Patent Application
20240277834
This application incorporates by reference a Sequence Listing submitted electronically with the application as an XML file entitled “COFER-101-SequenceListing.xml” created on Jan. 18, 2024 and having a size of 91,906 bytes.
The present disclosure relates to a nucleic acid molecule comprising 5′-UTR and/or 3′-UTR sequences that yield high translation levels. Aspects of the disclosure further relate to nucleic acid molecules suitable for use as a vaccine in the treatment and prevention of infectious diseases, including those caused by a coronavirus.
Nucleic acid vectors have multiple uses in both the treatment and study of human diseases. In molecular biology, nucleic acid vectors can be used to introduce disease-related genes or proteins of interest in cell or animal models as a means of assaying. Furthermore, there are now myriad therapeutic settings where expression of a nucleic acid sequences is desirable, including expression of a functional protein to treat a disease caused by a lack of said protein or as nucleic acid-based vaccines. Nucleic acid vectors generally comprise a simple structure, consisting of a coding sequence, encoding a peptide or protein of interest; 5′ and 3′-untranslated regions (UTRs), which aid in translation and stability of the vector; and a polyadenylation signal, which protects the vector from enzymatic degradation and plays a key role in translation. The constitutive parts of nucleic acid vectors can be modified to treat or model a specific disease.
Recent successes of nucleic acid vaccines during the COVID-19 pandemic has brought renewed interest to the field of nucleic acid-based therapies, particularly those for the expression of heterologous proteins of interest. For example, interest has now turned to pan-mRNA vaccines, where antigens from multiple disease-associated pathogens are administered simultaneously to provide pan-immunity against multiple seasonal pathogens (e.g., Clinical Trial NCT05596S734 evaluating mRNA vaccine candidates against COVID-19 and influenza).
Pan-vaccines would be greatly assisted by improvements to the nucleic acid vectors. For example, maximising or boosting translational efficiency from vectors might achieve high neutralisation responses against antigens at lower mRNA dose levels. This would enable multiple vectors encoding multiple antigens to be simultaneously administered without exceeding recommended mRNA dose amounts per vaccination. Moreover, boosting translational efficiency may lower costs associated with production of mRNA therapeutics by enabling efficacious responses at lower dose levels. Such an advantage would be applicable to any nucleic acid-based expressed biologic therapeutic approach (e.g., in vivo expressed antibodies, wild-type proteins, cancer neo-antigens, as well as traditional anti-pathogen vaccines).
The present disclosure relates to a nucleic acid molecule comprising at least one coding sequence flanked by and operably linked to 5′-and/or 3′-UTRs. The UTR(s) are engineered such that they increase translation of a protein of interest encoded for by the coding sequence. The coding sequence or sequences may encode for one or more peptides or fragments thereof of an infectious agent, such as the receptor binding domain or spike protein from one or more coronavirus variants. The molecule may also include the coding sequence of a multimerization unit, such that upon assembly a multimeric complex is formed.
Certain instances of the present disclosure are summarized below. This list is only exemplary and not exhaustive of all of the instances provided by this disclosure.
Those of skill in the art will understand that the drawings, described below, are for illustrative purposes only. The drawings are not intended to limit the scope of the present teachings in any way.
All references referred to are incorporated herein by reference in their entireties.
Many modifications and other instances of the disclosures set forth herein will come to mind to one skilled in the art to which these disclosures pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the disclosures are not to be limited to the specific instances disclosed and that modifications and other instances are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.
Units, prefixes and symbols may be denoted in their SI accepted form. Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively. Numeric ranges are inclusive of the numbers defining the range. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes. The terms defined below are more fully defined by reference to the specification as a whole.
The term “nucleic acid sequence” is intended to encompass a polymer of DNA or RNA, i.e., a polynucleotide, which can be single-stranded or double-stranded and which can contain non-natural or altered nucleotides e.g. modified uridine. The terms “nucleic acid” and “polynucleotide” as used herein refer to a polymeric form of nucleotides of any length, either ribonucleotides (RNA) or deoxyribonucleotides (DNA). These terms refer to the primary structure of the molecule, and thus include double-and single-stranded DNA, and double- and single-stranded RNA. The terms include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs and modified polynucleotides such as, though not limited to, methylated and/or capped polynucleotides. Nucleic acids are typically linked via phosphate bonds to form nucleic acid sequences or polynucleotides, though many other linkages are known in the art (e.g. phosphorothioates, boranophosphates, and the like).
The terms “polypeptide,” “peptide,” and “protein” are used interchangeably herein to refer to polymers of amino acids of any length. The polymer can be linear or branched, it can comprise modified amino acids, and it can be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulphide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labelling component. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), as well as other modifications known in the art. It is understood that, because the polypeptides of this disclosure are based upon antibodies, in some aspects, the polypeptides can occur as single chains or associated chains.
“Percent identity” refers to the extent of identity between two sequences (e.g. nucleic acid sequences). Percent identity can be determined by aligning two sequences, introducing gaps to maximize identity between the sequences. Percent identity should generally be calculated between the same types of nucleic acids, i.e. for DNA sequences or RNA sequences. Thus, it is understood, if a DNA sequence “corresponds to” an RNA sequence or if an RNA sequence “corresponds to” a DNA sequence, in a first step the RNA sequence is converted into the corresponding DNA sequence (in particular by replacing the uracils (U) by thymidines (T) throughout the sequence) or, vice versa, the DNA sequence is converted into the corresponding RNA sequence (in particular by replacing the T by U throughout the sequence). Alignments can be generated using programs known in the art. For purposes herein, alignment of nucleotide sequences can be performed with the blastn program set at default parameters (see National Center for Biotechnology Information (NCBI): ncbi.nlm.nih.gov). Identity can be calculated between two sequences can be calculated by multiplying the number of matches in the pair by 100 and dividing by the length of the aligned region, including gaps. Identity scoring only counts perfect matches. Gaps at the end of sequences are not included, and internal gaps are included in the length.
“5′-untranslated region (5′-UTR)” has the usual meaning recognised by a skilled person. It is the region of a nucleic acid molecule located 5′ of a coding sequence and which is not translated into protein. A 5′-UTR usually starts with the transcriptional start site and end before the start codon of the coding sequence.
“3′-untranslated region (3′-UTR)” has the usual meaning recognised by a skilled person. It is the region of a nucleic acid molecule located 3′ of a coding sequence and which is not translated into protein. A 3′-UTR is usually 3′ of a coding sequence. If the molecule comprises a polyadenylation signal, the 3′-UTR is usually between the coding sequence and the polyadenylation signal.
“Coding sequence” is a continuous stretch of DNA or RNA beginning with a start codon (e.g., methionine (ATG or AUG)) and ending with a stop codon (e.g., TAA, TAG or TGA, or UAA, UAG or UGA). A coding sequence typically encodes a polypeptide. The coding sequences disclosed herein are operably linked to the5′ and 3′ UTRs described herein.
“Messenger RNA (mRNA)” is any RNA that encodes a (at least one) protein (a naturally-occurring, non-naturally-occurring, or modified polymer of amino acids) and can be translated to produce the encoded protein in vitro, in vivo, in situ, or ex vivo. The skilled artisan will appreciate that, except where otherwise noted, nucleic acid sequences set forth in the instant application may recite “T”s in a representative DNA sequence but where the sequence represents RNA (e.g., mRNA), the “T”s would be substituted for “U”s. Thus, any of the DNAs disclosed and identified by a particular sequence identification number herein also disclose the corresponding RNA (e.g., mRNA) sequence complementary to the DNA, where each “T” of the DNA sequence is substituted with “U.”
A “nucleoside” refers to a compound containing a sugar molecule (e.g., a pentose or ribose) or a derivative thereof in combination with an organic base (e.g., a purine or pyrimidine) or a derivative thereof (also referred to herein as “nucleobase”). Nucleic acids can comprise a region or regions of linked nucleosides. Such regions 5 may have variable backbone linkages. The linkages can be standard phosphodiester linkages, in which case the nucleic acids would comprise regions of nucleotides (a “nucleotide” refers to a nucleoside, including a phosphate group).
“Expression” of a nucleic acid sequence refers to one or more of the following events: (1) production of an RNA template from a DNA sequence (e.g., by transcription); (2) processing of an RNA transcript (e.g., by splicing, editing, 5′ cap formation, and/or 3′ end processing) and (3) translation of an RNA into a polypeptide or protein.
The term “pharmaceutical composition” refers to a preparation which is in such form as to permit the biological activity of the active ingredient to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the composition would be administered. The composition can be sterile.
As used herein, the terms “subject” and “patient” are used interchangeably. The subject can be an animal. In some aspects, the subject is a mammal such as a non-human animal (e.g. cow, pig, horse, cat, dog, rat, mouse, monkey or other primate, etc.). In some aspects, the subject is a human.
As used in the present disclosure and claims, the singular forms “a”, “an”, and “the” include plural forms unless the context clearly dictates otherwise.
It is understood that wherever aspects are described herein with the language “comprising”, otherwise analogous aspects described in terms of “consisting of’ and/or “consisting essentially of” are also provided. In this disclosure, “comprises”, “comprising”, “containing” and “having” and the like can mean “includes”, “including”, and the like; “consisting essentially of” or “consists essentially” are open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art aspects.
Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive. The term “and/or” as used in a phrase such as “A and/or B” herein is intended to include both “A and B,” “A or B”, “A”, and “B”. Likewise, the term “and/or” as used in a phrase such as “A, B, and/or C” is intended to encompass each of the following aspects: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).
Any molecules, vectors, compositions, uses or methods provided herein can be combined with one or more of any of the other molecules, vectors, compositions, uses or methods provided herein.
The present disclosure provides a nucleic acid molecule comprising a 5′ untranslated region (5′-UTR), a coding sequence and a 3′ untranslated region (3′-UTR), wherein the coding sequence is operably linked to the 5′-UTR and the 3′-UTR and wherein
The nucleic acid molecule of the disclosure is a nucleic acid vector.
The 5′-UTR and 3′-UTR sequences of the disclosure are particularly useful for increasing translation levels of the coding sequence . . . . The examples demonstrate that the combination of 5′-and 3′-UTRs disclosed herein enhance translation levels of multiple proteins of interest, including GFP and an scFv-Fc (e.g., a therapeutic protein). The translation levels were greater than achieved compared to clinically validated UTR combinations derived from regulatory approved mRNA vaccine products (see
Levels of translation obtained with the UTRs of the present disclosure can be assessed by any appropriate assay available to a skilled person, for example, by measuring the concentration of a protein of interest encoded by the coding sequence, for example by detecting a marker protein, such as GFP, or a therapeutic protein such as an scFv-Fc or a vaccine antigen, such as a SARS-COV-2 spike protein.
The 5′-UTRs and 3′-UTRs of the disclosure are capable of increasing translation of a coding sequence, optionally in HeLa or A549 cells, compared to a 5′-UTR sequence derived from albumin, optionally comprising or consisting of the sequence set forth in SEQ ID NO:16 or a corresponding RNA sequence, and a 3′-UTR sequence derived from HSD17B4, optionally comprising or consisting of the sequence set forth in SEQ ID NO:17, or a corresponding RNA sequence.
In one instance, the 5′-UTR derived from a 5′-UTR of CHIT1 does not comprise a sequence comprising ATG, optionally the 5′-UTR derived from a 5′-UTR of CHIT1 does not comprise a sequence consisting of ATGGGCTGCAGCCTGCCGCTGA (SEQ ID NO: 35), or the corresponding RNA sequence.
The present disclosure further provides a deoxyribonucleic (DNA) molecule comprising a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and the 3′-UTR and wherein
The present disclosure further provides a ribonucleic (RNA) molecule comprising a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and the 3′-UTR and wherein
In one instance, the nucleic acid molecule of the present disclosure comprises a 5′-UTR comprising, or consisting of, the sequence of SEQ ID NO:19 or a sequence at least 80%, 85%, 90% or 95% identical thereto and a 3′-UTR comprising, or consisting of, the sequence of SEQ ID NO: 21 or a sequence at least 80%, 85%, 90% or 95% identical thereto. The present disclosure further provides a nucleic acid molecule comprising a 5′-UTR, a coding sequence and a 3′-UTR,
The examples show that these 5′-UTRs and/or these 3′UTRs are capable of increasing translation of the coding sequence as assessed in accordance with this disclosure.
The present disclosure further provides a deoxyribonucleic acid molecule comprising a 5′-UTR, a coding sequence and 3′-UTR, wherein the 5′-UTR comprises a sequence selected from SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5 or SEQ ID NO: 7 or a sequence at least 80%, 85%, 90% or 95% identical thereto and/or the 3′-UTR comprises a sequence selected from SEQ ID NO: 9, SEQ ID NO: 11 or SEQ ID NO: 12 or a sequence at least 80%, 85%, 90% or 95% identical thereto.
The present disclosure further provides a ribonucleic acid molecule comprising a 5′-UTR, a coding sequence and 3′-UTR, wherein the 5′-UTR comprises a sequence selected from SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6 or SEQ ID NO: 8 or a sequence at least 80%, 85%, 90% or 95% identical thereto and/or the 3′-UTR comprises a sequence selected from SEQ ID NO: 10, SEQ ID NO: 12 or SEQ ID NO: 14 or a sequence at least 80%, 85%, 90% or 95% identical thereto.
In one instance, the 5′-UTR of the present disclosure comprises a sequence at least 80%, 85%, 90% or 95% identical to a sequence selected from any one of SEQ ID NOS: 1 to 8, wherein the sequence is capable of increasing translation of the coding sequence, optionally in HeLa cells or A549 cells, compared to a reference 5′-UTR, optionally the HSD17B4 5′-UTR (SEQ ID NO: 17), when constant 3′-UTR sequences are included in both molecules. Constant 3′-UTR sequences mean the same 3′-UTR sequence is paired with the 5′-UTR of the present disclosure and the reference 5′-UTR.
In one instance, the 3′-UTR of the present disclosure comprises a sequence at least 80%, 85%, 90% or 95% identical to a sequence selected from any one of SEQ ID NOS: 9 to 14, wherein the sequence is capable of increasing translation of the coding sequence, optionally in Hela cells or A549 cells, compared to a reference 3′-UTR, optionally the albumin 3′-UTR (SEQ ID NO: 16), when constant 5′-UTR sequences are included in both molecules. Constant 5′-UTR sequences mean the same 5′-UTR sequence is paired with the 3′-UTR of the present disclosure and the reference 3′-UTR.
In one instance, the nucleic acid molecule of the disclosure comprises a 5′-UTR comprising a sequence at least 80%, 85%, 90% or 95% identical to a sequence selected from SEQ ID NO: 1, or the corresponding RNA sequence, and a 3′-UTR comprising a sequence at least 80%, 85%, 90% or 95% identical to a sequence selected from SEQ ID NO: 9, or the corresponding RNA sequence, wherein the 5′-UTR sequence and the 3′-UTR sequence are capable of increasing translation of the coding sequence, optionally in Hela cells or A549 cells, compared to translation by a nucleic acid molecule comprising a reference 5′-UTR, optionally the HSD17B4 5′-UTR (SEQ ID NO: 17, or the corresponding RNA sequence), and a reference 3′-UTR, optionally the albumin 3′-UTR (SEQ ID NO: 16, or the corresponding RNA sequence), operably linked to the coding sequence.
In one instance, the 5′-UTR consists of a sequence selected from any one of SEQ ID NOS: 1 to 8 or a sequence at least 80%, 85%, 90% or 95% identical thereto, where the sequence is capable of increasing translation of the coding sequence as assessed in accordance with this disclosure, and/or the 3′-UTR consists of a sequence selected from any one of SEQ ID NOS: 9 to 14 or a sequence at least 80%, 85%, 90%, 95% or 98% identical thereto, where the sequence is capable of increasing translation of the coding sequence as assessed in accordance with this disclosure.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 5′-UTR comprises a sequence derived from the human chitinase-1 (CHIT1) 5′-UTR, optionally a sequence according to SEQ ID NO: 1 or SEQ ID NO: 2, or a sequence at least 80%, 85%, 90% or 95% identical thereto. The examples show that this 5′-UTR is capable of increasing translation of the coding sequence as assessed in accordance with this disclosure.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 3′-UTR comprises a sequence derived from the human citrate synthase (CS) 3′ UTR, optionally a sequence according to SEQ ID NO: 9 or SEQ ID NO: 10, or a sequence at least 80%, 85%, 90% or 95% identical thereto. The examples show that this 3′-UTR is capable of increasing translation of the coding sequence as assessed in accordance with this disclosure.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 5′-UTR comprises a sequence derived from the human chitinase 1(CHIT1) 5′ UTR and wherein the 3′-UTR comprises a sequence derived from the human citrate synthase (CS) 3′-UTR. The examples show that a nucleic acid molecule comprising these 5′ and 3′-UTRs yield the highest translation levels of multiple proteins of interest in multiple cell lines compared to clinically validated 5′ and 3′-UTR combinations.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 5′-UTR comprises a sequence derived from the human protein kinase CAMP-activated catalytic subunit beta (PRKACB) 5′ UTR, optionally a sequence according to SEQ ID NO: 3 or SEQ ID NO: 4, or a sequence at least 80%, 85%, 90% or 95% identical thereto, that is capable of increasing expression of the coding sequence as assessed in accordance with this disclosure.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 3′-UTR comprises a sequence derived from the human chitinase-1 (CHIT1) 3′-UTR, optionally a sequence according to SEQ ID NO: 11 or SEQ ID NO: 12, or a sequence at least 80%, 85%, 90% or 95% identical thereto, that is capable of increasing expression of the coding sequence as assessed in accordance with this disclosure.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 5′-UTR comprises a sequence derived from the human protein kinase cAMP-activated catalytic subunit beta (PRKACB) 5′-UTR, that is capable of increasing expression of the coding sequence as assessed in accordance with this disclosure and wherein the 3′-UTR comprises a sequence derived from the chitinase-1 (CHIT1) 3′-UTR, optionally a sequence according to SEQ ID NO: 5, that is capable of increasing expression of the coding sequence as assessed in accordance with this disclosure.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 5′-UTR comprises a sequence derived from the glutamic-oxaloacetic transaminase 1 (GOT1) 5′ UTR, optionally a sequence according to SEQ ID NO: 5 or SEQ ID NO: 6, or a sequence at least 80%, 85%, 90% or 95% identical thereto, that is capable of increasing expression of the coding sequence as assessed in accordance with this disclosure.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 5′-UTR comprises a sequence derived from the glucuronidase beta (GUSB1) 5′ UTR, optionally a sequence according to SEQ ID NO: 7 or SEQ ID NO: 8, or a sequence at least 80%, 85%, 90% or 95% identical thereto, that is capable of increasing expression of the coding sequence as assessed in accordance with this disclosure.
In one instance, the nucleic acid molecule comprises a 5′-UTR, a coding sequence and a 3′-UTR, wherein the coding sequence is operably linked to the 5′-UTR and 3′-UTR and wherein the 3′-UTR comprises a sequence derived from the pyruvate kinase L/R (PKLR) sequence, optionally a sequence according to SEQ ID NO: 13 or SEQ ID NO: 14, or a sequence at least 80%, 85%, 90% or 95% identical thereto, that is capable of increasing expression of the coding sequence as assessed in accordance with this disclosure.
Table 1 sets out the UniProt (Release 2022_04) codes for the genes referred to in accordance with the disclosure:
In an instance, the 5′-UTR and/or 3′-UTR sequences of the disclosure include sequences 85%, 86%, 87%, 88%, 89%, 90%, 91%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to the sequences disclosed herein, where the sequences are capable of increasing expression of the coding sequence as assessed in accordance with this disclosure.
The nucleic acid molecule of the disclosure can be, for example, a plasmid, an episome, a cosmid or a phage. Suitable vectors and methods of vector preparation are well known in the art (see, e.g., Sambrook et al., Molecular Cloning, a Laboratory Manual, 3rd edition, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (2001), and Ausubel et al., Current Protocols in Molecular Biology, Greene Publishing Associates and John Wiley & Sons, New York, N.Y. (1994)).
In one instance, the nucleic acid molecule of the present disclosure is a closed circular molecule or a linear molecule.
In various instances, the nucleic acid molecule according to the disclosure comprises, in a 5′ to 3′ direction of transcription, a promoter, a 5′-UTR and a 3′-UTR flanking a coding sequence and a polyadenylation signal.
In one instance, the nucleic acid molecule of the disclosure further comprises a 5′-cap structure, optionally a cap1 structure. Further suitable cap structures and approaches for generating suitable cap structures are disclosed in WO2017/053297 and Tusup et al., Design of in vitro Transcribed mRNA Vectors for Research and Therapy, Chim Int J Chem. 2019; 73(5):391-394, both of which are hereby incorporated by reference. 5′-capping of polynucleotides may be completed concomitantly during the in vitro-transcription reaction using the following chemical RNA cap analogs to generate the 5′-guanosine cap structure according to manufacturer protocols: 3′-O-Me-m7G(5′)ppp(5′) G [the ARCA cap]; G(5′)ppp(5′)A; 35 G(5′)ppp(5′)G; m7G(5′)ppp(5′)A; m7G(5′)ppp(5′)G (New England BioLabs, Ipswich, MA). 5′-capping of modified RNA may be completed post-transcriptionally using a Vaccinia Virus Capping Enzyme to generate the “Cap 0” structure: m7G(5′)ppp(5′)G (New England BioLabs, Ipswich, MA). Cap 1 structure may be generated using both Vaccinia Virus Capping Enzyme and a 2′-0 methyl-transferase to generate: m7G(5′)ppp(5′)G-2′-O-methyl. Cap 2 structure may be generated from the Cap 1 structure followed by the 2′-O-methylation of the 5′antepenultimate nucleotide using a 2′-0 methyl-transferase. Cap 3 structure may be generated from the Cap 2 structure followed by the 2′-O-methylation of the 5′-preantepenultimate nucleotide using a 2′-0 methyl-transferase. Enzymes may be derived from a recombinant source. Further suitable means for generating suitable cap structures are disclosed in WO2016/193226, which is hereby incorporated by reference.
In one instance, the nucleic acid molecule of the disclosure comprises a promoter that is any promoter for a DNA-dependent RNA polymerase. For example, T7 (optionally comprising or consisting of the sequence TAATACGACTCACTATAAGG (SEQ ID NO: 15), T3, SP6 or Syn5 RNA polymerases.
In some instances, the nucleic acid molecule disclosed herein comprises a polyadenylation signal (Poly A tail). The Poly A tail is a long sequence of adenine residues which lies at the 3′ end of the molecule. The role of the Poly A tail is two-fold. The Poly A tail is essential for translation, with Poly(A) binding proteins (PABP) recruiting translation factors to enhance translation levels. Furthermore, the Poly A tail increases the stability of a nucleic acid molecule by PABP binding poly(A) in mRNA and protecting it against exonuclease digestion. In mRNA, the poly A tail is also known to play a key role in the transport of mRNA from the nucleus to the ribosomes (Shlake, T., et al., RNA Biol., (2012), 9(11), 1319-1330). In one instance, the nucleic acid molecule of the disclosure comprises a Poly A tail of about 50 to about 500 adenosine nucleotides. For example, the poly A tail may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290 or 300 adenosines. In some instances, the poly A tail contains 50 to 250 adenosines. In some instances, the poly A tail contains 60 to 100 adenosines. In some instances, the poly A tail contains 70, 71, 72, 73, 74, 75, 76, 77, 78, 79 or 80 adenosines. In some instances, the poly A tail contains 77 adenosines.
In one instance of the disclosure, the nucleic acid molecule comprises a split Poly(A) tail. A split Poly(A) tail can comprise at least two adenosine containing elements, optionally of between 30 and 60 adenosines each, separated by a spacer optionally of between 1 and 25 nucleotides.
In one instance, the nucleic acid molecule of the disclosure is a ribonucleic acid (RNA) molecule.
In one instance, the ribonucleic acid (RNA) molecule is mRNA.
In some instances, the coding sequence disclosed herein comprises a leader sequence. A leader sequence may encode a signal peptide. In some instances, the signal peptide is fused to the expressed therapeutic protein. In such instances, the leader sequence and the gene of interest are within the same open reading frame (ORF).
Signal peptides, comprising the N-terminal 15-60 amino acids of proteins, are typically needed for the translocation across the membrane on the secretory pathway and control entry of most proteins to the secretory pathway. In eukaryotes, the signal peptide of a nascent precursor protein (pre-protein) directs the ribosome to the rough endoplasmic reticulum (ER) and initiates the transport of the growing peptide chain across it for processing. ER processing produces mature proteins, in which the signal peptide is typically cleaved by resident signal peptidases, at least for secreted proteins.
A signal peptide may have a length of 15-60 amino acids. For example, a signal peptide may have a length of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, or 60 amino acids. In some instance, a signal peptide has a length of 20-60, 25-60, 30-60, 35-60, 40-60, 45-60, 50-60, 55-60, 15-55, 20-55, 25-55, 30-55, 35-55, 40-55, 45-55, 50-55, 15-50, 20-50, 25-50, 30-50, 35-50, 40-50, 45-50, 15-45, 20-45, 25-45, 30-45, 35-45, 40-45, 15-40, 20-40, 25-40, 30-40, 35-40, 15-35, 20-35, 25-35, 30-35, 15-30, 20-30, 25-30, 15-25, 20-25, or 15-20 amino acids. In some instances, the signal peptide has the following sequence: MPLLLLLPLLWAGALA (SEQ ID NO: 34).
In some instances, the nucleic acid molecule provided herein is not chemically modified and comprises the standard nucleotides adenine (A), thymine (T) or uracil (U), where the nucleic acid molecule is an RNA, guanine (G) or cytosine (C).
In some instances, the nucleic acid molecule comprises modified nucleotides. Many modified nucleotides are known in the art, such as disclosed in WO2007/024708, which is hereby incorporated by reference. Modifications can include either naturally occurring modifications or non-naturally occurring modifications. Modifications can include those at the sugar, backbone or nucleobase protein of the nucleotide and/or nucleoside as well known in the art.
In some instances, the nucleic acid molecules herein may include natural (i.e., standard) nucleotide or nucleoside, non-naturally or naturally occurring modified nucleotides or nucleosides, or any combination thereof.
In one instance, wherein the nucleic acid molecule is an RNA, the RNA may comprise standard A, G and C nucleotides and modified U nucleotides.
In some instances, the nucleic acid molecule comprising the modified nucleoside or nucleotide (e.g., a “modified RNA nucleic acid molecule”) exhibits reduced immunogenicity in a cell or organism relative to an unmodified RNA nucleic molecule comprising the same sequence.
In some instances, modified nucleosides in nucleic acid molecules provided herein (e.g., RNA nucleic acid molecules such as mRNA) comprise N1-methyl-pseudouridine (m1Ψ), 1-ethyl-pseudouridine (e1Ψ), 5-methoxy-uridine (mo5U), 5-methyl-cytidine (m5C), and/or pseudouridine (Ψ). In some instances, modified nucleotides in nucleic acid molecules (e.g., RNA nucleic acid molecules, such as mRNA) comprise 5-methoxymethyl uridine, 5-methylthio uridine, 1-methoxymethyl pseudouridine, 5-methyl cytidine, and/or 5-methoxy cytidine. In some instances, the RNA nucleic acid molecule includes a combination of at least two (e.g., 2, 3, 4 or more) of any of the aforementioned modified nucleobases.
In some instances, the nucleic acid molecule provided herein comprises N1-methyl-pseudouridine (m1Ψ) at one or more or all uridine positions of the nucleic acid molecule.
In some instances, the nucleic acid molecule comprises 5-methoxy-uridine (mo5U) at one or more or all uridine positions of the nucleic acid molecule.
In some instances, the nucleic acid molecule comprises from about 1% to about 100% modified nucleotides (either in relation to overall nucleotide content or in relation to one or more types of nucleotide (i.e., any one or more of A, G, U, T or C). In some instances, the nucleic acid molecule comprises any intervening percent of modified nucleotide content. For example, from 1% to 20%, from 1% to 25%, from 1% to 50%, from 1% to 60%, from 1% to 70%, from 1% to 80%, from 1% to 90%, from 1% to 95%, from 10% to 20%, from 10% to 25%, from 10% to 50%, from 10% to 60%, from 10% to 70%, from 10% to 80%, from 10% to 90%, from 10% to 95%, from 10% to 100%, from 20% to 25%, from 20% to 50%, from 20% to 60%, from 20% to 70%, from 20% to 80%, from 20% to 90%, from 20% to 95%, from 20% to 100%, from 50% to 60%, from 50% to 70%, from 50% to 80%, from 50% to 90%, from 50% to 95%, from 50% to 100%, from 70% to 80%, from 70% to 90%, from 70% to 95%, from 70% to 100%, from 80% to 90%, from 80% to 95%, from 80% to 100%, from 90% to 95%, from 90% to 100%, and from 95% to 100%. The remaining percentage is accounted for by unmodified A, G, U, T or C.
The nucleic acid molecules may contain at a minimum 1% and at maximum 100% modified nucleotides, or any intervening percentage, such as at least 5% modified nucleotides, at least 10% modified nucleotides, at least 25% modified nucleotides, at least 50% modified nucleotides, at least 80% modified nucleotides, or at least 90% modified nucleotides. For example, the nucleic acids may contain a modified pyrimidine such as a modified uracil or cytosine. In some instances, at least 5%, at least 10%, at least 25%, at least 50%, at least 80%, at least 90% or 100% of the uracil in the nucleic acid is replaced with a modified uracil (e.g., a 5-substituted uracil). The modified uracil can be replaced by a compound having a single unique structure, or can be replaced by a plurality of compounds having different structures (e.g., 2, 3, 4 or more unique structures). In some instances, at least 5%, at least 10%, at least 25%, at least 50%, at least 80%, at least 90% or 100% of the cytosine in the nucleic acid is replaced with a modified cytosine (e.g., a 5-substituted cytosine). The modified cytosine can be replaced by a compound having a single unique structure, or can be replaced by a plurality of compounds having different structures (e.g., 2, 3, 4 or more unique structures).
In some instances, the nucleic acid molecules is an mRNA in which the uridine is replaced by a compound having a single unique structure. In some instances, the single unique structure is N1-methyl-pseudouridine. In some instances, the nucleic acid molecule comprises at least 5%, at least 10%, at least 25%, at least 50%, at least 80%, at least 90% or 100% N1-methyl-pseudouridine.
In one instance the mRNA comprises a modified nucleobase. In some instances, the modified nucleobase is modified adenine (A), cytosine (C), uracil (U) and guanine (G).
In one instance, the modified nucleobase is modified U. In some instances, the modified U is 1-methylpseudouridine (m1Ψ) and pseudouridine (Ψ), such as is disclosed in WO2007/024708, which is hereby incorporated by reference.
In one instance, the nucleic acid molecules of the present disclosure comprise UTR sequences comprising 5-methoxy-uridine (mo5U) at one or more or all uridine positions of the nucleic acid molecule. The molecule can comprise at least 25% ratio of modified uridine to unmodified uridine, including 25% to 50%, or at least 50%.
The examples show that modifying uridine in a 5′-UTR sequence derived from the human CHIT1 5′-UTR and in a 3′-UTR sequence derived from the human citrate synthase (CS) 3′-UTR results in a particularly substantial increase in translation.
In one instance, the nucleic acid molecules of the present disclosure comprise sequences comprising N1-methyl-pseudouridine (m1Ψ) at one or more or all uridine positions of the nucleic acid molecule. The molecule can comprise at least 75% ratio of modified uridine to unmodified uridine, including 100%.
In one instance, the nucleic acid molecule of the disclosure comprises a coding sequence encoding a therapeutic protein or peptide, optionally a wild-type sequence of a human protein or an antibody, or antigen binding fragment thereof.
Thus, the nucleic acid molecule of the disclosure can be useful in gene therapies.
In some instances, the coding sequence is not CHIT1, GUSB1, PRKACB, GOT1, PKLR or CS.
In one instance, the nucleic acid molecule of the disclosure comprises a coding sequence encoding a disease-associated antigen (DAA). This molecule of the disclosure is a vaccine vector.
Nucleic acid vaccine vectors pose substantial advantages over conventional vaccination approaches. In terms of safety, RNA based vaccines are non-infectious, unlike live or live attenuated vaccination approaches. Furthermore, RNA vaccines do not integrate into the genome and therefore are not a risk for mutagenesis. Moreover, both DNA and RNA-based vaccines have proved highly efficacious against many infectious agents, including Zika, Influenza, Rabies and SARS-COV-2. Nucleic acid-based vaccines offer a cheap, fast and easily-scalable alternative to conventional vaccination approaches (Pardi, N., et al., Nature Reviews, (2018), 17, 261-279).
In one instance of the disclosure, the disease-associated antigen can be a viral antigen, a bacterial antigen or a tumour-associated antigen.
After entering a cell, the coding sequence of a DNA molecule can undergo transcription and translation, or the coding sequence of an RNA molecule can undergo translation to produce the antigenic protein or fragments thereof of an antigen.
Upon production of the antigen, the exposure of the host immune system to the protein or protein fragment can stimulate an immune response. This immune response may comprise the stimulation of antibody production by B cells and the production of memory B cells, capable of producing antibodies against the antigen or fragment thereof of a specified infectious agent. Upon infection with the same infectious agent, the host immune system is primed against this antigen or antigenic protein fragment, reducing the time-span of the immune response against the infectious agent. Therefore, reducing or preventing the onset of symptoms in response to infection.
In one instance of the disclosure, the nucleic acid molecule comprises a sequence encoding a nano antigen particle. The antigen may be an antigen as described anywhere herein.
In one instance, the nucleic acid molecule comprises a coding sequence that encodes a multimerization unit. In one instance, the multimerization unit is a ferritin protein. The multimerization unit may be the scaffold for the nano antigen particle. In some instances, the ferritin is a Helicobacter pylori ferritin. In some instances, the nucleic acid molecule comprises a sequence that encodes an antigenic protein and a ferritin protein, wherein the antigenic protein and ferritin assemble to form a nano antigen particle.
In one instance of the disclosure, the coding sequence further encodes a linker. The linker can be encoded between the DAA and the multimerization unit, optionally a ferritin protein, such that the DAA is fused to the multimerization unit in the encoded molecule.
In one instance, the nucleic acid molecule comprises RNA 5′- and 3′-UTR sequences and RNA coding sequence, optionally mRNA sequence.
The recent Covid-19 pandemic has led to an urgent need for improved vaccines that target coronaviruses of concern. To date several variants of SARS-COV-2 have been identified with some of the most infectious among these being the Delta and Omicron variants. Vaccines currently approved for the treatment of SARS-COV-2 all encompass stimulating immunity against the SARS-COV-2 spike protein. Although, a number of mutations in the receptor binding domain of the spike protein have been identified in new variants of SARS-COV-2, which is thought to have led to increased vaccine resistance in newly emerging variants (Zhao, J. et al., Environmental research, (2022), 206(112240)). Research estimates that current vaccines are around three to five fold less potent against the Delta variant than the Alpha variant of SARS-COV-2 (Planas, D. et al., Nature, (2021), 596, 276-280).
Accordingly, there is an ongoing need for improved vaccines in general, including those useful in the prevention and treatment of coronaviruses.
Accordingly, one instance of the disclosure provides a nucleic acid molecule as described herein encoding a coronavirus (CoV) antigen. In one instance, the nucleic acid molecule comprises RNA 5′-and 3′-UTR sequences and RNA coding sequence. In one instance, the coronavirus antigen can be selected from SARS-COV-1 and/or SARS-COV-2. In one instance, the nucleic acid molecule encodes a SARS-COV-2 antigen selected from one or more of the following variants: Wuhan, Alpha, Beta, Delta and Omicron, optionally BA.1, BA.2, BA.2.86, BA.3, BA.4/5, BQ.1, BQ.1.1, JN.1, XBB.1 and XBB.1.5.
The coronavirus virion comprises a large number of glycosylated spike (S) proteins projecting from the surface of the virion. These S proteins form trimer structures, and mediate virus entry into host cells, making it a primary target for vaccine design.
The coronavirus spike protein is 1273 amino acids in length and comprises a signal peptide, and S1 and S2 subunits. The S1 subunit contains a receptor-binding domain (RBD) that recognizes and binds to a specific host cell receptor, angiotensin-converting enzyme 2 (ACE2). The S2 subunit mediates viral cell membrane fusion.
Thus, in one instance, the nucleic acid molecule comprises a sequence encoding an S protein or antigenic fragment thereof. Upon delivery into a host cell, the S protein is translated and processed in the host cell, resulting in the presentation of a trimerized S protein on a host cell surface.
In some instances, the nucleic acid molecule comprises a sequence that encodes a CoV S protein and a ferritin protein, wherein the CoV S protein and ferritin assemble to form a nano antigen particle.
The S protein can be stabilised in a pre-fusion conformation. Further, the S protein can comprise K986P and/or V987P mutations.
In one instance, the nucleic acid molecule of the present disclosure encodes an antigenic fragment thereof that is a receptor binding domain (RBD). In one instance, the antigenic fragment is a RBD of a SARS-COV-2 S protein. In one instance, the antigenic fragment is a RBD of a SARS-COV-1 S protein.
In some instances, it may be advantageous to fuse a fragment of an antigenic protein to the ferritin in the nano antigen particle. In one instance, the fragment of the antigenic protein may be the RBD. The RBDs in the nano antigen particle may be derived from antigens of the same infectious agent i.e. be monovalent, or the RBDs of the nano antigen particle may be derived from antigens of more than one infectious agent i.e. be multivalent.
The nucleic acid molecules as provided herein, in some instances, encode fusion proteins that comprise vaccine antigens linked to multimerization units. In some instances, such multimerization units impart desired properties to an antigen encoded by the nucleic acid molecule. For example, the examples show that multimerization units improve the immunogenicity of an antigen (e.g., the COVID spike protein), as compared to the immunogenicity of the same antigen expressed without the multimerization units. Furthermore, the multimerization units provided herein improve the pan-variant response against an antigen. For example, a nucleic acid molecule provided herein comprising a coding sequence encoding a COVID spike protein-multimerization unit fusion protein elicits a broader immune response against SARs-COV-2 variants compared to spike proteins alone.
In some instances, the multimerization unit is a protein that can self-assemble into protein nanoparticles that are highly symmetric, stable, and structurally organized, with diameters of 10-150 nm, a highly suitable size range for optimal interactions with various cells of the immune system. In some instances, viral proteins or virus-like particles can be used to form stable nanoparticle structures. Examples of such viral proteins are known in the art. For example, in some instances, the multimerization units is a hepatitis B surface antigen (HBsAg). HBsAg forms spherical particles with an average diameter of ˜22 nm and which lacked nucleic acid and hence are non-infectious (Lopez-Sagaseta, J. et al. Computational and Structural Biotechnology Journal 14 (2016) 58-68). In some instances, the multimerization unit is a hepatitis B core antigen (HBcAg) self-assembles into particles of 24-31 nm diameter, which resembled the viral cores obtained from HEY-infected human liver. HBcAg produced in self-assembles into two classes of differently sized nanoparticles of 300 A and 360 A diameter, corresponding to 180 or 240 protomers. In some instances, the antigen is fused to HBSAG or HBcAG to facilitate self-assembly of nanoparticles displaying the antigen.
In some instances, the multimerization unit is selected from the following self-assembling proteins: ferritin, lumazine synthase and encapsuling.
Ferritin is a protein whose main function is intracellular iron storage. Ferritin is made of 24 subunits, each composed of a four-alpha-helix bundle, that self-assemble in a quaternary structure with octahedral symmetry (Cho K. J. et al. J Mol Biol. 2009; 390:83-98). Several high resolution structures of ferritin have been determined, confirming that Helicobacter pyloriferritin is made of 24 identical protomers, whereas in animals, there are ferritin light and heavy chains that can assemble alone or combine with different ratios into particles of 24 subunits (Granier T. et al. J Biol Inorg Chem. 2003; 8:105-111; Lawson D. M. et al. Nature. 1991; 349:541-544). Ferritin self-assembles into nanoparticles with robust thermal and chemical stability. Thus, the ferritin nanoparticle is well-suited to carry and expose antigens.
Lumazine synthase (LS) is also well-suited as a nanoparticle platform for antigen display. LS, which is responsible for the penultimate catalytic step in the biosynthesis of riboflavin, is an enzyme present in a broad variety of organisms, including archaea, bacteria, fungi, plants, and eubacteria (Weber S. E. Flavins and Flavoproteins. Methods and Protocols, Series: Methods in Molecular Biology. 2014). The LS monomer is 150 amino acids long, and consists of beta-sheets along with tandem alpha-helices flanking its sides. A number of different quaternary structures have been reported for LS, illustrating its morphological versatility: from homopentamers up to symmetrical assemblies of 12 pentamers forming capsids of 150 A diameter. Even LS cages of more than 100 subunits have been described (Zhang X. et al. J Mol Biol. 2006; 362:753-770).
Encapsulin, a novel protein cage nanoparticle isolated from thermophile Thermotoga maritima, may also be used as a platform to present antigens on the surface of self-assembling nanoparticles. Encapsulin is assembled from 60 copies of identical 31 kDa monomers having a thin and icosahedral T=1 symmetric cage structure with interior and exterior diameters of 20 and 24 nm, respectively (Sutter M. et al. Nat Struct Mol Biol. 2008, 15: 939-947). Although the exact function of encapsulin in T. maritima is not clearly understood yet, its crystal structure has been recently solved and its function was postulated as a cellular compartment that encapsulates proteins such as DyP (Dye decolorizing peroxidase) and Flp (Ferritin like protein), which are involved in oxidative stress responses (Rahmanpour R. et al. FEES J. 2013, 280: 2097-2104).
In some instances, the nucleic acid molecule provided herein comprises a coding sequence encoding a coronavirus antigen (e.g., a SARS-COV-2 spike (S) protein) fused to a ferritin sub-unit.
In some instances, the nucleic acid molecules disclosed herein encode fusion proteins. In such instances, the each of the domains of the fusion protein (e.g., the antigen and the multimerization unit), may be separated by a coding sequence encoding a linker sequences. The linker sequence may be self-cleaving. In other words, the linker may be a self-cleavable linker. In other instances, the linker may be a protease-sensitive linker. In some instances, the linker may be a glycine-serine linker.
In some instances, the self-cleaving linker is selected from an F2A linker, P2A linker, T2A linker, E2A linker, and combinations thereof. This family of self-cleaving peptide linkers, referred to as 2A peptides, has been described in the art (see for example, Kim, J. H. et al. (2011) PLOS ONE 6:e18556).
In some instances, the glycine-serine linker has the following amino acid sequence: GSGGSG (SEQ ID NO: 28). In some instances, the glycine-serine linker is encoded by SEQ ID NO: 29 or SEQ ID NO: 30.
The skilled person will appreciate that other art-recognized linkers may be suitable for use in the constructs of the disclosure (e.g., encoded by the nucleic acid molecules provided herein). The skilled person will likewise appreciate that other polycistronic constructs (nucleic acid molecules encoding more than one antigen/polypeptide separately within the same molecule) may be suitable for use as provided herein.
The nucleic acid vaccine vectors of the present disclosure can be manufactured according to in vitro transcription. In vitro transcription of RNA is known in the art and is described in International Publication WO2014/152027, which is incorporated by reference herein in its entirety. In some instances, the RNA of the present disclosure is prepared in accordance with any one or more of the methods described in WO2018/053209 and WO2019/036682, each of which is incorporated by reference herein. In overview, a DNA template is generated, typically as a linearized plasmid, followed by in vitro transcription to synthesize the RNA, alongside or followed by capping.
The 5′ cap can be added by a multi-step enzymatic reaction or via co-transcription. In co-transcriptional capping, a cap analog, such as CleanCap® AG, is added directly to the in vitro transcription mixture. Alternatively, enzymatic capping using vaccinia virus capping enzyme is performed separately to the in vitro transcription.
Following purification, the mRNA product can be encapsulated in a lipid nanoparticle (LNP).
The present disclosure also provides a pharmaceutical composition comprising a nucleic acid molecule or LNP as defined anywhere herein and a pharmaceutical carrier.
In one instance, the pharmaceutical composition is a monovalent composition comprising a nucleic acid molecule according to the disclosure encoding a first antigen, or an immunogenic fragment or immunogenic variant thereof.
In one instance, the pharmaceutical composition is a bivalent composition comprising a further nucleic acid molecule according to the disclosure encoding a second antigen, or an immunogenic fragment or immunogenic variant thereof, wherein the second antigen is different to the first antigen.
The present disclosure further provides a composition comprising a first nucleic acid molecule according to the disclosure, wherein the disease-associated antigen is a Delta variant S protein. In one instance, the disease-associated antigen of a first nucleic acid molecule is a Wuhan variant S protein.
In one instance, the composition according to the disclosure can further include a second nucleic acid molecule encoding an Omicron variant S Protein, optionally variant BA.1, BA.2, BA.2.86, BA.3, BA.4/5, BQ.1, BQ.1.1, JN.1, XBB.1 or XBB.1.5.
In one instance, the second nucleic acid molecule encodes Omicron variant S Protein BA.4/5.
In one instance, the second nucleic acid molecule encodes Omicron variant S Protein XBB.1.5.
In one instance of the disclosure, the composition comprises:
In one instance of the disclosure, the composition comprises:
In one instance of the disclosure, the first nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO: 25 and/or the second nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO:27.
In one instance of the disclosure, the first nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO: 25 and/or the second nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO:42.
In one instance of the disclosure, the first nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:37 and the second nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:38. In one instance, the first nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:37 and the second nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:38.
In one instance of the disclosure, the first nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:37 and the second nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:43. In one instance, the first nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:37 and the second nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:43.
In one instance, the first nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 40 and the second nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 41.
In one instance, the first nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 40 and the second nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 41.
In one instance, the first nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 40 and the second nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 44.
In one instance, the first nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 40 and the second nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 44.
In one instance of the disclosure, the composition comprises:
In one instance of the disclosure, the composition comprises:
In one instance of the disclosure, the first nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO:23 and the second nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO:27.
In one instance of the disclosure, the first nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO:23 and the second nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO:42.
In one instance of the disclosure, the first nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:36 and the second nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:38. In one instance, the first nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:36 and the second nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:38.
In one instance of the disclosure, the first nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:36 and the second nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:43. In one instance, the first nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:36 and the second nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:43.
In one instance, the first nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 39 and the second nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 41.
In one instance, the first nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 39 and the second nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 41.
In one instance, the first nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 39 and the second nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 44.
In one instance, the first nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 39 and the second nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 44.
In one instance, the first and/or second nucleic acid molecule of any composition of the disclosure comprises 80% to 100% N1-methyl-pseudouridine (m1Ψ) at uridine positions of the nucleic acid molecule.
In one instance, the first and/or nucleic acid vector(s) comprise a 5′-cap structure, optionally a cap 1 structure.
In one instance, the first and/or second nucleic acid molecule of the composition comprises a T7 promoter sequence, optionally the RNA sequence corresponding to the sequence set forth in SEQ ID NO: 15.
In one instance, the first and/or second nucleic acid molecule of the composition encodes a glycine-serine linker, optionally with the sequence of SEQ ID NO: 28.
In one instance, the first and/or second nucleic acid molecule of the composition comprises a Poly A tail of between 70 and 90 adenosine nucleotides.
In one instance, the first and/or second nucleic acid molecule of the composition comprise a leader sequence. The leader sequence will be cleaved from the mature, expressed antigen. In one instance, the leader sequence encodes the following amino acid sequence: MPLLLLLPLLWAGALA (SEQ ID NO: 34).
The present disclosure further provides a monovalent composition comprising a nucleic acid molecule according to the disclosure, wherein the disease-associated antigen is an Omicron variant S Protein, optionally variant BA.1, BA.2, BA.2.86, BA.3, BA.4/5, BQ.1, BQ.1.1, JN.1, XBB.1 or XBB.1.5.
In one instance, the nucleic acid molecule encodes Omicron variant S Protein BA.4/5.
In one instance, the nucleic acid molecule encodes Omicron variant S Protein XBB.1.5.
In one instance of the disclosure, the composition comprises a nucleic acid molecule comprising a 5′-UTR comprising a sequence at least 95% identical to the sequence of SEQ ID NO: 19 and a 3′-UTR comprising a sequence at least 95% identical to the sequence of SEQ ID NO: 21, operably linked to a coding sequence, wherein the coding sequence comprises a sequence encoding an Omicron variant S protein, a linker and a ferritin protein, wherein the encoded protein is a Delta variant S protein—ferritin fusion protein.
In one instance of the disclosure, the composition comprises a nucleic acid molecule comprising a 5′-UTR comprising or consisting of the sequence of SEQ ID NO: 19 and a 3′-UTR comprising or consisting of the sequence of SEQ ID NO: 21, operably linked to a coding sequence, wherein the coding sequence comprises a sequence encoding an Omicron S protein, a linker and a ferritin protein, wherein the encoded protein is a Delta variant S protein—ferritin fusion protein.
In one instance of the disclosure, the nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO:27.
In one instance of the disclosure, the nucleic acid molecule comprises a coding sequence as set forth in SEQ ID NO:42.
In one instance of the disclosure, the nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:38. In one instance, the nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:38.
In one instance of the disclosure, the nucleic acid molecule comprises a sequence as set forth in SEQ ID NO:43. In one instance, the nucleic acid molecule consists of a sequence as set forth in SEQ ID NO:43.
In one instance, the nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 41.
In one instance, the nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 41.
In one instance, the nucleic acid molecule comprises a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 44.
In one instance, the nucleic acid molecule contains a coding sequence that encodes for the polypeptide sequence set forth in SEQ ID NO: 44.
In one instance, the nucleic acid molecule of the composition comprises 80% to 100% N1-methyl-pseudouridine (m1Ψ) at uridine positions of the nucleic acid molecule.
In one instance, nucleic acid vector comprises a 5′-cap structure, optionally a cap 1 structure.
In one instance, the nucleic acid molecule of the composition comprises a T7 promoter sequence, optionally the RNA sequence corresponding to the sequence set forth in SEQ ID NO: 15.
In one instance, the nucleic acid molecule of the composition encodes a glycine-serine linker, optionally with the sequence of SEQ ID NO: 28.
In one instance, the nucleic acid molecule of the composition comprises a Poly A tail of between 70 and 90 adenosine nucleotides.
In one instance, the nucleic acid molecule of the composition comprises a leader sequence. The leader sequence will be cleaved from the mature, expressed antigen. In one instance, the leader sequence encodes the following amino acid sequence: MPLLLLLPLLWAGALA (SEQ ID NO: 34).
In all instances of the disclosure, the sequence encoding the antigen may be further optimized via mutation to increase protein stability (such as the structure of the CoV spike protein or the RBD), maximise protein translation and reduce unwanted side effects.
Said compositions may comprise an effective amount of the nucleic acid molecule as defined herein. An effective amount of the nucleic acid molecule to be employed therapeutically will depend, for example, upon the therapeutic objectives, the route of administration, and the condition of the patient. In one instance, the effective amount of the nucleic acid molecule as defined anywhere herein within the pharmaceutical composition is effective to treat or prevent a disease associated with coronavirus infection.
The composition is a pharmaceutically acceptable (e.g., physiologically acceptable) composition, which comprises a carrier, preferably a pharmaceutically acceptable (e.g., physiologically acceptable) carrier. The pharmaceutically acceptable carrier may include one or more excipients. Pharmaceutically acceptable excipients are known and include carriers, excipients, or stabilizers that are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Any suitable carrier can be used within the context of the disclosure, and such carriers are well known in the art. The choice of carrier will be determined, in part, by the particular site to which the composition may be administered and the particular method used to administer the composition. The physiologically acceptable excipient may be an aqueous pH buffered solution. Examples of physiologically acceptable excipients include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as Ethylenediaminetetraacetic acid (EDTA); sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN™, polyethylene glycol (PEG), and PLURONICS™.
The composition optionally can be sterile. The composition can be frozen or lyophilized for storage and reconstituted in a suitable sterile carrier prior to use. The compositions can be generated in accordance with conventional techniques described in, e.g., Remington: The Science and Practice of Pharmacy, 21st Edition, Lippincott Williams & Wilkins, Philadelphia, PA (2001).
The compositions can be administered intravenously. The composition can also be administered parenterally or subcutaneously.
Methods of administering a pharmaceutical composition as defined herein include, but are not limited to, parenteral administration (e.g., intradermal, intramuscular, intraperitoneal, intravenous and subcutaneous), epidural, and mucosal (e.g., intranasal and oral routes). In a specific example, a pharmaceutical composition is administered intranasally, intramuscularly, intravenously, or subcutaneously. The compositions may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, intranasal mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local. Each dose may or may not be administered by an identical route of administration.
Various delivery systems are known and can be used to administer a prophylactic or therapeutic agent (e.g., a nucleic acid molecule as disclosed herein), including, but not limited to, encapsulation in liposomes, microparticles, microcapsules, construction of a nucleic acid as part of a retroviral or other vector, etc. In addition, pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.
The present disclosure relates to nucleic acid molecules that can be suitable for use as vaccine vectors.
Lipid nanoparticles (LNPs) may be used as a platform for vaccine vector delivery. LNPs may comprise ionizable cationic lipids, cholesterol, phospholipids (such as distearoylphosphatidylcholine), and polyethylene glycol (PEG)-lipid. lonizable cationic lipids participate in nanoparticle packaging by interacting with negatively charged RNA molecules. Upon administration, LNPs are rapidly cleared from injected tissues, and are therefore less likely to induce inflammation and tissue damage.
Thus, in one instance of the present disclosure, the nucleic acid molecules as described anywhere herein are packaged into a delivery system. In one instance the delivery system is an LNP. Thus, the present disclosure also relates to LNPs comprising a nucleic acid molecule as described anywhere herein.
In one instance, the LNPs comprise nucleic acid molecules as described anywhere herein, wherein the nucleic acid molecule encodes an antigenic protein. In one instance, the LNPs comprise one or more nucleic acid molecules as described anywhere herein, wherein the molecules encode a CoV S protein.
The present disclosure provides for a nucleic acid molecule described herein for use in medicine.
In one instance, a nucleic acid molecule of the disclosure encoding a therapeutic protein or peptide is useful for treating a disease or condition characterised by a lack of said therapeutic protein or peptide.
In one instance, a nucleic acid molecule of the disclosure encoding a disease-associated antigen is useful as a nucleic acid vaccine vector.
Following patient administration, the coding sequence will be transcribed and translated, in the case of a DNA sequence, and translated in the case of an RNA sequence, into the antigenic protein or fragment of an antigenic protein that it encodes for. The production of these antigenic proteins or antigenic protein fragments will stimulate an immune response, leading to the production of neutralising antibodies. Upon infection by a corresponding infectious agent, the presence of neutralising antibodies and memory B cells will increase the speed of the immune response, minimising the severity and length of symptom onset.
The vaccine vectors of the present disclosure may be used as a preventative therapy against a target antigen that causes disease. In one instance of the present disclosure, the vaccine vectors may be used in the prevention of CoV and, in particular, SARS-COV-2.
The vaccine vectors of the present disclosure may also be used as a treatment against a target antigen that has infected a subject. In one instance of the present disclosure, the vaccine vectors may be used in the treatment of CoV and, in particular, SARS-COV-2.
The present disclosure further provides a method of the prevention or treatment of a disease or condition comprising administering a nucleic acid molecule as described anywhere herein to a patient in need thereof. The present disclosure also relates to a nucleic acid molecule as described anywhere herein for use in a method of manufacture of a medicament useful in the prevention or treatment of a disease. In one instance, the disease is caused by CoV. In one instance, the disease is COVID-19.
Further, the present disclosure relates to a method of inducing an immune response in a subject, the method comprising administering a nucleic acid molecule, combination, composition, pharmaceutical composition or formulation as described anywhere herein to the subject.
In one instance, the subject is human.
Here we describe 5′-UTR and 3′-UTR sequences that enhance expression of coding sequences, including in the context of mRNA vaccine vectors.
The following examples further illustrate the disclosure but should not be construed as in any way limiting its scope.
5′-UTR candidate sequences (shown in Table 2 below) were cloned with eGFP and a reference 3′-UTR sequence (albumin, as used in a CureVac vector described, for example, in EP2831240). The cloning was either done using restriction sites (RE) or seamless. The 5′ end of the 5′-UTR contained T7 promoter sequence.
The template for IVT were generated by PCR using Phusion PCR mix (NEB). The upstream primers contain T7 promoter sequence and the downstream primer contained reverse compliment of end of 3′-UTR of respective clone, along with T80 sequence. The resulting PCR product contain sequence encoding relevant sequence in following order: T7 promoter—5′-UTR-eGFP-3′-UTR-A80. The PCR reaction was then treated with DPNI to digest template DNA and purified using PCR purification kit.
mRNA Synthesis Using in Vitro Transcription (IVT):
The template generated for IVT using PCR were used to prepare mRNA using NEB IVT kits that uses T7 RNA polymerase. The protocol was modified to include CleanCap® (AG). The T7 polymerase incorporates CleanCap® (AG) at the start of each mRNA, giving a cap 1 structure at the 5′ end. The mRNA was either produced using unmodified nucleotide or using modified uridine (5′methoxy uridine) in 25% ratio with unmodified uridine. After the reaction completes, the DNA-template was digested using RNase free DNase. mRNA transcripts contained a 5′-CAP-1-5′-UTR-eGFP coding sequence—3′-UTR-A80. mRNA was then purified using silica column and resuspended in water.
Lung A549 cells were grown in T175 flasks in A549 complete medium (Ham's F-12K supplemented with 10% FBS) at 37° C. 5% CO2. Cells were harvested using accutase for 5 min 37° C., then counted, washed and replated. 100,000 cells in 100 μl media were seeded in each well (96W plates) the day before. On the day of transfection, old media was aspirated and 140 μl of media was added to each well. 1 μl of 100 ng/μl of mRNA was diluted in 4 μl of OptiMEM, and 0.3 μl Lipofectamine 2000 was diluted in 4.7 μl OptiMEM. Then mRNA and Lipofectamine complex were mixed by vortexing and spun down before incubating for 5-10 min at RT. 10 μl of mRNA and Lipofectamine mix was added to each well.
Hela cells were grown in T175 flasks in HeLa complete medium (Minimum Essential Medium MEM, supplemented with 10% FBS and 1% non-essential amino acids) at 37° C. 5% CO2. Cells were harvested using accutase for 5 min 37° C., then counted, washed and replated in collagen treated plates. 100,000 cells in 100 μl media were seeded in each well (96W plates, collagen treated) the day before transfection. On the day of transfection, old media was aspirated and 140 μl of media was added to each well. 1 μl of 100 ng/μl of mRNA was diluted in 4 μl of OptiMEM, and 0.3 μl Lipofectamine 2000 was diluted in 4.7 μl OptiMEM. Then mRNA and Lipofectamine complex were mixed by vortexing and spun down before incubating for 5-10 min at RT. 10 μl of mRNA and Lipofectamine mix was added to each well.
Quantification of eGFP Expression:
eGFP fluorescence was detected using incucyte machine that captures images from the live cells. The fluorescence was measured from the images using Incucyte software in relative fluorescence units (RFU). The data reported in the Figures shows eGFP fluorescence 24 h post-transfection.
Table 2 shows expression levels by the candidate 5′-UTRs. Sequences for candidate 5′-UTRs are shown in SEQ ID Nos:1-8.
The inclusion of a candidate 5′-UTR (Table 2) was shown to increase the expression of eGFP encoding mRNAs in A549 cells, when compared to eGFP expression with both a control 5′-UTR (HSD17B4) and control 3′-UTR (albumin) (
This result was substantiated in Hela cells, in which replacement of the control 5′-UTR with a candidate 5′-UTR (Table 2) was shown to increase eGFP-encoding mRNA expression (
Methods:
3′-UTR candidate sequences (shown in Table 3 below) were cloned with eGFP and a reference 5′-UTR sequence (HSD17B4, as used in a CureVac vector, described, for example, in EP2831240). The cloning was either done using restriction sites (RE) or seamless. The 5′ end of 5′-UTR contained T7 promoter sequence.
The template for IVT were generated by PCR using Phusion PCR mix (NEB). The upstream primers contain T7 promoter sequence and the downstream primer contained reverse compliment of end of 3′-UTR of respective clone, along with T80 sequence. The resulting PCR product contain sequence encoding relevant sequence in following order: T7 promoter—5′-UTR-eGFP-3′-UTR-A80. The PCR reaction was then treated with DPNI to digest template DNA and purified using PCR purification kit.
mRNA Synthesis Using in Vitro Transcription (IVT):
The template generated for IVT using PCR were used to prepare mRNA using NEB IVT kits that uses T7 RNA polymerase. The protocol was modified to include CleanCap® (AG). The T7 polymerase incorporates CleanCap® (AG) at the start of each mRNA, giving cap 1 structure at the 5′ end. The mRNA was either produced using unmodified nucleotide or using modified uridine (5′methoxy uridine) in 25% ratio with unmodified uridine. After the reaction completes, the DNA-template was digested using RNase free DNase. mRNA transcripts contained a 5′-CAP-1-5′-UTR-eGFP-3′-UTR-A80. mRNA was then purified using silica column and resuspended in water.
Lung A549 cells were grown in T175 flasks in A549 complete medium (Ham's F-12K supplemented with 10% FBS) at 37° C. 5% CO2. Cells were harvested using accutase for 5 min 37° C., then counted, washed and replated. 100,000 cells in 100 μl media were seeded in each well (96W plates) the day before. On the day of transfection, old media was aspirated and 140 μl of media was added to each well. 1 μl of 100 ng/μl of mRNA was diluted in 4 μl of OptiMEM, and 0.3 μl Lipofectamine 2000 was diluted in 4.7 μl OptiMEM. Then mRNA and Lipofectamine complex were mixed by vortexing and spun down before incubating for 5-10 min at RT. 10 μl of mRNA and Lipofectamine mix was added to each well.
HeLa cells were grown in T175 flasks in HeLa complete medium (Minimum Essential Medium MEM, supplemented with 10% FBS and 1% non-essential amino acids) at 37° C. 5% CO2. Cells were harvested using accutase for 5 min 37° C., then counted, washed and replated in collagen treated plates. 100,000 cells in 100 μl media were seeded in each well (96W plates, collagen treated) the day before transfection. On the day of transfection, old media was aspirated and 140 μl of media was added to each well. 1 μl of 100 ng/μl of mRNA was diluted in 4 μl of OptiMEM, and 0.3 μl Lipofectamine 2000 was diluted in 4.7 μl OptiMEM. Then mRNA and Lipofectamine complex were mixed by vortexing and spun down before incubating for 5-10 min at RT. 10 μl of mRNA and Lipofectamine mix was added to each well. 1
Quantification of eGFP Expression:
eGFP fluorescence was detected using incucyte machine that captures images from the live cells. The fluorescence was measured from the images using Incucyte software in relative fluorescence units (RFU). The data reported in the Figures shows eGFP fluorescence 24 h post-transfection.
Table 3 shows expression levels by the candidate 3′-UTRs. Sequences for candidate 3′-UTRs are shown in SEQ ID NO NOs:9 to 14.
The addition of a candidate 3′-UTR (Table 3) was shown to increase the expression of eGFP encoding mRNAs in A549 cells, when compared to eGFP expression with both a control 3′-UTR (albumin) and control 3′-UTR (HSD17B4) (
This result was replicated in Hela cells, in which replacement of the control 3′-UTR (albumin) with a candidate 3′-UTR (Table 3) was shown to increase eGFP encoding mRNA expression (
A combination of selected 5′-UTRs (Table 2) along with selected 3′-UTRs (Table 3) were assessed, to determine whether a combinatory approach could further increase eGFP mRNA expression. The following combinations were assayed: GOT1/CHIT1, GOT1/CS, PRKACB/CHIT1, PRKACB/CS, CHIT1/CHIT1 and CHIT1/CS.
The 5′-UTRs and 3′-UTRs were cloned with eGFP as the ORF. The cloning was either done using restriction sites (RE) or seamless. The 5′ end of 5′-UTR contained T7 promoter sequence.
The template for IVT were generated by PCR using Phusion PCR mix (NEB). The upstream primers contain T7 promoter sequence and the downstream primer contained reverse compliment of end of 3′-UTR of respective clone, along with T80 sequence. The resulting PCR product contain sequence encoding relevant sequence in following order: T7 promoter—5′-UTR-ORF-3′-UTR-A80. The PCR reaction was then treated with DPNI to digest template DNA and purified using PCR purification kit.
mRNA Synthesis Using in Vitro Transcription (IVT):
The template generated for IVT using PCR were used to prepare mRNA using NEB IVT kits that uses T7 RNA polymerase. The protocol was modified to include CleanCap® (AG). The T7 polymerase incorporates CleanCap® (AG) at the start of each mRNA, giving cap 1 structure at the 5′ end. The mRNA was either produced using unmodified nucleotide or using modified uridine (5′methoxy Uridine) in 25% ratio with unmodified uridine. After the reaction completes, the DNA-template was digested using RNase free DNase. mRNA transcripts contained a 5′-CAP-1-5′-UTR-ORF-3′-UTR-A80. mRNA was then purified using silica column and resuspended in water.
Lung A549 cells were grown in T175 flasks in A549 complete medium (Ham's F-12K supplemented with 10% FBS) at 37° C. 5% CO2. Cells were harvested using accutase for 5 min 37° C., then counted, washed and replated. 100,000 cells in 100 μl media were seeded in each well (96W plates) the day before. On the day of transfection, old media was aspirated and 140 μl of media was added to each well. 1 μl of 100 ng/μl of mRNA was diluted in 4 μl of OptiMEM, and 0.3 μl Lipofectamine 2000 was diluted in 4.7 μl OptiMEM. Then mRNA and Lipofectamine complex were mixed by vortexing and spun down before incubating for 5-10 min at RT. 10 μl of mRNA and Lipofectamine mix was added to each well.
Quantification of eGFP Expression:
eGFP fluorescence was detected using incucyte machine that captures images from the live cells. The fluorescence was measured from the images using Incucyte software in relative fluorescence units (RFU). The data reported in the Figures shows eGFP fluorescence 24 h post-transfection.
It was previously shown that the incorporation of selected 5′-UTRs and 3′-UTRs with control 3′-UTRs and 5′-UTRs, respectively, could increase the expression of an eGFP (see Examples 1 and 2).
The eGFP mRNA expression with combinations of these 5′-UTRs and 3′-UTRs were compared to expression with a control 5′-UTR (HSD17B4) and a 3′-UTR (albumin). In all instances, eGFP mRNA expression with a combination of a candidate 5′-UTR and a candidate 3′-UTR was increased, in comparison to control in A549 cells (
In order to study whether the combination of UTRs work as well for increasing expression levels independent of the gene of interest, the combinations were tested for scFv expression. This was again performed in both wild-type mRNA and modified mRNA.
The 5′-UTRs and 3′-UTRs were cloned with scFv-Fc encoding mRNA. The cloning was either done using restriction sites (RE) or seamless. The 5′ end of 5′-UTR contained T7 promoter sequence.
The template for IVT were generated by PCR using Phusion PCR mix (NEB). The upstream primers contain T7 promoter sequence and the downstream primer contained reverse compliment of end of 3′-UTR of respective clone, along with T80 sequence. The resulting PCR product contain sequence encoding relevant sequence in following order: T7 promoter—5′-UTR-ORF-3′-UTR-A80. The PCR reaction was then treated with DPNI to digest template DNA and purified using PCR purification kit.
mRNA Synthesis Using in Vitro Transcription (IVT):
The template generated for IVT using PCR were used to prepare mRNA using NEB IVT kits that uses T7 RNA polymerase. The protocol was modified to include CleanCap® (AG). The T7 polymerase incorporates CleanCap® (AG) at the start of each mRNA, giving cap 1 structure at the 5′ end. The mRNA was either produced using unmodified nucleotide or using modified uridine (5′methoxy uridine) in 25% ratio with unmodified uridine. After the reaction completes, the DNA-template was digested using RNase free DNase. mRNA transcripts contained a 5′-CAP-1-5′-UTR-ORF-3′-UTR-A80. mRNA was then purified using silica column and resuspended in water.
Lung A549 cells were grown in T175 flasks in A549 complete medium (Ham's F-12K supplemented with 10% FBS) at 37° C. 5% CO2. Cells were harvested using accutase for 5 min 37° C., then counted, washed and replated. 100,000 cells in 100 μl media were seeded in each well (96W plates) the day before. On the day of transfection, old media was aspirated and 140 μl of media was added to each well. 1 μl of 100 ng/μl of mRNA was diluted in 4 μl of OptiMEM, and 0.3 μl Lipofectamine 2000 was diluted in 4.7 μl OptiMEM. Then mRNA and Lipofectamine complex were mixed by vortexing and spun down before incubating for 5-10 min at RT. 10 μl of mRNA and Lipofectamine mix was added to each well. 100 μl supernatant was collected at specified timepoints.
scFv-Fc Quantification:
Cell supernatant (sup) was harvested from the cells transfected with scFv-Fc mRNA after 24 hours. The sups were frozen at −80 C until quantified. For quantification, cis-bio kit for Fc quantification was used. The principle for quantification is based on competitive immunoassay using HTRF technology. hFc-tagged proteins (or antibody) can displace the binding between IgG labelled with d2 and PAb anti-human Fc labelled with Cryptate. Specific signal (i.e. energy transfer) is inversely proportional to the concentration of human Fc in the sample or standard. A standard curve from known concentrations of scFv-Fc is produced and the signal from sups of scFv-Fc transfected cells was interpolated using this standard curve to quantify the amount of scFv-Fc present in the sup. The concentration of scFv-Fc was measured in ng/ml. The data shown in the Figures reports scFv-Fc levels 24 h post transfection.
Once again, the scFv mRNA expression with combinations of these 5′-UTRs and 3′-UTRs were compared to expression with a control 5′-UTR (HSD17B4) and a 3′-UTR (albumin). Interestingly, as with eGFP fluorescence levels in Example 3, the PRKACB/CHIT resulted in the highest expression levels when wild-type mRNA was used (
Therefore, out of all novel UTRs tested, whether alone or in combination, the CHIT/CS and PRKACB/CHIT combinations generated the greatest increase in expression levels, agnostic of the gene of interest or whether the mRNA comprised modified or wild-type U.
Next, one of the optimum UTR combinations (CHIT/CS) was tested head-to-head against mRNA comprising putative UTR pairs from Moderna and Pfizer/BioNTech (mRNA Comp A and mRNA Comp B) using the UTR sequences reported on 14 Apr. 2021 by Andrew Fire and colleagues at Stanford University via GitHub. This time, modified mRNA comprised 100%5′methoxy uridine (rather than 25%, as in Examples 1-4).
mRNA constructs encoding the EGFP reporter and employing the CHIT1 5′-UTR (SEQ ID NO: 19) paired with a CS 3′-UTR (SEQ ID NO:21) were designed (mRNA_AZ). In parallel, mRNA comparator A and mRNA comparator B constructs were designed to encode EGFP flanked by the putative UTR sequences from each of the COVID vaccines mentioned above. The cloning was performed by Gibson-based assembly methods. Each plasmid possessed a T7 promoter sequence upstream of each 5′ UTR and a poly A track of 80 basepairs long downstream of the 3′ UTR with a single BspQI site for subsequent linearization. All EGFP coding sequences were identical. The full 5′-UTR and 3′-UTR sequences comprising sequences derived from CHIT1 and CS UTRs are shown below (SEQ ID Nos: 19 and 21, respectively).
The template for IVT were generated following plasmid purification from bacterial cells in a manner similar to as outlined in Examples 1-4.
mRNA Synthesis Using in Vitro Transcription (IVT):
The template generated for IVT was used to prepare mRNA using NEB IVT kits employing T7 RNA polymerase. The protocol was modified to include CleanCap® (AG). The T7 polymerase incorporates CleanCap® (AG) at the start of each mRNA, giving a cap 1 structure at the 5′ end. The mRNA was either produced using unmodified nucleotide or using modified uridine (N1-methylpseudouridine) at 100%. Both mRNA comp A and mRNA comp B (the mRNAs comprising the putative UTRs derived from the GitHub database) contained 100% modified U. After the reaction completed, the DNA template was digested using RNase-free DNase. mRNA was then purified using silica column and resuspended in water.
Purified mRNA was transfected into either BHK-21 or HEK293 cells with Lipofectamine MessengerMAX transfection reagent (ThermoFisher) per manufacturer's protocol. EGFP fluorescence was detected using an IncuCyte instrument which captures images from live, RNA-transfected cells over the course of 96 hours. The fluorescence was measured from the images using IncuCyte software as relative fluorescence units (arbitrary units).
The mRNAs employing the 5′-UTR CHIT1 (SEQ ID NO: 19) and 3′-UTR CS (SEQ ID NO: 21) UTR set generated the highest levels of EGFP expression in both BHK-21 (
The overall purpose of this study was to determine the immunogenicity of a candidate SARS-CoV-2 mRNA vaccine comprising the mCHIT/CS UTR combination in mice and naïve non-human primates. The mRNA vaccine encoded a stabilised Spike (S) protein-ferritin subunit fusion protein that, when expressed, assembles into a nanoparticle for high concentration antigen display.
Groups of naïve BALB/c mice (n=6 per group) were administered LNP-formulated mRNA vaccines twice (21 days apart) as 50 μl injections intramuscularly in the thigh muscle. Fourteen days after the second vaccination, mice were bled and sera obtained to perform SARS-COV-2 pseudovirus-based neutralization assays. Both the magnitude and breadth of neutralizing antibody (nAb) responses among the different groups were evaluated using a panel of pseudoviruses bearing the following SARS-COV-2 Spike proteins of interest: Delta, Wuhan (D614G), BA.1, BA.2 and BA.4/5. Sigmoidal curves, taking averages of triplicates at each serum dilution, were generated, and 50% (ID50) neutralizing activity was calculated, considering uninfected cells to represent 100% neutralization and cells transduced with only virus to represent 0% neutralization.
Groups of naïve cynomolgus non-human primates (NHPs; n=6 per group) were administered LNP-formulated mRNA vaccines twice (28 days apart) as 1 ml injections intramuscularly. Each animal received a 10 μg dose per vaccination. Fourteen days after the second vaccination, NHPs were bled and sera obtained to perform SARS-COV-2 pseudovirus-based neutralization assays. Both the magnitude and breadth of neutralizing antibody (nAb) responses among the different groups were evaluated using a panel of pseudoviruses bearing the following SARS-CoV-2 Spike proteins of interest: Delta, Wuhan (D614G), BA.1, BA.2 and BA.4/5. Sigmoidal curves, taking averages of triplicates at each serum dilution, were generated, and 50% (ID50) neutralizing activity was calculated, considering uninfected cells to represent 100% neutralization and cells transduced with only virus to represent 0% neutralization.
In both the mouse and NHP studies, groups were administered either a Delta S protein ferritin construct (Delta FL VLP) or a Delta S protein only-encoding mRNA (Delta FL Spike). This enabled comparison of the immunogenicity and reactogenicity profiles of the mRNA-based nanoparticle vaccine approach compared to the Spike-only approach used in tozinameran and elasomeran. Both delta FL VLP and Delta FL Spike constructs comprised the CHIT1/CS UTR combination disclosed herein.
The results, shown in
Table 4 below demonstrates the mRNA VLP/FL spike fold change for the data in
1Fold change = mRNA VLP geometric mean titre (GMT)/mRNA FL spike GMT
2p-values calculated using two-sided t-test
This suggests that broadly neutralising responses are obtainable from a single vaccine construct when mRNA is used to launch a nanoparticle antigen. This may lead to better efficacy against multiple existing, and possibly future, variants of concern, without the requirement for boosters to be independently generated each time a novel dominant variant emerges.
GTGAGGAAGCCTAAATAAACCTAGCGTACGTAAAAAATGGAAAGAACCTAGCGTACG
AGUGAGGAAGCCUAAAUAAACCUAGCGUACGUAAAAAAUGGAAAGAACCUAGCGUAC
MPLLLLLPLLWAGALASQCVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPF
MPLLLLLPLLWAGALASQCVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPF
MPLLLLLPLLWAGALASQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSN
This application claims benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 63/480,749, filed Jan. 20, 2023, which is incorporated by reference herein.
| Number | Date | Country | |
|---|---|---|---|
| 63480749 | Jan 2023 | US |
