Compositions for use in treatment of acne
This invention relates to compositions (e.g. immunogenic compositions) which can be used to immunise against C. acnes . The compositions comprise C. acnes antigens and antigen combinations, used in the form of nucleic acids (e.g. mRNAs) encoding antigenic proteins or in the form of recombinant protein antigens.
1 . A nucleic acid comprising a nucleotide sequence encoding a modified Cutibacterium acnes ( C. acnes ) Christie-Atkins-Munch-Petersen factor 2 (CAMP2) polypeptide, wherein the modified C. acnes CAMP2 polypeptide comprises an amino acid sequence comprising a C. acnes CAMP2 polypeptide sequence and a transmembrane domain sequence, wherein the nucleic acid is a messenger RNA (mRNA).
2 . The nucleic acid of claim 1 , wherein:
(A) (a) the transmembrane domain sequence is positioned at the C terminus of the modified C. acnes CAMP2 polypeptide; and/or
(b) the transmembrane domain sequence comprises a viral transmembrane domain sequence, which is selected from the group consisting of: an influenza hemagglutinin (HA) transmembrane domain sequence, a SARS COV-2 spike transmembrane domain sequence, a VZV gB transmembrane domain sequence, a VZV gE transmembrane domain sequence, a VZV gI transmembrane domain sequence, a VZV gK transmembrane domain sequence, a measles F-protein transmembrane domain sequence, a rubella E1 protein transmembrane domain sequence, a rubella E2 protein transmembrane domain sequence, a mumps F-protein transmembrane domain sequence, an Ebola GP protein transmembrane domain sequence and a rabies transmembrane domain sequence; and/or
(B) the modified C. acnes CAMP2 polypeptide comprises a non-native secretion signal peptide sequence wherein:
(a) the secretion signal peptide sequence is positioned at the N terminus of the modified C. acnes CAMP2 polypeptide; and/or
(b) the secretion signal peptide sequence is a viral secretion signal peptide sequence, which is selected from the group consisting of: an influenza hemagglutinin (HA) secretion signal peptide sequence, a SARS COV-2 spike secretion signal peptide sequence, a VZV gB secretion signal peptide sequence, a VZV gE secretion signal peptide sequence, a VZV gI secretion signal peptide sequence, a VZV gK secretion signal peptide sequence, a measles F-protein secretion signal peptide sequence, a rubella E1 protein secretion signal peptide sequence, a rubella E2 protein secretion signal peptide sequence, a mumps F-protein secretion signal peptide sequence, an Ebola GP protein secretion signal peptide sequence, a smallpox 6 kDa IC protein secretion signal peptide sequence and a rabies G protein secretion signal peptide sequence.
3 . The nucleic acid of claim 1 , wherein the transmembrane domain comprises an amino acid sequence selected from the group consisting of sequences set forth by SEQ ID NO: 208-209 and 241-253.
4 . The nucleic acid of claim 1 , wherein
the mRNA comprises a 5′ cap, at least one 5′ untranslated region (5′ UTR), at least one 3′ untranslated region (3′ UTR), and/or at least one polyadenylation (poly(A)) sequence.
5 . The nucleic acid of claim 1 , wherein:
(a) the modified C. acnes CAMP2 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 207 and SEQ ID NO: 5-9, or a sequence having at least 60% identity thereto; and/or
(b) the nucleic acid comprises a nucleotide sequence selected from the group consisting of sequences set forth by SEQ ID NO: 90-94 and SEQ ID NO: 391-392, or a sequence having at least 50% identity thereto; and/or
(c) the nucleic acid is a mRNA comprising or consisting of the following structural elements:
(i) a 5′ cap with the following structure:
(ii) a 5′ untranslated region (5′ UTR) having the nucleic acid sequence according to SEQ ID NO: 265;
(iii) a protein coding region having the nucleic acid sequence selected from the group consisting of sequences set forth by SEQ ID NO: 90-91 and SEQ ID NO: 391-392;
(iv) a 3′ untranslated region (3′ UTR) having the nucleic acid sequence according to SEQ ID NO: 266; and
(v) a poly A tail.
6 . A composition comprising the nucleic acid of claim 1 .
7 . The composition of claim 6 , wherein the composition further comprises one or more of:
(i) a nucleic acid comprising a nucleotide sequence encoding a C. acnes dermatan sulfate-adhesin 1 (DsA1) polypeptide;
(ii) a nucleic acid comprising a nucleotide sequence encoding a C. acnes dermatan sulfate-adhesin 2 (DsA2) polypeptide;
(iii) a nucleic acid comprising a nucleotide sequence encoding a C. acnes putative iron-transport protein (PITP) polypeptide;
(iv) a nucleic acid comprising a nucleotide sequence encoding a chimeric C. acnes DsA1/DsA2 polypeptide; and
(v) a nucleic acid comprising a nucleotide sequence encoding a chimeric C. acnes DsA1/DsA2/PITP polypeptide.
8 . The composition of claim 6 , wherein the composition comprises:
(A) a first mRNA comprising or consisting of the following structural elements:
(i) a 5′ cap;
(ii) a 5′ UTR having the nucleic acid sequence according to SEQ ID NO: 265;
(iii) a protein coding region having the nucleic acid sequence according to SEQ ID NO: 91;
(iv) a 3′ UTR having the nucleic acid sequence according to SEQ ID NO: 266; and
(v) a poly A tail;
(B) a second mRNA comprising or consisting of the following structural elements:
(i) a 5′ cap;
(ii) a 5′ UTR having the nucleic acid sequence according to SEQ ID NO: 265;
(iii) a protein coding region having the nucleic acid sequence according to SEQ ID NO: 113;
(iv) a 3′ UTR having the nucleic acid sequence according to SEQ ID NO: 266; and
(v) a poly A tail; and
(C) a third mRNA comprising or consisting of the following structural elements:
(i) a 5′ cap;
(ii) a 5′ UTR having the nucleic acid sequence according to SEQ ID NO: 265;
(iii) a protein coding region having the nucleic acid sequence according to SEQ ID NO: 115;
(iv) a 3′ UTR having the nucleic acid sequence according to SEQ ID NO: 266; and
(v) a poly A tail;
wherein the 5′ cap has the following structure:
9 . The composition of claim 6 , wherein:
the composition comprises a total of about 45 μg, about 120 μg, or about 225 μg of the one or more nucleic acid(s).
10 . A composition comprising a nucleic acid comprising a nucleotide sequence encoding a C. acnes CAMP2 polypeptide and one or more of:
(i) a nucleic acid comprising a nucleotide sequence encoding a C. acnes DsA1 polypeptide;
(ii) a nucleic acid comprising a nucleotide sequence encoding a C. acnes DsA2 polypeptide;
(iii) a nucleic acid comprising a nucleotide sequence encoding a C. acnes PITP polypeptide;
(iv) a nucleic acid comprising a nucleotide sequence encoding a chimeric C. acnes DsA1/DsA2 polypeptide; and
(v) a nucleic acid comprising a nucleotide sequence encoding a chimeric C. acnes DsA1/DsA2/PITP polypeptide.
11 . The composition of claim 10 , wherein the composition comprises the nucleic acid according to (iii) and/or the nucleic acid according to (iv).
12 . The composition of claim 10 , wherein
any two or more nucleic acids are located on the same nucleic acid molecule or on different nucleic acid molecules.
13 . The composition of claim 10 , wherein:
(a) the C. acnes CAMP2 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 203, SEQ ID NO: 43-58, SEQ ID NO: 1-4, SEQ ID NO: 10-16 and SEQ ID NO: 339-363 or a sequence having at least 60% identity thereto;
(b) the C. acnes DsA1 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 204, SEQ ID NO: 17-19 and SEQ ID NO: 59-61, or a sequence having at least 75% identity thereto;
(c) the C. acnes DsA2 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 205, SEQ ID NO: 20-27 and SEQ ID NO: 62-69 or a sequence having at least 75% identity thereto;
(d) the C. acnes PITP polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 206, SEQ ID NO: 31-37, and SEQ ID NO: 73-79 or a sequence having at least 75% identity thereto;
(e) the chimeric C. acnes DsA1/DsA2 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 28-30, SEQ ID NO: 39, SEQ ID NO: 70-72 and SEQ ID NO: 81, or a sequence having at least 90% identity thereto; and/or
(f) the chimeric C. acnes DsA1/DsA2/PITP polypeptide comprises (i) a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 28-30, SEQ ID NO:
39, SEQ ID NO: 70-72 and SEQ ID NO: 81, or a sequence having at least 90% identity thereto; and (ii) a PITP polypeptide sequence.
14 . A nucleic acid comprising a nucleotide sequence encoding a chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide, wherein the chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide comprises:
(a) a chimeric C. acnes DsA1/DsA2 polypeptide;
(b) an immunogenic fragment of a C. acnes PITP polypeptide; and
(c) a C. acnes CAMP2 polypeptide or an immunogenic fragment thereof.
15 . The nucleic acid comprising a nucleotide sequence encoding a chimeric C acnes DsA1/DsA2/PITP/CAMP2 polypeptide of claim 14 , wherein:
i, the chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide comprises a first conserved sub-domain (CSD1) of a C. acnes DsA1 polypeptide, a second conserved sub-domain (CSD2) of a C. acnes DsA2 polypeptide and a third conserved sub-domain (CSD3) of a C. acnes DsA1 polypeptide;
ii, the immunogenic fragment of a C. acnes PITP polypeptide in (b) comprising an extended neocarzinostatin family domain (ENFD) of a C. acnes PITP polypeptide comprises the sequence corresponding to amino acid residues 1-133 or residues 1-146 of SEQ ID NO: 73 or a sequence having at least 90% identity thereto; and/or
iii. (c) is (1) a C. acnes CAMP2 polypeptide; or (2) an immunogenic fragment of a C. acnes CAMP2 polypeptide comprising a N-terminal domain of a C. acnes CAMP2 polypeptide.
16 . The nucleic acid of claim 14 , wherein:
(i) the chimeric C acnes DsA1/DsA2/PITP/CAMP2 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 374-375;
(ii) the chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide comprises a sequence according to SEQ ID NO: 373 and a transmembrane domain sequence,
(iii) the nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 377-382 and 384-389; and/or
(iv) the nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide comprises a sequence according to SEQ ID NO: 384 and a sequence according to SEQ ID NO: 395; or a sequence according to SEQ ID NO: 385 and a sequence according to SEQ ID NO: 396.
17 . A chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide encoded by the nucleic acid of claim 14 .
18 . A composition, optionally an immunogenic composition, comprising the nucleic acid as defined in claim 14 .
19 . A composition, optionally an immunogenic composition, comprising the chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide as defined in claim 17 .
20 . An immunogenic composition comprising a nucleic acid comprising a nucleotide sequence encoding a C. acnes CAMP2 polypeptide, wherein the nucleic acid is a mRNA.
21 . A method of treating or preventing C. acnes infection in a subject, the method comprising administering the nucleic acid of claim 1 to the subject.
22 . A method of treating or preventing at least one symptom of a C. acnes infection in a subject, the method comprising administering the composition of claim 10 to the subject.
23 . A method of treating or preventing at least one symptom of a C. acnes infection in a subject, the method comprising administering the nucleic acid of claim 14 to the subject.
24 . A method of treating or preventing at least one symptom of a C. acnes infection in a subject, the method comprising administering the polypeptide of claim 17 to the subject.
25 . A method of treating or preventing at least one symptom of a C. acnes infection in a subject, the method comprising administering the immunogenic composition of claim 20 to the subject.
26 . The nucleic acid of claim 1 , wherein the mRNA is unmodified.
27 . The nucleic acid of claim 1 , wherein the mRNA comprises at least one chemical modification.
28 . The nucleic acid of claim 1 , wherein the mRNA is a self-replicating mRNA.
29 . The nucleic acid of claim 1 , wherein the mRNA is a non-replicating mRNA.
30 . The nucleic acid of claim 5 , wherein the polyA tail comprises at least 75 adenosine nucleotides or at least 100 adenosine nucleotides.
31 . The composition of claim 6 , wherein the composition is in a frozen liquid form or in a lyophilized form.
32 . The composition of claim 7 , wherein:
the modified C. acnes CAMP2 polypeptide comprises a sequence having at least 60% identity to SEQ ID NO: 207;
the chimeric C. acnes DsA1/DsA2 polypeptide comprises a sequence having at least 90% identity to SEQ ID NO: 70; and
the C. acnes PITP polypeptide comprises a sequence having at least 75% identity to SEQ ID NO: 73.
33 . The composition of claim 6 , wherein the composition further comprises a nucleic acid comprising a nucleotide sequence encoding a chimeric C. acnes DsA1/DsA2 polypeptide and a nucleic acid comprising a nucleotide sequence encoding a C. acnes PITP polypeptide, wherein:
the modified C. acnes CAMP2 polypeptide comprises or consists of a sequence according to SEQ ID NO: 207;
the chimeric C. acnes DsA1/DsA2 polypeptide comprises or consists of a sequence according to SEQ ID NO: 70; and
the C. acnes PITP polypeptide comprises or consists of a sequence according to SEQ ID NO: 73.
34 . The composition of claim 7 , wherein:
the nucleotide sequence encoding the modified C. acnes CAMP2 polypeptide comprises a sequence having at least 50% identity to SEQ ID NO: 91;
the nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2 polypeptide comprises a sequence having at least 75% identity to SEQ ID NO: 113; and
the nucleotide sequence encoding the C. acnes PITP polypeptide comprises a sequence having at least 50% identity to SEQ ID NO: 115.
35 . The composition of claim 6 , wherein the composition further comprises a nucleic acid comprising a nucleotide sequence encoding a chimeric C. acnes DsA1/DsA2 polypeptide and a nucleic acid comprising a nucleotide sequence encoding a C. acnes PITP polypeptide, wherein:
the nucleotide sequence encoding the modified C. acnes CAMP2 polypeptide comprises or consists of a sequence according to SEQ ID NO: 91;
the nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2 polypeptide comprises or consists of a sequence according to SEQ ID NO: 113; and
the nucleotide sequence encoding the C. acnes PITP polypeptide comprises or consists of a sequence according to SEQ ID NO: 115.
36 . The composition of claim 6 , wherein the composition further comprises a lipid nanoparticle (LNP).
37 . The composition of claim 36 , wherein any one or more nucleic acids are encapsulated in the LNP.
38 . The composition of claim 7 , wherein any two or more nucleic acids are co-encapsulated in a single LNP.
39 . The composition of claim 33 , wherein the nucleic acid comprising a nucleotide sequence encoding the modified C. acnes CAMP2 polypeptide, the nucleic acid comprising a nucleotide sequence encoding the C. acnes PITP polypeptide, and the nucleic acid comprising a nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2 polypeptide are encapsulated in an LNP.
40 . The composition of claim 33 , wherein the nucleic acid comprising a nucleotide sequence encoding the modified C. acnes CAMP2 polypeptide, the nucleic acid comprising a nucleotide sequence encoding the C. acnes PITP polypeptide, and the nucleic acid comprising a nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2 polypeptide are co-encapsulated in a single LNP.
41 . The composition of claim 33 , wherein the nucleic acid comprising a nucleotide sequence encoding the modified C. acnes CAMP2 polypeptide, the nucleic acid comprising a nucleotide sequence encoding the C. acnes PITP polypeptide, and the nucleic acid comprising a nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2 polypeptide are present in a weight ratio of 1:1:1.
42 . The composition of claim 35 , wherein the nucleic acid comprising a nucleotide sequence encoding the modified C. acnes CAMP2 polypeptide, the nucleic acid comprising a nucleotide sequence encoding the C. acnes PITP polypeptide, and the nucleic acid comprising a nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2 polypeptide are co-encapsulated in a single LNP.
43 . The composition of claim 35 , wherein the nucleic acid comprising a nucleotide sequence encoding the modified C. acnes CAMP2 polypeptide, the nucleic acid comprising a nucleotide sequence encoding the C. acnes PITP polypeptide, and the nucleic acid comprising a nucleotide sequence encoding the chimeric C. acnes DsA1/DsA2 polypeptide are present in a weight ratio of 1:1:1.
44 . The composition of claim 7 , wherein any two or more nucleic acids are encapsulated in separate LNPs.
45 . The composition of claim 36 , wherein: the LNP comprises at least one cationic lipid and wherein the cationic lipid is selected from the group consisting of OF-02, cKK-E10, IM-001, IS-001 and GL-HEPES-E3-E12-DS-4-E10; and/or
the LNP comprises a polyethylene glycol (PEG) conjugated (PEGylated) lipid, a cholesterol-based lipid, and a helper lipid.
46 . The composition of claim 45 , wherein the LNP comprises GL-HEPES-E3-E12-DS-4-E10, DMG-PEG2000, cholesterol and DOPE.
47 . The composition of claim 46 , wherein the LNP comprises GL-HEPES-E3-E12-DS-4-E10 at a molar ratio of 40%, DMG-PEG2000 at a molar ratio of 1.5%, cholesterol at a molar ratio of 28.5%, and DOPE at a molar ratio of 30%.
48 . The composition of claim 10 , wherein the composition is an immunogenic composition.
49 . The composition of claim 10 , wherein the composition is in a frozen liquid form or in a lyophilized form.
50 . The composition of claim 10 , wherein the C. acnes DsA1 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 204, SEQ ID NO: 17-19 and SEQ ID NO: 59-61, or a sequence having at least 75% identity thereto.
51 . The composition of claim 10 , wherein the C. acnes DsA2 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 205, SEQ ID NO: 20-27 and SEQ ID NO: 62-69 or a sequence having at least 75% identity thereto.
52 . The composition of claim 10 , wherein the C. acnes PITP polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 206, SEQ ID NO: 31-37, and SEQ ID NO: 73-79 or a sequence having at least 75% identity thereto.
53 . The composition of claim 10 , wherein the chimeric C. acnes DsA1/DsA2 polypeptide comprises a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 28-30, SEQ ID NO: 39, SEQ ID NO: 70-72 and SEQ ID NO: 81, or a sequence having at least 90% identity thereto.
54 . The composition of claim 10 , wherein the chimeric C. acnes DsA1/DsA2/PITP polypeptide comprises (i) a sequence selected from the group consisting of sequences set forth by SEQ ID NO: 28-30, SEQ ID NO: 39, or SEQ ID NO: 70-72 and SEQ ID NO: 81, or a sequence having at least 90% identity thereto; and (ii) a PITP polypeptide sequence.
55 . The nucleic acid of claim 14 , wherein the immunogenic fragment of a C. acnes PITP polypeptide of (b) comprises an extended neocarzinostatin family domain (ENFD) of a C. acnes PITP polypeptide.
56 . The nucleic acid of claim 15 , wherein the chimeric C. acnes DsA1/DsA2 polypeptide of (a) comprises a sequence according to SEQ ID NO: 70, or a sequence having at least 90% identity thereto.
57 . The nucleic acid of claim 15 , wherein the C. acnes CAMP2 polypeptide of (c) (1) comprises SEQ ID NO: 203 or a sequence having at least 90% identity thereto.
58 . The nucleic acid of claim 15 , wherein the chimeric C. acnes DsA1/DsA2/PITP/CAMP2 polypeptide comprises a transmembrane domain sequence.
59 . The nucleic acid of claim 58 , wherein the transmembrane domain sequence comprises an amino acid sequence according to SEQ ID NO: 84.
60 . The composition of claim 11 , wherein the C. acnes CAMP2 polypeptide comprises a sequence according to SEQ ID NO: 203 or a sequence having at least 60% identity thereto; the chimeric C. acnes DsA1/DsA2 polypeptide comprises a sequence according to SEQ ID NO: 70 or a sequence having at least 90% identity thereto; and the C. acnes PITP polypeptide comprises a sequence according to SEQ ID NO: 73 or a sequence having at least 75% identity thereto.
61 . A composition comprising:
a messenger RNA (mRNA) comprising a nucleotide sequence encoding a modified C. acnes CAMP2 polypeptide comprising or consisting of a sequence according to SEQ ID NO: 207;
a mRNA comprising a nucleotide sequence encoding a chimeric C. acnes DsA1/DsA2 polypeptide comprising or consisting of a sequence according to SEQ ID NO: 70; and
a mRNA comprising a nucleotide sequence encoding a C. acnes PITP polypeptide comprising or consisting of a sequence according to SEQ ID NO: 73,
wherein the mRNAs are encapsulated in an LNP.
62 . The composition of claim 61 , wherein the mRNAs are co-encapsulated in the same LNP.
63 . The composition of claim 61 , wherein the mRNAs are present in a weight ratio of 1:1:1.
64 . The composition of claim 61 , wherein the mRNAs are present in a weight ratio of 1:1:1 and are co-encapsulated in the same LNP.
65 . A method of generating an immune response against a C. acnes infection in a subject, the method comprising administering the composition of claim 10 to the subject.
66 . A method of generating an immune response against a C. acnes infection in a subject, the method comprising administering the nucleic acid of claim 14 to the subject.
67 . A method of generating an immune response against a C. acnes infection in a subject, the method comprising administering the polypeptide of claim 17 to the subject.
68 . A method of generating an immune response against a C. acnes infection in a subject, the method comprising administering the immunogenic composition of claim 20 to the subject.