K, P115E, and/or N166R.
Then, Hall et al. have engineered a luciferase derived from the 19 kDa subunit of the luciferase from Oplophorus with improved stability called nanoLuc, NLuc as well as nanoKAZ with the following mutations: A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, 190V, P115E, Q124K, Y138I, and N166R (Hall M P, Unch J, Binkowski B F, Valley M P, Butler B L, Wood M G, Otto P, Zimmerman K, Vidugiris G, Machleidt T, Robers M B, Benink H A, Eggers C T, Slater M R, Meisenheimer P L, Klaubert D H, Fan F, Encell L P, Wood K V. Engineered luciferase reporter from a deep sea shrimp utilizing a novel imidazopyrazinone substrate. ACS Chem Biol. 2012 Nov. 16; 7(11):1848-57).
However, the properties of the nanoKAZ luciferase still need to be improved.
Now, the applicant has found that the specific mutants of nanoKAZ have improved solubility and/or catalytic activity and/or photon emission per mol of catalyzed substrate compared to nanoKAZ especially with newly patented substrates (WO2018/197727, Coutant et al., 2019, 2020).
Thus, the present invention relates to a luciferase having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% amino acid sequence identity to the amino acid sequence SEQ ID NO: 1 and comprising at least one amino acid substitution selected from the group consisting of:
For the purposes of comparing two closely-related polynucleotide or polypeptide sequences, the “% identity” between a first sequence and a second sequence may be calculated using an alignment program, such as BLAST® (available at blast.ncbi.nlm.nih.gov, last accessed 9 Mar. 2015) using standard settings. The % identity is the number of identical residues divided by the number of residues in the reference sequence, multiplied by 100. The % identity figures referred to above and in the claims are percentages calculated by this methodology. An alternative definition of % identity is the number of identical residues divided by the number of aligned residues, multiplied by 100. Alternative methods include using a gapped method in which gaps in the alignment, for example deletions in one sequence relative to the other sequence, are accounted for in a gap score or a gap cost in the scoring parameter. For more information, see the BLAST® fact sheet available at ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_BLASTGuide.pdf, last accessed on 9 Mar. 2015.
The luciferase may comprise at least 1, at least 2, at least 3, at least 4, at least 5, at least 6 or at least 7 or 1, 2, 3, 4, 5, 6 or 7 amino acid substitutions selected from the group consisting of:
In one embodiment, the tryptophan (W) at a position corresponding to the position 134 of SEQ ID NO: 1 is substituted with a threonine (T). In an alternative embodiment, the tryptophan (W) at a position corresponding to the position 134 of SEQ ID NO: 1 is substituted with a glutamate (E),
In one embodiment, the tryptophan (W) at a position corresponding to the position 163 of SEQ ID NO: 1 is substituted with a threonine (T). In an alternative embodiment, the tryptophan (W) at a position corresponding to the position 163 of SEQ ID NO: 1 is substituted with a glutamate (E),
In one embodiment, the tyrosine (Y) at a position corresponding to the position 116 of SEQ ID NO: 1 is substituted with a phenylalanine (F).
In one embodiment, the tryptophan (W) at a position corresponding to the position 134 of SEQ ID NO: 1 is substituted with a threonine (T),
In one embodiment, the tryptophan (W) at a position corresponding to the position 163 of SEQ ID NO: 1 is substituted with a threonine (T),
In one embodiment, the isoleucine (I) at a position corresponding to the position 56 of SEQ ID NO: 1 with an alanine (A).
In one embodiment, the tyrosine (Y) at a position corresponding to the position 116 of SEQ ID NO: 1 is substituted with a phenylalanine (F) and the tryptophan (W) at a position corresponding to the position 134 of SEQ ID NO: 1 is substituted with a threonine (T),
In one embodiment, the tyrosine (Y) at a position corresponding to the position 116 of SEQ ID NO: 1 is substituted with a phenylalanine (F) and the cysteine (C) at a position corresponding to the position 166 of SEQ ID NO: 1 is substituted with a serine (S).
In one embodiment, the tyrosine (Y) at a position corresponding to the position 18 of SEQ ID NO: 1 is substituted with an arginine (R), the leucine (L) at a position corresponding to the position 48 of SEQ ID NO: 1 is substituted with a lysine (K), the tryptophan (W) at a position corresponding to the position 134 of SEQ ID NO: 1 is substituted with a glutamate (E) and the tryptophan (W) at a position corresponding to the position 163 of SEQ ID NO: 1 is substituted with a glutamate (E).
In one embodiment, the tyrosine (Y) at a position corresponding to the position 18 of SEQ ID NO: 1 is substituted with an arginine (R), the leucine (L) at a position corresponding to the position 48 of SEQ ID NO: 1 is substituted with a lysine (K), the tryptophan (W) at a position corresponding to the position 134 of SEQ ID NO: 1 is substituted with a glutamate (E), the tryptophan (W) at a position corresponding to the position 163 of SEQ ID NO: 1 is substituted with a glutamate (E) and the cysteine (C) at a position corresponding to the position 166 of SEQ ID NO: 1 is substituted with a serine (S).
In one embodiment, the tyrosine (Y) at a position corresponding to the position 18 of SEQ ID NO: 1 is substituted with an arginine (R), the leucine (L) at a position corresponding to the position 48 of SEQ ID NO: 1 is substituted with a lysine (K), the tyrosine (Y) at a position corresponding to the position 116 of SEQ ID NO: 1 is substituted with a phenylalanine (F), the tryptophan (W) at a position corresponding to the position 134 of SEQ ID NO: 1 is substituted with a glutamate (E) and the tryptophan (W) at a position corresponding to the position 163 of SEQ ID NO: 1 is substituted with a glutamate (E).
In one embodiment, the tyrosine (Y) at a position corresponding to the position 18 of SEQ ID NO: 1 is substituted with an arginine (R), the leucine (L) at a position corresponding to the position 48 of SEQ ID NO: 1 is substituted with a lysine (K), the tyrosine (Y) at a position corresponding to the position 116 of SEQ ID NO: 1 is substituted with a phenylalanine (F), the tryptophan (W) at a position corresponding to the position 134 of SEQ ID NO: 1 is substituted with a glutamate (E), the tryptophan (W) at a position corresponding to the position 163 of SEQ ID NO: 1 is substituted with a glutamate (E) and the cysteine (C) at a position corresponding to the position 166 of SEQ ID NO: 1 is substituted with a serine (S).
The present invention also relates to a luciferase having an amino acid sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, 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, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO 17.
The amino acid sequence of the various luciferases are disclosed in the table 1 below.
Preferably, the luciferase has the amino acid sequence SEQ ID NO: 1 to SEQ ID NO: 11, more preferably SEQ ID NO: 2, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10 or SEQ ID NO: 11. Most preferably the luciferase has the amino acid sequence SEQ ID NO: 8, SEQ ID NO: 11 or SEQ ID NO: 6
The present invention also relates to a polypeptide having a luciferase activity comprising 2 or 3 amino acid sequences selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, 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, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO 17.
Such polypeptide may have the amino acid sequence selected from the group consisting of SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44 and SEQ ID NO: 45. The present invention also relates to a polypeptide with a luciferase activity having the amino acid sequence SEQ ID NO: 46.
MTGGQQMGRDLYDDDDKDPMVSKGEELIKENMRSKLYLEGSVNGHQFKCTHEGEGKPYEGKQTNRIKVVEGG
PLPFAFDILATHFMYGSKVFIKYPADLPDYFKQSFPEGFTWERVMVFEDGGVLTATQDTSLQDGELIYNVKV
RGVNFPANGPVMQKKTLGWEPSTETMYPADGGLEGRCDKALKLVGGGHLHVNFKTTYKSKKPVKMPGVHYVD
RRLERIKEADNETYVEQYEHAVARYSNLGGG
FTLEDFVGDWRQTAGYNLDQVLEQGGVSSLFQNLGVSVTPI
GSVNGHQFKCTHEGEGKPYEGKQTNRIKVVEGGPLPFAFDILATHFMYGSKVFIKYPADLPDYFKQSFPEGE
TWERVMVFEDGGVLTATQDTSLQDGELIYNVKVRGVNFPANGPVMQKKTLGWEPSTETMYPADGGLEGRCDK
ALKLVGGGHLHVNFKTTYKSKKPVKMPGVHYVDRRLERIKEADNETYVEQYEHAVARYSNLGGGMDELYK
The luciferase of the invention may have one or more heterologous amino acid sequences at the N-terminus, C-terminus, or both, which optionally directly or indirectly interact with a molecule of interest. The heterologous sequence may be a tag, such as a tag for purification purpose or a peptide or protein of interest. The luciferase may be also linked to an organic molecule (such as an organic molecule binder).
Affinity tags may be used at the C-end of the luciferase amino-acid sequence for purification, for secondary binding probe, for bead binding, for solid substrate binding purpose. Examples of amino acid sequence of such tags are given in the table 3 below.
The peptide or protein of interest may be selected from the group consisting for a variable domain of a camelid heavy-chain antibody (VHH), a single-chain variable fragment (scFv), a variable regions of a heavy chain (VH), an immunoglobulin (Ig), interleukine, cytokine, chemokine, receptor ectodomain, peptidic antigen, peptidic allergen, receptor ectodomain, viral capsid peptidic fragment, bacteria surface peptidic fragment and cell surface peptidic fragment but not limited to.
Linkers may be inserted in between the amino-end of the peptide of interest (eg. VHH, scFv, VH, Ig but not limited to) or the organic molecule binder and the carboxy-end luciferase for articulating the two domains. Linkers may have from 0 to 10 residues. In one embodiment, the amino-end of the peptide of interest or the organic molecule binder and the carboxy-end luciferase amino-acid sequence for articulating the two domains may be linked directly, without the use of a linker.
The amino acid sequence of linkers are disclosed in the table 4 below.
When necessary or required for detection or measurement purpose linkers are inserted in between the amino-end protein binder domain (VHH, scFv, VH, Ig but not limited to), organic molecule binder or peptidic sequence of interest and the carboxy-end luciferase articulating the two domains with a protease-specific cleavage site for luciferase releasing purpose. Amino acid sequence of such thrombin-specific cleavable linkers are the following with from 5 to 14 residues. Thrombin cleavage sites are disclosed in the table 5 below.
In particular, the present invention also relates to a fusion protein comprising the luciferase of the invention. The luciferase may be linked to a peptide of interest.
As mentioned above, the peptide of interest may be selected from the group consisting for a variable domain of a camelid heavy-chain antibody (VHH), a single-chain variable fragment (scFv), a variable regions of a heavy chain (VH), an immunoglobulin (Ig), interleukine, cytokine, chemokine, receptor ectodomain, peptidic antigen, peptidic allergen, receptor ectodomain, viral capsid peptidic fragment, bacteria surface peptidic fragment and cell surface peptidic fragment but not limited to.
Suitably the luciferase or the fusion protein comprising the luciferase of the invention are recombinant. Recombinant means that the luciferase or the fusion protein is the product of at least one of mutation or cloning steps, or other procedures that result in a luciferase that is distinct from a luciferase found in nature, in particular distinct from the luciferase of Oplophorus found in the nature.
The present invention also relates to a polynucleotide encoding the luciferase of the invention or the fusion protein comprising the luciferase of the invention.
Suitably the polynucleotides of the invention are recombinant. As mentioned above, recombinant means that the polynucleotide is the product of at least one of cloning, restriction or ligation steps, or other procedures that result in a polynucleotide that is distinct from a polynucleotide found in nature.
The polynucleotide may further encode a polypeptide of interest linked to the luciferase, wherein the polypeptide of interest and the luciferase are capable of being expressed as a fusion protein.
Advantageously, the polynucleotide may be codon-optimized for expression of the luciferase of the invention or of the fusion protein comprising the luciferase in a host cell.
The polynucleotide of interest may comprise a nucleotide sequence selected from the group consisting of SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 60, SEQ ID NO: 61 and SEQ ID NO: 62. These nucleotide sequences of embodiments of expression-optimized polynucleotide are summarized in the table 6 below.
The present invention also relates to a vector comprising the polynucleotide of the invention.
As used herein, vector (or plasmid) refers to discrete elements that are used to introduce heterologous DNA into cells for either expression or replication thereof.
Selection and use of such vehicles are well-known to those of skill in the art. An expression vector includes vectors capable of expressing DNAs that are operatively linked with regulatory sequences, such as promoters, that are capable of effecting expression of such DNA fragments. Thus, an expression vector refers to a recombinant DNA construct, such as a plasmid, a phage, recombinant virus or other vector that, upon introduction into an appropriate host cell, results in expression of the cloned DNA. Appropriate expression vectors are well known to those of skill in the art.
A recombinant vector is a vector comprising a recombinant polynucleotide.
Advantageously, the vector comprises the polynucleotide operably linked to a promoter.
As used herein, operatively linked refers to the functional relationship of DNA with regulatory and effector sequences of nucleotides, such as promoters, enhancers, transcriptional and translational stop sites, and other signal sequences.
For example, operative linkage of DNA to a promoter refers to the physical and functional relationship between the DNA and the promoter such that the transcription of such DNA is initiated from the promoter by an RNA polymerase that specifically recognizes, binds to and transcribes the DNA.
As used herein, a promoter refers to a segment of DNA that controls transcription of the DNA to which it is operatively linked.
The polynucleotide or the vector of the invention may be into a cell, typically a prokaryote or eukaryote cell. The vector may be conservative in the cytoplasm or the polynucleotide could be integrated in the genome using lentiviral vector or genome edition (i.e. CRISPR-Cas9 but not limited to).
Therefore, the present invention also relates to a cell comprising the polynucleotide of the invention or the expression vector of the invention.
In one embodiment, the luciferase or the fusion protein comprising the luciferase is secreted from the prokaryotic or eukaryotic cell, expressed in the cytoplasm or in the periplasm in the case of bacteria.
In one embodiment, the luciferase or the fusion protein comprising the luciferase is synthesized in vitro using transcription and translation kit.
The present invention also relates to a non-human transgenic animal comprising the cell or the polynucleotide or the vector of the invention.
The present invention also relates to a kit comprising:
Preferably, the kit comprises the luciferase or the fusion protein and the substrate. Coelenterazine is the natural substrate for the shrimp Oplophorus luciferase but improvement in signals may be obtained with furimazine.
Consequently, the substrate may be selected from the group consisting of coelenterazine, furimazine or derivatives thereof.
Derivatives of furimazine and their O-acetylated moieties in their steady-state as pro-substrates are disclosed in the patent application WO2018/197727 A1. Such derivatives of furimazine provide a better bioluminescence signals in term of intensity, signal-to-noise ratio and/or duration.
Consequently, the substrate may be selected in the group consisting in:
These substrates are respectively disclosed in WO2018/197727 A1 with the following names Q3, Q12, Q16, Q21, Q14, Q18, Q20, Q27, Q28, Q29, Q34, Q36, Q41, Q51, Q54, Q56, Q58, Q61, Q72, Q73, Q81, Q82, Q83, Q84, Q85, Q101, Q100, Q99, Q98, Q97, Q96, Q105, Q107, Q108, Q117, Q121, Q124, Q127, Q129, Q131, Q132, Q135, Q143 and Q149.
In a preferred embodiment, the substrate is 8-(2,3-difluorobenzyl)-2-((5-methylfuran-2-yl)methyl)-6-phenylimidazo[1,2-a]pyrazin-3(7H)-one (Q-108 as disclosed in Table 1 page 129 of WO2018/197727 A1).
The present invention also relates to a method for producing the luciferase of the invention comprising the step of:
The present invention also relates to a method of producing the luciferase of the invention or the fusion protein comprising the luciferase of the invention comprising the steps of:
The present invention also relates the use of the luciferase of the invention or of the fusion protein comprising the luciferase of the invention in a luminescence reaction; the use comprising the addition of a substrate for the luciferase.
The present invention provides a method comprising the steps of:
(a) exposing the luciferase or the fusion protein to a substrate and
(b) detecting luminescence.
Prior to the exposition, a polynucleotide according to the invention may be introduced into a cell and/or the luciferase or the fusion protein may be expressed.
The method may be in vitro, ex vivo or in vivo.
Fusion Protein
As mentioned in the summary of the invention, the present invention relates to a fusion protein comprising:
In one embodiment the fusion protein comprises
A single-chain variable fragment (scFv) is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a linker.
In another embodiment the fusion protein comprises:
VHH are variable domain of a camelid heavy-chain antibody. Indeed, in members of the family Camelidae a significant proportion of serum antibodies are homodimeric IgGs with a molecular weight of about 80 kD (Hamers-Casterman et al. 1993 Nature, 363, 446-448). These heavy chain immunoglobulins (Ig) contain three domains and their variable region is referred to as VHH. Recombinant VHHs (˜12-14 kD in size) constitute intact antigen-binding domains and exhibit a broad antigen-binding repertoire. Their hypervariable regions are expanded and exhibit unique characteristics, such as the substitution of three to four hydrophobic framework residues (which interact with the VL in conventional antibodies) by more hydrophilic amino acids. To stabilize the enlarged CDRs, VHHs may possess in addition of the canonical disulfide bond, an extra disulfide bound between CDR1 and CDR3 in dromedaries and CDR2 and CDR3 in llamas (Harmsen and De Haard 2007 Appl Microbiol Biotechnol., 77, 13-22; Muyldermans 2001 J Biotechnol., 74, 277-302). The extended CDR3 loop can adopt a convex conformation, whereas conventional paratopes are limited to concave or flat structures (Muyldermans 2001 J Biotechnol., 74, 277-302). These features allow VHHs to recognize unique epitopes that are poorly immunogenic for conventional antibodies (Lafaye et al. 2009 Mol Immuno., 46, 695-704; Wernery 2001 J Vet Med B Infect Dis Vet Public Health., 48, 561-568). Although VHHs are by definition monovalent antibodies, which by default exclude any avidity effect, their biological activity measured as IC50 in vitro can be similar to conventional, bivalent antibody molecules (Thys et al. 2010 Antiviral Res., 87, 257-264). The VHH may be selected among known VHHs. Examples of known VHHs that can be used according to the invention are disclosed in the table 3 below.
Therefore, the VHH of the fusion protein according to the invention may have the amino acid sequence selected from the group consisting of SEQ ID NO: 57, SEQ ID NO: 58 and SEQ ID NO: 59.
VHH to be used according the invention may be also selected from a library.
Methods, such as phage display, have been described to select antigen-specific VHH from VHH libraries of immunized camels or llamas. The VHH genes are cloned in phage display vectors, the antigen binders are obtained by panning and selected VHH are expressed in bacteria. The recombinant VHHs have a number of advantages compared with the conventional antibody fragments (Fab or scFv), because only one domain has to be cloned and because these VHHs are well expressed, highly soluble in aqueous environments and are stable at high temperature.
VHH may be also be custom designed, screened from synthetic libraries derivatized from camelid VHH scaffold or from humanized scFv scaffold.
For example, the VHH is obtainable by the method comprising the steps of:
(a) immunizing a camelid, preferably a Lama pacos, with the immunoglobulin or a fragment thereof,
(b) isolating peripheral lymphocytes of the immunized camelid, obtaining the total RNA and synthesizing the corresponding cDNAs (methods are known in the art; for instance see Lafaye et al. 1995 Res Immunol., 146, 373-82; Erratum in: 1996, Res Immunol., 147, 61),
(c) constructing a library of cDNA fragments encoding VHH domains,
(d) transcribing the VHH domain-encoding cDNAs obtained in step (c) to mRNA using PCR, converting the mRNA to ribosome display format, and selecting the VHH domain by ribosome display.
The polynucleotide encoding for the VHH and the polynucleotide encoding a polypeptide with a luciferase activity may be inserted in a vector. The polynucleotide encoding for the VHH and the polynucleotide encoding the polypeptide with a luciferase activity are linked so as the fusion protein of the invention to be expressed.
The vector may be then introduced into a cell, for example by transformation of a bacterial cell, so as the cell expresses the fusion protein.
The N-terminal domain and the C-terminal domain of the fusion protein and/or the VHH and the polypeptide with a luciferase activity may be linked via a linker. Preferred linkers have the amino acid sequence selected from the group consisting of GS, AAA, SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 26.
The fusion protein may comprise one or more heterologous amino acid sequences at the N-terminus, C-terminus, or both. In particular, it may comprise a tag such as poly-histidine tag for purification purpose.
The present invention also relates to a polynucleotide encoding the fusion protein of the invention as well as to a vector comprising this polynucleotide.
Suitably the fusion protein of the invention or the polynucleotide encoding thereof are recombinant.
Advantageously, the vector comprises the polynucleotide operably linked to a promoter.
Advantageously, the polynucleotide may be codon-optimized for expression of the fusion protein.
The polynucleotide or the vector of the invention may be into a cell.
Therefore, the present invention also relates to a cell comprising the polynucleotide of the invention or the vector of the invention.
The immunoglobulin against which the VHH is directed may be from a human or a non-human animal, preferably a human.
The immunoglobulin may be an IgG1, IgG2, IgG3, IgG4, IgA, IgM, IgD or IgE. Preferably, the immunoglobulin is an IgG, an IgE, an IgM or an IgA. The immunoglobulin of interest will depend on the aim of the assay. For example, when the aim of an assay is to diagnosis an allergy, IgE mainly and IgG secondarily will be preferred. IgM may be used to diagnose a recent infection in blood. IgG may be used to diagnose an older infection in blood. IgA may be used to diagnose infection in blood, mucosa or saliva.
Typically, the immunoglobulin is directed against an antigen.
The antigen may be selected from the group consisting of an allergen, a virus, a bacteria, a fungus and a parasite or a fragment or part thereof.
For example, allergen may be components, mainly proteins, of milk in particular cow's milk, soy, egg, wheat, cod, seafood, shellfish, fishes, nuts, peanut, D. pteronyssinus, Alternaria, cat, dog, grass or birch pollen, dust mite, anaesthetics (curare but not limited to), antibiotics (amoxicillin but not limited to), latex, fabrics, venoms (from wasp and bees but not limited to).
Virus may be for example severe acute respiratory syndrome coronavirus 2 (SARS CoV2) or severe acute respiratory syndrome coronavirus 1 (SARS CoV1). Fragment of virus may comprise an isolated protein from the virus, synthesized or expressed as recombinant, such as protein Spike (S) or Nucleoprotein (N) or fragments corresponding to structural or functional domains or fragment of any size.
The immunoglobulin may also be an auto-antibody.
In a preferred embodiment, the VHH is directed against the constant fragment (Fc) of the immunoglobulin.
In one embodiment, the polypeptide with a luciferase activity is a luciferase having the amino acid sequence SEQ ID NO: 1.
The polypeptide with a luciferase activity may have at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% amino acid sequence identity to the amino acid sequence SEQ ID NO: 1.
In one embodiment, the polypeptide with a luciferase activity is a mutant luciferase as disclosed above.
Thus, the polypeptide with a luciferase activity may have at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% amino acid sequence identity to the amino acid sequence SEQ ID NO: 1 and comprising at least one amino acid substitution selected from the group consisting of:
The polypeptide having a luciferase activity may have an amino acid sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, 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, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, and SEQ ID NO 17.
The polypeptide having a luciferase activity may also have the amino acid sequence selected from the group consisting of SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45 and SEQ ID NO: 46.
The present invention also relates to a kit comprising:
As mentioned above, coelenterazine is the natural substrate for the shrimp Oplophorus luciferase but improvement in signals may be obtained with furimazine.
Consequently, the substrate may be selected from the group consisting of coelenterazine, furimazine or derivatives thereof.
Derivatives of furimazine are disclosed in the patent application WO2018/197727 A1.
Such derivatives of furimazine provide a better bioluminescence signals in term of intensity, signal-to-noise ratio and/or duration.
Consequently, the substrate may be selected in the group consisting in:
These substrates are respectively disclosed in WO2018/197727 A1 with the following names Q3, Q12, Q16, Q21, Q14, Q18, Q20, Q27, Q28, Q29, Q34, Q36, Q41, Q51, Q54, Q56, Q58, Q61, Q72, Q73, Q81, Q82, Q83, Q84, Q85, Q101, Q100, Q99, Q98, Q97, Q96, Q105, Q107, Q108, Q117, Q121, Q124, Q127, Q129, Q131, Q132, Q135, Q143 and Q149.
In a preferred embodiment, the substrate is 8-(2,3-difluorobenzyl)-2-((5-methylfuran-2-yl)methyl)-6-phenylimidazo[1,2-a]pyrazin-3(7H)-one (Q-108 as disclosed in Table 1 page 129 of WO2018/197727 A1).
The kit may also comprises reagents for the detection of luciferase activity, a control and/or support.
Preferably, the antigen is immobilized on the support. The support may be a slide, a plate, for example a multi-well plate, a strip, for example a strip a nitrocellulose or PVDF membrane or paper, a tube, a disk, a loop, a stick, a propeller, a fibre or an assemblage of fibers.
The present invention also relates to the use of the fusion protein of the invention for detecting and/or quantifying the immunoglobulin in a sample.
The sample may be for example selected from the group consisting of whole blood, serum, plasma, cerebrospinal fluid, sperm, urine, nasopharyngeal smear, oropharyngeal smear, vaginal smear, stool, sweat, saliva, tracheal washing and bronchial washing.
The present invention also relates to a method for detecting the presence of an immunoglobulin in a sample comprising the steps of:
(a) contacting the sample with the fusion protein of the invention,
(b) adding a substrate for the polypeptide with a luciferase activity and
(c) detecting the luminescence.
Typically, the polypeptide with a luciferase activity is the polypeptide with a luciferase activity of the fusion protein of the invention.
Since the level of immunoglobulin in the sample may be also measured by the mean to the emitted luminescence, the present invention also relates to a method for quantifying the level of an immunoglobulin in a sample comprising the steps of:
(a) contacting the sample with the fusion protein of the invention,
(b) adding a substrate for the polypeptide with a luciferase activity and
(c) quantifying the luminescence.
Typically, the polypeptide with a luciferase activity is the polypeptide with a luciferase activity of the fusion protein of the invention.
The methods of the invention may also comprise a step of immobilizing the antigen to a support and/or a step of providing a support where the antigen is immobilized on.
The immobilization may be performed by either by surface adsorption, chemical linkage or non-covalent interaction.
The methods may comprise a step of contacting the sample with the immobilized antigen.
The interaction of the fusion protein with the immunoglobulin may be challenged either by dilution, heating or addition of salt, acid, base, or organic or mineral buffer or any competitor for the interaction, or by lateral flow or acoustic frequency
When detecting the luminescence, the number of photons per second may be counted eventually according to their wavelength.
The methods may also comprise a step of comparing to the luminescence emitted to a control.
The present invention also relates to a method for quantifying the level of an immunoglobulin per affinity interval in a sample for evaluating the affinity range of a polyclonal immunoglobulin mixture comprising the steps of:
(a) contacting the sample with an immobilized antigen in the presence of dilution series of the free antigen,
(b) contacting the sample with the fusion protein of the invention and
(c) adding a substrate for the polypeptide with a luciferase activity,
(d) quantifying the luminescence and plot light intensity versus antigen concentration.
Typically, the immunoglobulin of which level is quantified is the immunoglobulin to which the antibody of the fusion protein is directed. The antigen is the antigen to which the immunoglobulin is directed. The polypeptide with a luciferase activity is the polypeptide with a luciferase activity of the fusion protein of the invention.
The invention will be further illustrated by the following figures and examples.
However, these examples and figures should not be interpreted in any way as limiting the scope of the present invention.
NanoKAZ/nanoLuc results of an intensive mutagenesis for optimizing enzyme production and light intensity with the smallest length from the catalytic domain of the luciferase from Oplophorus gracilirostris. However beyond improvement of the catalytic activity of the enzyme, four observations invite finding mutations overcoming 1) enzyme inactivation by reaction products, 2) reaction inhibition by high substrate concentration, 3) low quantum yield of the oxidation reaction, 4) propensity of the enzyme to be adsorbed by material surface (tube, well, membrane . . . ).
Material and Methods:
nanoKAZ (SEQ NO:1) is an optimized sequence of the catalytic domain of the luciferase from Oplophorus gracilirostris. (WO2012/061530).
The gene nanoKAZ (SEQ NO:33 [jaz526]) has been synthetized by Eurofins (Germany) with carboxy-end His6-tag and flanking region corresponding to the pET23 sequence (Novagen). PCR purified pET23 vector and the synthetic gene were assembled according to the Gibson method assembling complementary fragments using the NEBuilder HiFi assembly master mix (New England BioLabs). Single or dual mutations have been introduced by PCR in SEQ ID NO: 2 [jaz544], 3 [jaz583], 4 [jaz584], 5 [jaz560], 6 [jaz585], 7 [jaz619]. The gene of SEQ NO:40 [jaz536]) has been synthetized by Eurofins (Germany) with carboxy-end His6-tag and flanking region corresponding to the pET23 sequence (Novagen). Single or dual mutations SEQ NO 41 [jaz570], 42 [jaz572], 43 [jaz573] have been introduced by PCR. in Multiple mutations have been introduced by the Gibson method assembling complementary fragments of the gene carrying specific mutations using NEBuilder HiFi assembly master mix (New-England Biolabs).
Genes SEQ ID NO: 42 [JAZ621] with duplication of SEQ ID NO: 1, SEQ ID NO: 43 [JAZ622] with double substitution of the tyrosine (Y) at a position 116 by a phenylalanine (F) in the duplication of SEQ ID NO: 1, SEQ ID NO: 44 [JAZ476] with triplication of SEQ ID NO: 1, SEQ ID NO: 45 [JAZ620] with triple substitution of the tyrosine (Y) at a position 116 by a phenylalanine (F) in the triplication of SEQ ID NO: 1 and SEQ ID NO: 46 [Scoprii68] substitutions of the tyrosine (Y) at a position 116 by a phenylalanine (F) of Antares sequence encompassing SEQ ID NO: 1 were all synthesized by Eurofins (Germany) with carboxy-end His6-tag and flanking region corresponding to the pET23 sequence (Novagen).
The products (5 mL) were used to transform NEB 5-alpha competent E. coli and grown overnight on LB/Agar/ampicillin in Petri dish. Isolated colonies were grown in liquid medium, plasmids were isolated and nucleotide sequence was performed to confirm the presence of the mutations at the correct positions.
Results:
The mutation of the residue tyrosine at position 116 by a phenylalanine (SEQ ID NO: 2 [JAZ544]) increased by 250% the catalytic activity of the nanoKAZ with the furimazine and 1400% with Q108 by reference with nanoKAZ/furimazine. Duplication (SEQ ID NO: 45) or triplication of the mutated catalytic domain (SEQ ID NO: 45) increase the catalytic activity by 2600% and 3500% respectively. Substrate diffusion rate is limiting the 2- or 3-fold expected improvement of the activity of the single domain (1400%). We have shown that luciferase activity is decreasing with time with a rate depending on the substrate nature (Coutant et al 1999). Decreasing activity is fast with Q80 and slow with Q103. Unfortunately, higher is the light emission, fastest is the enzyme inactivation. There is a compromise between light intensity (flash) or long (glow) lifetime. We have shown that decreasing is due to the enzyme inactivation. Mutation of cysteine 166 by a residue serine (SEQ ID NO: 7 [JAZ619]) reduces the rate of inactivation.
Mutation of tryptophan at position 134 by a threonine (SEQ ID NO: 3 [JAZ583]) in the vicinity of the hydrophobic back pocket mildly reduces the inhibition by high concentration of substrate. We counted 1 photon every 1460 molecules of furimazine catalyzed by a molecule of nanoKAZ (SEQ ID NO: 1) at room temperature at furimazine concentration at the maximal reaction rate (54 microM). The choice of substrate modulate this quantum yield from very low to moderate. Lower is the substrate concentration, higher is the quantum yield but unfortunately lower is the reaction rate and lower is the photon emission. Mutation of the residue tyrosine at position 116 by a phenylalanine (SEQ ID NO: 2 [JAZ544]) improves moderately the photon emission count. Mutations of tryptophans at position 134 (SEQ ID NO: 3 [JAZ583]) and 163 (SEQ ID NO: 4 [JAZ584]) pointing out at the protein surface, are the most effective for improving the solubility of the enzyme and reducing surface adsorption affecting assays with higher noise.
Combination of mutations is giving improved properties in terms of light intensity, lifetime, and solubility. Best compromises are selected according to the specific properties required by the application: light intensity/expected sensibility, lifetime/experiment duration, solubility/experimental conditions.
Several sequences allow an increased signal by duplication or triplication of the catalytic domain. They are mainly used for in vitro or in vivo imaging application requiring light intensity for live imaging, fast kinetics or deep tissue observation. For diagnosis their application in assays are not useful as they increase the signal and the noise. Noticeably diffusion rate of substrate to active site are limiting activity if the substrate concentration is low.
Two color applications with a single substrate but two luciferases as reporter can be performed by using one of sequences from 1 to 15 and the Antares or Scorpii (SEQ NO: 48) which emits redshifted photons through energy resonance transfer from the nanoKAZ to the mOrange derived from Discosoma sp. red fluorescent protein (Shaner Nc, Campbell Re, Steinbach Pa, Giepmans Bng, Palmer Ae, Tsien Ry (2004). Nature Biotechnology, 22(12), 1567-1572).
Materials and Method
Human Plasma
Plasma samples from patients with peanut allergy were obtained as part of their enrolment into an institutional review board—approved clinical trial of oral immunotherapy in children and adults with peanut allergy (peanut oral immunotherapy study: safety, efficacy and discovery; ClinicalTrials.gov Identifier: NCT02103270, US). Peanut allergy was defined as having a reaction to a double-blind, placebo-controlled food challenge to peanut (with reactions elicited with 500 mg of peanut protein) and a positive skin prick test response to peanut (wheal 5 mm). Plasma samples from healthy donors were obtained from the French blood bank (Etablissement Francais du Sang, EFS).
Fusion Protein Anti-IgE sdAb026-nanoKAZ
Design and Synthesis of Plasmid Encoding the Anti-IgE Nanobody-Luciferase Fusion Protein (pET23-sdAb026-Nanokaz)
nanoKAZ is an optimized sequence of the catalytic domain of the luciferase from Oplophorus gracilirostris (WO2012/061530).
The gene nanoKAZ has been synthetized by Eurofins (Germany) with carboxy-end
His6-tag and flanking region corresponding to the pET23 sequence (Novagen). pET23 plasmid has been amplified with the forward and reverse oligonucleotides (Fwd:5′CTCGAGCACCACCACCACCACCAC3′ (SEQ ID NO: 47); Rvr:5′GGTATATCTCCTTCTTAAAGTTAAAC3′ (SEQ ID NO: 48), Eurofins) using a Q5 DNA polymerase, dNTP mix (New England BioLabs). PCR product was purified by electrophoresis on agarose gel (1%, Macherey Nagel). Purified pET23 vector and the synthetic gene were assembly (pET23-nanoKAZ) using NEBuilder HiFi assembly master mix (New England BioLabs).
The slgE—binding moiety is issued from a humanized heavy chain antibody of alpaca selected against sIgE (single-domain antibody, sdAb026) (Jabs F, Plum M, Laursen N S, Jensen R K, Molgaard B, Miehe M, et al. Trapping IgE in a closed conformation by mimicking CD23 binding prevents and disrupts FcepsilonRI interaction. Nat Commun 2018; 9:7, WO2014/087010 A1). sdAb026 recognizes the constant Cc3 region of human IgE. sdAb026 has an affinity for IgE similar to that of the therapeutic anti-IgE antibody omalizumab (KD 1.4 nM vs. 2.6 nM, respectively3,5), and was reported to inhibit interactions between IgE and the two receptors FcεRI and CD23.
The gene sdab026 has been synthetized by Eurofins with flanking regions corresponding to the pET23-nanoKAZ sequence. Synthetic gene sdab026 has been amplified with the corresponding forward and reverse oligonucleotides (Fwd: 5′ATGGTCTTCACACTCGAAGATTTC3′ (SEQ ID NO: 49); Rvr: 5′CATGGTATATCTCCTTCTTAAAGTTAAA3′(SEQ ID NO: 50); Eurofins) using a Q5 DNA polymerase and dNTP mix.
PCR products were purified by electrophoresis on agarose gel. Purified pET23-nanoKAZ vector and the synthetic gene sdAb026 were assembled using NEBuilder HiFi assembly master mix (New-England Biolabs).
The assembled products (5 mL) were used to transform NEB 5-alpha competent E. coli and grown overnight on LB/Agar/ampicillin in Petri dish. Isolated colonies were grown in liquid medium, plasmids were isolated and nucleotide sequence was performed to confirm the presence of the sdabs026-nanoKAZ insert.
The full sequence of anti-IgE nanobody luciferase tandem sdAb026-nanoKAZ ([nanobody anti-IgE]-[nanoKAZ]-[His6]) is shown in the table below:
ATGGCGGAGGTCCAGTTGCT
TGAGAGTGGTGGGGGTCTTG
TTCAGCCAGGGGGCTCCCTT
CGTCTTAGTTGTGCCGCATC
CGGTTTCACATTCGGCAATT
ACGACATGGCGTGGGTCCGA
CAAGCTCCCGGCAAACGCCC
TGAGTGGGTATCGTCTATTG
ATACGGGGGGAGATATAACA
CACTACGCAGACAGTGTGAA
GGGGAGGTTCACAATCTCTC
GGGACAACGCAAAGAACACC
TTATACTTGCAGATGAATAG
CCTGAGACCGGAGGACACTG
CTGTGTATTGGTGCGCTACC
GATGAAGAATATGCCCTCGG
CCCAAACGAATTTGATTATT
ACGGACAGGGAACTCTGGTG
ACTGTGTCATCAGCTGCCGC
CCTGGAG
ATGGTCTTCACAC
TCGAAGATTTCGTTGGGGAC
TGGCGACAGACAGCCGGCTA
CAACCTGGACCAAGTCCTTG
AACAGGGAGGTGTGTCCAGT
TTGTTTCAGAATCTCGGGGT
GTCCGTAACTCCGATCCAAA
GGATTGTCCTGAGCGGTGAA
AATGGGCTGAAGATCGACAT
CCATGTCATCATCCCGTATG
AAGGTCTGAGCGGCGACCAA
ATGGGCCAGATCGAAAAAAT
TTTTAAGGTGGTGTACCCTG
TGGATGATCATCACTTTAAG
GTGATCCTGCACTATGGCAC
ACTGGTAATCGACGGGGTTA
CGCCGAACATGATCGACTAT
TTCGGACGGCCGTATGAAGG
CATCGCCGTGTTCGACGGCA
AAAAGATCACTGTAACAGGG
ACCCTGTGGAACGGCAACAA
AATTATCGACGAGCGCCTGA
TCAACCCCGACGGCTCCCTG
CTGTTCCGAGTAACCATCAA
CGGAGTGACCGGCTGGCGGC
TGTGCGAACGCATTCTGGCG
CTCGAGCACCACCACCACCA
MAEVQLLESGGGLVQPGGSL
RLSCAASGFTFGNYDMAWVR
QAPGKRPEWVSSIDTGGDIT
HYADSVKGRFTISRDNAKNT
LYLQMNSLRPEDTAVYWCAT
DEEYALGPNEFDYYGQGTLV
TVSSAAALE
MVFTLEDFVGD
WRQTAGYNLDQVLEQGGVSS
LFQNLGVSVTPIQRIVLSGE
NGLKIDIHVIIPYEGLSGDQ
MGQIEKIFKVVYPVDDHHFK
VILHYGTLVIDGVTPNMIDY
FGRPYEGIAVFDGKKITVTG
TLWNGNKIIDERLINPDGSL
LFRVTINGVTGWRLCERILA
LEHHHHHH
The estimated molecular weight (MW) of sdAb026-nanoKAZ calculated from sequence is 34.1 kD.
Expression, Purification and Validation of Anti-IgE Nanobody-Luciferase Fusion Protein (sdAb026-nanoKAZ)
pET23-sdab026-nanokaz was used to transform E. coli BL21 (DE3, New-England Biolabs) to achieve high expression in E. coli. Cells were grown at 18° C. and IPTG (Sigma-Aldrich) was added to induce sdAb026-nanoKAZ production. After harvesting the cells by centrifugation (1.5 L), the pellet was resuspended in 50 mM Tris-HCl pH 8.0, 50 mM NaCl with protease inhibitor (Sigma-Aldrich) and lysozyme (0.1 mg/mL, Sigma-Aldrich). Cells were disrupted by freezing-thawing cycle lysis method. DNase I (Sigma-Aldrich) was then added to remove DNA from the sample.
The crude extract was centrifuged 30 min at 1250 g. The supernatant was collected and NaCl (500 mM), Imidazole (20 mM, Sigma-Aldrich) and Triton X-100 (0.1%, Sigma-Aldrich) were added. The cleared lysate was loaded on an equilibrated Hi-Trap 5 mL-column (GE-Healthcare) at 4 mL/min using an AKTA pure chromatography system (GE-Healthcare). The column was washed with 20 volumes of column with a running buffer (50 mM Tris-HCl pH 8.0, NaCl 50 mM, 20 mM imidazole) at 5 mL/min. The sdAb026-nanoKAZ was eluted with a gradient of imidazole from 20 mM to 200 mM in 50 mM Tris-HCl pH 8.0, 50 mM NaCl at 5 mL/min and fractions of 1 mL were collected in 96-deepwell plate (GE-Healthcare). Catalytic activity of fractions was profiled using a luminometer Hydex by diluting 107 fold the fraction in PBS with 27 μM of furimazine. The fractions of high activity were pooled, and loaded on a 1 mL HiTrap Q column (GE-Healthcare) equilibrated in 50 mM Tris-HCl pH 8.0, NaCl 50 mM. The protein was eluted in 50 mM MES pH 6.5, 50 mM NaCl at 1 mL/min at 18° C. using the AKTA pure chromatography system. The fractions of 500 μL were collected in 96-deepwell plate and their activities were assayed as described above. The fractions of high activity were pooled. The quality of the purified protein was assessed by loading an aliquot (10 μL) on a stain-free SDS gel (4-15% Mini-PROTEAN® TGX Stain-Free™ Protein Gels, Bio-Rad).
The gel was activated by UV trans-illumination for 5 min (Bio-Gel Doc XR Imaging System). Tryptophan residues undergo an UV-induced reaction with trihalo compounds and produce a fluorescence signal imaged. An UV-spectrum (240-300 nm) was acquired for evaluating the concentration of sdAb026-nanoKAZ from the solution absorption at 280 nm. The specific activity is about 1015 acquired photons/second/mg of sdAb026-nanoKAZ with furimazine in PBS at 23° C. The optimal activity is reached for a substrate (furimazine) concentration from 10 to 30 μM (plateau at about 10 times the KM=2 μM). Beyond 30 μM the dipolar moments of the substrates out of the nanoKAZ catalytic site are quenching the photon emission of the catalyzed substrate in the active site. Quenching efficiency depends on dipolar moment of substrates. Substrate catalysis inactivates stochastically the nanoKAZ and the life time of enzyme depends on substrates and catalysis rate. Light emission intensity has been optimized by using optimal conditions according to kinetics parameters according to specific substrates from a thorough enzymatic study of nanoKAZ and its 30 mutants and the catalysis of 172 distinct substrates.
IgE Luciferase Immunosorbent Assay (Lu LISA) Protocol
White 96-well plates with flat bottom (Fluoronunc C96 Maxisorp, Nunc) were coated by adsorption with either 10 μg/mL of peanut extract (F171, Greer laboratories), 10 μg/mL of Ara H1 (NA-AH1-1, Indoor Technology), 10 μg/mL of Ara H2 (RP-AH2-1, Indoor Technology), 5 μg/mL of ovalbumin (OVA, Sigma-Aldrich) or 1 μg/mL of dust mite DER p2 (2B12NA-DP2-1, Indoor Technology) in 50 μL/well of NaHCO3 50 mM buffer pH 9.5 (Sigma) for 2 hours at room temperature. Target immobilization is the main factor of success or failure of the method as the maximum of target should be immobilized while presenting the allergenic domain accessible to sIgE for binding. Adsorption on Maxisorp® plates favours charge interaction. Alternatives to adsorption are covalent binding of targets through carboxylic, amine or sulfhydryl moieties or glycosylation at the functionalized well surface. Wells were emptied and the coating was saturated with bovine serum albumin (Sigma) at 100 μg/mL in NaHCO3 for 1 hour at room temperature. Wells were washed four times with 100 μL of PBS/Tween 20 0.1%. Recombinant anti-OVA human chimeric IgE (clone X4A4D12/G9/H8, a kind gift from Arkab), anti-dust mite p2 human chimeric IgE (clone CH1, a kind gift from Arkab), or plasma from peanut allergic subjects were diluted in PBS or in a pool of plasma from healthy donors, as indicated. Sample dilutions were incubated 1 hour at room temperature in their respective allergen-coated wells, 50 μL/well. Wells were washed four times with 100 μL PBS/Tween 20 0.1%. Purified sdAb026-nanoKAZ 1 ng/mL (1·109 RLU·s−1·mL−1) in PBS was loaded (50 μL/well) and incubated 30 min at room temperature. Wells were washed four times with 100 μL of PBS/Tween 20 0.1%. Plates can be stored at this step in PBS until measurements. Just before reading, each wells were emptied and loaded with 50 μL of furimazine (8-benzyl-2-(furan ylmethyl)-6-phenylimidazo[1,2-a]pyrazin-3(7H)-one) at 27 μM (about 10 times the KM of nanoKAZ, 2 μM). The plate was orbitally shaked for 5 seconds and the light emission intensity was integrated 1 sec per well using a multi-well plate luminometer (LB960 Centro, Berthold).
For processing an affinity spectra from LuLISA competition assay, mixtures of the same concentration of serum or plasma sample, 0.5 μL in 50 μL, with 3 by 3 dilution series of the free allergen from 10 μM to 0.7 μM in PBS along 16 allergen-coated wells of a 384-well plate or with 10 by 10 dilution series of the free allergen from 10 μM to 1 μM along 8 allergen-coated wells of a 96-well plate. Values should be adapted to IgE affinities. 1 to 3 hours of incubation for reaching equilibrium or at the nearest. Wells were washed four times with 100 μL PBS/Tween 20 0.1%. Purified sdAb026-JAZ572 (1 ng/mL) is preferred to sdAb026-nanoKAZ for higher signal and lower background especially for high concentration of free allergen while IgE binding to immobilized allergen is low in so long incubation time. Eventually Tween 20 0.1%, BSA 0.1 mg/mL, or gelatine 0.1 mg/mL might be used for reducing background. Milk should be avoided for IgE assays in potentially allergic patients. Wells were washed four times with 100 μL PBS/Tween 20 0.1%. Just before reading, each wells were emptied and loaded with 50 μL of hikazine-108 (8-benzyl-2-(furan-2-ylmethyl)-6-phenylimidazo[1,2-a]pyrazin-3(7H)-one) at 13.5 μM. The plate was orbitally shaked for 1 seconds and the light emission intensity was integrated 0.5 sec per well using a multi-well plate luminometer (LB960 Centro, Berthold). Bioluminescence intensity is displayed versus target concentration as a bar graph.
IgE Immunocap
ImmunoCAP analysis was performed on shipped samples by Phadia, Thermo Fisher.
IgE ELISA Protocol
Clear, flat bottom 96- or 384-well plates (Maxisorp, Nunc) were coated as described above, 2 hours at room temperature. Wells were emptied and the coating was saturated with 50 μL of bovine serum albumin (Sigma) at 100 μg/mL in PBS for 1 hour at room temperature. Wells were washed four times with 100 μL of PBS/Tween 20 0.1% (Sigma). Recombinant anti-OVA human chimeric IgE (clone X4A4D12/G9/H8, a kind gift from Arkab), anti-dust mite p2 human chimeric IgE (clone CH1, a kind gift from Arkab), or plasma from peanut allergic subjects were diluted in PBS and incubated 1 hour at room temperature in their respective allergen-coated wells, 50 mL/well. Wells were washed four times with 100 μL of PBS/Tween 20 0.1%. 50 μL of goat IgG anti-human IgE conjugated with alkaline phosphatase diluted (1:700 in PBS, Sigma-Aldrich) were loaded in each well and incubated 1 hour at room temperature. Wells were washed four times with 100 μL of PBS/Tween 20 0.1%. All wells were emptied, 50 μL of phosphatase substrate pNPP 1 mg/mL (4-Nitrophenyl phosphate disodium salt, Sigma-Aldrich) were added per well, incubated 3 hours at room temperature or overnight at 4° C. Absorbance was measured at 405 nm with a multi-well plate spectrophotometer (Sapphire, Tecan) and compared with LuLISA results.
Statistical Analysis
Differences in IgE levels between plasma samples from healthy donors and peanut allergic subjects were compared using an unpaired Mann-Whitney U test. P values <0.05 are considered statistically significant.
Blood Samples from Fingertip
Tests have been performed with a healthy volunteer to set up a project application for blood sampling from a reduced cohort of allergic patients at the Trousseau Hospital for an IgE LuLISA assay in parallel with ImmunoCAP and ELISA.
The tests have been performed after decontamination of the fingertip with alcohol using a lancing device with sterile disposable lancets usually performed for glucose assay for diabetic patient auto-survey. One μL is pipetted and mixed to 50 μL of a solution of PBS, BSA (50 μg/mL), heparin (10 Ul/mL), sdAb026-nanoKAZ (1 ng) preloaded inside a 1000 μL tip (single use) ended by a paper filter framed by to polyethylene filter plugs. The diluted blood is filtered through the tip end and loaded in a 96-well plate pre-coated with the specific allergen and incubated at room temperature for 5 min. The well is washed with PBS and 100 μL of luciferase substrate (furimazine analogs) is added and bioluminescence is immediately measured during 1 second using a plate-luminometer (LB960 centro, Berthold). Measurements are performed in parallel with negative and positive controls for internal calibration.
Results
Sensitive and Specific Detection of Allergen-Specific IgE by Luciferase-Linked Immunosorbent Assay (LuLISA)
To establish a proof-of-concept for the specific detection of sIgE using LuLISA, dilution series in PBS of recombinant IgE, IgG1 (the major IgG subclass) or IgG4 (the main IgG subclass overproduced during allergen-specific immunotherapy) directed against the house dust mite allergen Der p 2 were prepared. The 3 groups of samples were analyzed using IgE LuLISA.
As expected, a concentration-dependent signal arose only for the sample containing anti-Der p 2 sIgE, with a detection limit of ˜5×10−13 M sIgE (˜1 pg/mL; ˜0.0004 kUA/L) (
A similar experiment was performed on recombinant human anti-ovalbumin IgE. Recombinant human anti-ovalbumin (OVA) IgE were diluted in PBS at the indicated concentration and incubated with plate-bound OVA. Bioluminescent detection of antibody levels was performed by LuLISA using the anti-IgE sdAb026-nanoKAZ.
It was also obtained high sensitivity with recombinant anti-ovalbumin (OVA) IgE, which was detectable by LuLISA at concentrations as low as 5 pg/mL (0.002 kUA/L) (
Recombinant anti-ovalbumin (OVA) IgE was diluted in PBS at the indicated concentrations. Levels of OVA sIgE were assessed in aliquots from the same dilution sample using LuLISA or ELISA. The sensitivity of LuLISA was also much higher than that of standard ELISA for the detection of sIgE (
Next, it was compared the dynamic range and sensitivity of IgE LuLISA versus standard ImmunoCAP, using recombinant OVA sIgE diluted in plasma pooled from 30 healthy donors (
It was performed similar experiments with dilution series of a plasma sample from a highly peanut allergic subject, which was again diluted in a pool of plasma from 30 healthy donors (
It was then studied the influence of the concentration of the anti-IgE nanobody-luciferase fusion protein on bioluminescent detection of IgE by Lu LISA. 1 μL of plasma from a peanut allergic subjects (peanut-specific IgE ImmunoCAP values: 2186 kU/L) was diluted in 50 μL of PBS and incubated with plate-bound peanut extract (PBS alone was used as a control). Bioluminescent detection of peanut-specific IgE levels was performed by LuLISA at the indicated concentration of anti-IgE nanobody-luciferase tandem (sdAb026-nanoKAZ). Dilution series of the anti-IgE nanobody-luciferase fusion protein gave a concentration-dependent signal at a fixed (1:50) dilution of this peanut allergic plasma sample, and confirmed the very low bioluminescent background signal of the IgE LuLISA (
Altogether, these results indicate that the IgE LuLISA has a very high sensitivity and specificity, and could thus potentially be used to quantify IgE in samples from patients with very low sIgE. The main advantage of the IgE LuLISA over ImmunoCAP is that it requires extremely low volume of sample. In the case of the sample from the peanut-allergic patient used in
It was then sought to further validate this approach by measuring sIgE against total peanut extract, or against the major peanut allergens Ara h 1 and Ara h 2 using 1 μL of plasma from 31 healthy donors (obtained from the French blood bank EFS with unknown allergic status) and 82-105 peanut-allergic subjects (collected upon their enrolment into the institutional review board—approved peanut oral immunotherapy study: safety, efficacy and discovery trial; ClinicalTrials.gov identifier: NCT02103270). Dilution series from reference samples with titrated high peanut sIgE were used for assay calibration, to ensure that all plasma samples were analysed within the linear range of detection of our method (
As expected, significantly higher levels of peanut sIgE, Ara h 1 sIgE and Ara h 2 sIgE were detected in plasma samples from peanut allergic subjects as compared to healthy donors (
Head-to-head comparison between LuLISA and ImmunoCAP in allergic patients showed a high correlation between both methods (R2=0.89, 0.84 and 0.83 for peanut sIgE, Ara h 1 sIgE and Ara h 2 sIgE, respectively) (
Altogether, these results demonstrate that the IgE LuLISA is highly sensitive and accurate for the clinical detection of sIgE, and requires very low volumes of plasma.
Besides ImmunoCAP, several other methods have been reported for the detection of sIgE, including IMMULITE and, more recently, isotype-specific agglutination-PCR (ISAP) (Hamilton R G et al. 2008, Tsai C T et al., 2018). IMMULITE appears to be the closest method to LuLISA as it uses a chemiluminescent approach to detect sIgE. However, the reported detection limit for sIgE with IMMULITE is the same as for ImmunoCAP (0.1 kUA/L). Similarly to LuLISA, detection of sIgE by ISAP can be performed using 1 μl of clinical sample. However, the two tests are based on different approaches as ISAP requires chemically-synthesized allergen-DNA (for each type of allergen) and secondary anti-IgE antibody-DNA conjugate for the detection of sIgE by quantitative PCR.
IgE LuLISA was used in a strip test (lateral flow) for a serum IgE testing on baby allergic to milk. Result is shown in
Such test aims proofing the application of LuLISA in emergency conditions for detecting IgE specific for curare (anaesthetics), amoxicillin (antibiotics) and latex (gloves) in patients attending surgery or for detection of allergy to milk compounds in new born babies in paediatric emergency.
The blood sampling from fingertip is adapted for a sIgE LuLISA of patients treated by omaluzimab in a routinely and timely manner for adjusting the injected doses with the amount of the detected free sIgE.
The low amount of sample required and the extended performance of LuLISA versus ELISA allow extended application as the plotting of affinity profile or spectra for serum with potentially more than one molecular species of IgE. LuLISA competition is performed using a series of allergen dilution mixed with a constant concentration of serum. IgE detected amount is correlated to light intensity. IgE detected amount per allergen concentration interval is a way to evaluate the presence of very high (sub-picomolar), high (nanomolar), medium (10 to 100's nanomolar) or low (micromolar and beyond) affinity immunoglobulin for the allergen. Higher affinity, stronger saturation and aggregation of IgE receptors at the surface of mastocytes, basophiles and macrophages, higher histaminic and cytokinic response with higher risk of anaphylactic shock. Affinity spectra are a relevant tool for the follow up of patient under desensibilizing treatment for orienting the therapeutic strategy from stopping the challenge with increasing amounts of allergen, controlling the short term response with anti-histaminic or clearing the high affinity IgE with competitor of the IgG Fc receptor binding site (Omaluzimab).
In summary, the IgE LuLISA is a new method for the detection of sIgE of ultra-high sensitivity requiring only very small (1 μL or less) plasma sample volumes. The use of bioluminescence offers markedly increased sensitivity over classical colorimetric (ELISA) or fluorescent (ImmunoCAP) IgE detection methods with an extended dynamic range of concentration. The method is fully automatable and uses commercialized plates and a standard luminometer for the bioluminescent detection of IgE. Thus, IgE LuLISA should be very cost-effective over conventional ImmunoCAP.
Material and Methods:
Human Plasmas and Serums
The samples were obtained from serums of the CORSER cohort (n=164; IcareB), from serums of the observation and monitoring protocol of the Intensive Medicine and Resuscitation service of Assistance Publique des Hopitaux de Paris (APHP) Cochin (n=20) in longitudinal follow-up and from healthy donors of Etablissement Francais du Sang (EFS) sampled in December 2019 (frozen plasmas n=20, frozen serums n=20). Prepandemic frozen sera from 664 healthy donors were obtained from the French blood bank (Etablissement Francais du Sang, EFS).
Fusion Protein Anti-IgG Nanobody-Luciferase
Design and Synthesis of Plasmid Encoding the Anti-IgG Nanobody-Luciferase Fusion Protein (pET23-Fc1-nanoKAZ or pET23-Fc10-nanoKAZ, with Fc1 Coding for SEQ ID NO: 62 and Fc10 Coding for SEQ ID NO: 63 and Jaz572 for SEQ ID NO: 10 Respectively or pET23-Fc1-Jaz572 or pET23-Fc10-Jaz572, with Fc1 Coding for SEQ ID NO: 62 and Fc10 Coding for SEQ ID NO: 63 and Jaz572 for SEQ ID NO: 10 Respectively)
nanoKAZ is an optimized sequence of the catalytic domain of the luciferase from Oplophorus gracilirostris (WO2012/061530). Jaz572 (SEQ ID NO: 10 is derived from the nanoKAZ with an improved catalytic activity increasing photo emission and signal and a reduced aggregation and surface adsorption behavior reducing noise contributing for a better signal noise ratio.
The gene nanoKAZ and JAZ572 have been synthetized by Eurofins (Germany) with carboxy-end His6-tag and flanking region corresponding to the pET23 sequence (Novagen). pET23 plasmid has been amplified with the forward and reverse oligonucleotides (Fwd:5′CTCGAGCACCACCACCACCACCAC3′ (SEQ ID NO:47); Rvr:5′GGTATATCTCCTTCTTAAAGTTAAAC3′ (SEQ ID NO: 48), Eurofins) using a Q5 DNA polymerase, dNTP mix (New England BioLabs). PCR product was purified by electrophoresis on agarose gel (1%, Macherey Nagel). Purified pET23 vector and the synthetic gene were assembly (pET23-nanoKAZ or pET23-jaz572) using NEBuilder HiFi assembly master mix (New England BioLabs).
The IgG-binding moiety is issued from a humanized heavy chain antibody of alpaca selected against IgG (single-domain antibody) (U.S. Pat. No. 10,259,886 B2). FC1 recognizes the constant fragment region of human IgG1, IgG2, IgG3 and IgG4 with the following dissociation constants at equilibrium: KD 0.57 nM, 1.73 nM, 47.8 nM, 0.30 nM respectively with a KD for all IgG of 3.25 nM (U.S. Pat. No. 10,259,886 B2). FC10 recognizes the constant fragment region of human IgG1, IgG2, IgG3 and IgG4 with the following dissociation constants at equilibrium: KD 2.62 nM, 7.29 nM, 8.99 nM, 12.3 nM respectively with a KD for all IgG of 3.25 nM (U.S. Pat. No. 10,259,886 B2). The gene fc1 and fc10 has been synthetized by Eurofins with flanking regions corresponding to the pET23-nanoKAZ sequence. Synthetic gene fc1 or fc10 have been amplified with the corresponding forward and reverse oligonucleotides using a Q5 DNA polymerase and dNTP mix.
PCR products were purified by electrophoresis on agarose gel. Purified pET23-nanoKAZ and pET23-jaz572 vectors and the synthetic gene fc1 or fc10 were assembled using NEBuilder HiFi assembly master mix (New-England Biolabs).
The assembled products (5 mL) were used to transform NEB 5-alpha competent E. coli and grown overnight on LB/Agar/ampicillin in Petri dish. Isolated colonies were grown in liquid medium, plasmids were isolated and nucleotide sequence was performed to confirm the presence of the fc1-nanoKAZ or fc10-nanoKAZ-fc1-jaz573, fc10-jaz573 inserts.
The full sequence of anti-IgG nanobody luciferase tandem FC1-nanoKAZ or FC10-nanoKAZ ([nanobody anti-IgG]-[nanoKAZ-]-[His6]) are shown as examples in the table below:
ATGCAGGTCCAATTGCAAGA
GTCAGGGGGCGGCCTGGTCC
AACCAGGCGGTAGCCTCCGC
CTGTCGTGCGCGGCCTCCGG
GGGTACATCTATTCGTATCG
GTTCGATTAATGCACTGGCT
TGGTACCGGCAGGCTTTAGG
CAATCAGCGCGAACTGGTTG
CAGCGGTGACCGAAGGCGGT
AGCACGAACTATGCCGATTT
TGTAAAAGGACGTTTCACCA
TCAGCCGCGATAACGCGCAG
AACATGATGTATCTTCAGAT
GAATTCCCTGAAACCGGAAG
ATACGGCAGTTTATTATTGT
AATGCGGACAAGGTACTGTA
CTCTCGTGGCGGATACTATA
GCGTGGCCAACGACCTATGG
GGTCAGGGCACCCAGGTGAC
TGTGAGTAGT
ATGGTTTTCA
MQVQLQESGGGLVQPGGSLR
LSCAASGGTSIRIGSINALA
WYRQALGNQRELVAAVTEGG
STNYADFVKGRFTISRDNAQ
NMMYLQMNSLKPEDTAVYYC
NADKVLYSRGGYYSVANDLW
GQGTQVTVSSMVFTLEDFVG
DWRQTAGYNLDQVLEQGGVS
ATGCAAGTACAGTTGCAGGA
GAGTGGAGGCGGATTAGTAC
AAGCTGGCGATTCTCTTCGG
ATTTCGTGTCGCGCATCGGG
TCTGACTGTGAACGATCTGT
ATATGGGTTGGTTTCGACAG
GCGCCGGGCAAGGAACGCGA
ATTTGTCGGTCGTGTTACTC
CAGGGGACAACACGGACTAT
ACATATTACGTGGACAGCGT
GAAAGGGCGTTTCACCATCA
GCCGTGATTCCGCCAAAAAT
ACCGTGTATCTCCAGATGAA
TTCTCTGAAACTGGAAGATA
CCGCCGTCTACCTGTGCGCG
GGCCGCCGCTTCGGTAGTTC
CGAGTGGGATTACTGGGGTC
AGGGCACCCAAGTTACGGTT
AGCTCA
ATGGTTTTCACCCT
MQVQLQESGGGLVQAGDSLR
ISCRASGLTVNDLYMGWFRQ
APGKEREFVGRVTPGDNTDY
TYYVDSVKGRFTISRDSAKN
TVYLQMNSLKLEDTAVYLCA
GRRFGSSEWDYWGQGTQVTV
SS
MVFTLEDFVGDWRQTAGY
The estimated molecular weight (MW) of FC1-nanoKAZ and FC10-nanoKAZ calculated from sequence are 34115 and 33588 Daltons respectively.
Expression, Purification and Validation of Anti-IgG Nanobody-Luciferase Fusion Proteins were Identical to Those of Anti IgE Nanobody-nanoKAZ (sdAb026-nanoKAZ)
Protocol of Detection of IgG Specific of Proteins N and S of SARS-COV2 by Luciferase Linked-Immunosorbent Assay (LuLISA)
IgG Luciferase Immunosorbent Assay (LuLISA) Protocol
White 96- or 384-well plates with flat bottom (Fluoronunc C96 Maxisorp, Nunc) were coated by adsorption with either 1 μg/mL of Nucleoprotein, Spike or their fragments, in 50 μL/well of phosphate buffer saline pH 7.4 (Sigma) for 2 hours at room temperature or overnight at 4° C. Adsorption on Maxisorp® plates favours charge interaction. Alternatives to adsorption are covalent binding of targets through carboxylic, amine or sulfhydryl moieties or glycosylation at the functionalized well surface or coating with poly-lysine. Wells were emptied eventually but not necessarily neutralize with BSA (1 mg/mL) or skimmed milk 3%. Wells were washed 3 to 6 times with 100 μL of PBS/Tween 20 0.1%. Dilutions of serum (typically 1/200), plasma or body fluid were incubated from 30 min to 1 hour at room temperature in their respective antigen-coated wells, 50 μL/well in phosphate buffer saline with eventually skimmed milk 3%, bovine serum albumin 1 mg/mL, bovine serum 1-3% and/or Tween 20 0.1%. Wells were washed three to six times with 100 μL PBS/Tween 20 0.1%. Purified VHH-nanoKAZ 1 ng/mL (5·107 RLU·s−1·mL−1) in phosphate buffer saline with eventually skimmed milk 3%, bovine serum albumin 1 mg/mL or bovine serum 1-3% and/or Tween 20 0.1%, was loaded (50 μL/well) and incubated 20-30 min at room temperature. Wells were washed four times with 100 μL of PBS/Tween 20 0.1%. Plates can be stored at this step in PBS until measurements. Just before reading, each wells were emptied and loaded with 50 μL of furimazine (8-benzyl-2-(furan-2-ylmethyl)-6-phenylimidazo[1,2-a]pyrazin-3(7H)-one) at 27 μM of furmazine or 13 μM of Q108. The plate was orbitally shaked for 5 seconds and the light emission intensity was integrated 0.5-1 sec per well using a multi-well plate luminometer (LB960 Centro, Berthold).
Results
IgGs specific of protein N of SARS-CoV2 have been titrated by luciferase linked immunosorbent assay (LuLISA) in serums of the CORSER cohort (n=164; IcareB), in serums of the observation and monitoring protocol of the Intensive Medicine and Resuscitation service of Assistance Publique des Hopitaux de Paris (APHP) Cochin (n=20) in longitudinal follow-up and in serums and plasma of healthy donors of
Establishment Français du Sang (EFS) sampled in December 2019 (frozen plasmas n=20, frozen serums n=20).
Results are shown in
IgGs specific of protein Spike (S) of SARS-CoV2 have been titrated by LuLISA in serums from the observation and monitoring protocol of the Intensive Medicine and Resuscitation service of Assistance Publique des Hopitaux de Paris (APHP) Cochin (n=20) and in frozen serums from healthy donors of EFS (n=4).
Results are shown in
The correlation between the titration of IgG specific of protein N of SARS-CoV2 and IgG specific of protein S of SARS-CoV2 in serum from APHP-Cochin (n=20) and EFS (n=4) is shown in
Then it was compared the IgG of serums from patients (APHP-Cochin n=20) and frozen serums of healthy donors (EFS n=4) which were specific for SARS-CoV1 protein N and SARS CoV2 protein N as well as SARS CoV1 protein S and SARS-CoV2 protein S.
Results are shown in
An emergency test on a 96 well-plate which may be performed in 5 minutes has been assayed on serum from APHP-Cochin (n=20) and EFS (n=4) in duplicate by reducing the incubations time: 3 minutes for the incubation of sera at room temperature or even better at 37° C., 17 seconds per washing step (plate washer Zoom HT, Berthold) and 1 minute for the incubation of the anti-IgG VHH-nanoKAZ. The coefficient of determination R2 was 0.75. Results are shown in
Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present application.
| Number | Date | Country | Kind |
|---|---|---|---|
| 20315224.4 | Apr 2020 | WO | international |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2021/060829 | 4/26/2021 | WO |
