Chimpanzee adenoviral delivery of neoantigens

Abstract

Disclosed herein are chimpanzee adenoviral vectors that include neoantigen-encoding nucleic acid sequences derived from a tumor of a subject. Also disclosed are nucleotides, cells, and methods associated with the vectors including their use as vaccines.

Description

(19) *EP004699662A3* (11) EP 4 699 662 A3 (12) EUROPEAN PATENT APPLICATION (88) Date of publication A3: 29.07.2026 Bulletin 2026 / 31 (43) Date of publication A2: 25.02.2026 Bulletin 2026 / 09 (21) Application number: 25211455.8 (22) Date of filing: 22.11.2017 (51) International Patent Classification (IPC): A61K 31 / 7088 (2006.01) A61K 31 / 404 (2006.01) A61K 39 / 00 (2006.01) A61K 39 / 395 (2006.01) A61K 45 / 06 (2006.01) C12N 7 / 00 (2006.01) (52) Cooperative Patent Classification (CPC): (C-Sets available) A61K 45 / 06; A61K 31 / 7088; A61K 31 / 713; A61K 39 / 0011; A61K 39 / 001188; A61K 39 / 001191; A61P 35 / 00; A61P 35 / 02; A61P 37 / 04; C12N 7 / 00; A61K 2039 / 55544; A61K 2039 / 57; A61K 2039 / 585; C12N 2710 / 10043; C12N 2710 / 10071; (Cont.) (84) Designated Contracting States: AL AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO PL PT RO RS SE SI SK SM TR Designated Validation States: MA (30) Priority: 23.11.2016 US 201662425996 P 16.12.2016 US 201662435266 P 08.05.2017 US 201762503196 P 21.06.2017 US 201762523212 P (62) Document number(s) of the earlier application(s) in accordance with Art. 76 EPC: 17873940.5 / 3 544 607 (71) Applicant: Seattle Project Corp. Dover, DE 19901 (US) (72) Inventors: • BLAIR, Wade Emeryville, 94608 (US) • BULIK-SULLIVAN, Brendan Emeryville, 94608 (US) • BUSBY, Jennifer Emeryville, 94608 (US) • DERTI, Adnan Emeryville, 94608 (US) • GITLIN, Leonid Emeryville, 94608 (US) • GROTENBREG, Gijsbert Emeryville, 94608 (US) • JOOSS, Karin Emeryville, 94608 (US) • SCALLAN, Ciaran Daniel Emeryville, 94608 (US) • YELENSKY, Roman Emeryville, 94608 (US) (74) Representative: Elkington and Fife LLP Prospect House 8 Pembroke Road Sevenoaks, Kent TN13 1XR (GB) (54) CHIMPANZEE ADENOVIRAL DELIVERY OF NEOANTIGENS (57) Disclosed herein are chimpanzee adenoviral vectors that include neoantigen-encoding nucleic acid sequences derived from a tumor of a subject. Also dis- closed are nucleotides, cells, and methods associated with the vectors including their use as vaccines. EP 4 69 9 66 2 A 3 Processed by Luminess, 75001 PARIS (FR) (Cont. next page) (52) Cooperative Patent Classification (CPC): (Cont.) C12N 2710 / 14034; C12N 2710 / 16134; C12N 2710 / 16234 C-Sets A61K 31 / 7088, A61K 2300 / 00; A61K 31 / 713, A61K 2300 / 00 2 EP 4 699 662 A3 3 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 4 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 5 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 6 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 7 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 8 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 9 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 10 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 11 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 12 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 13 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 14 EP 4 699 662 A3 5 10 15 20 25 30 35 40 45 50 55 摘要 本文公开包括源于个体肿瘤的新抗原编码核酸序列的黑猩猩腺病毒载体。 还公开与所述载体相关的核苷酸、细胞及方法,包括所述载体作为疫苗的用 途。

Claims

1. An adenovirus vector comprising a neoantigen cassette, wherein the neoantigen cassette comprises one or more major histocompatibility complex (MHC) neoepitope-encoding nucleic acid sequences encoding an MHC neoepitope, wherein the MHC neoepitope is characterized by each of the following characteristics: (i) the MHC neoepitope is expressed in a tumor cell of a subject according to exome, transcriptome, or whole genome nucleotide sequencing data obtained from the subject; (ii) the MHC neoepitope comprises at least one alteration that makes the MHC neoepitope distinct from a corresponding wild-type peptide expressed in a normal cell of the subject according to the exome, transcriptome, or whole genome nucleotide sequencing data obtained from the subject; and (iii) the MHC neoepitope is predicted to be presented by an MHC allele on the surface of the tumor cell of the subject according to a deep-learning presentation model trained on peptide-MHC binding data.

2. The adenovirus vector of claim 1, wherein the deep-learning presentation model comprises a set of training peptide sequences identified as present in a plurality of samples and one or more MHC alleles associated with each training peptide sequence, wherein the training peptide sequences are identified through mass spectrometry on isolated peptides eluted from MHC alleles derived from the plurality of samples, optionally wherein the deep-learning presentation model comprises: a plurality of parameters identified at least based on a training data set comprising: labels obtained by mass spectrometry measuring the presence of peptides bound to at least one MHC allele identified as present in at least one of a plurality of samples; training peptide sequences encoded as numerical vectors including information regarding a plurality of amino acids that make up the peptide sequence and a set of positions of the amino acids in the peptide sequence; and at least one HLA allele associated with the training peptide sequences; and a function representing a relation between the numerical vector received as input and the presentation likelihood generated as output based on the numerical vector and the parameters.

3. The adenovirus vector of claim 1, wherein the one or more MHC neoepitope-encoding nucleic acid sequence comprises at least two MHC neoepitope-encoding nucleic acid sequences each encoding a respective MHC neoepitope, wherein each MHC neoepitope is characterized by each of the following characteristics: (i) each MHC neoepitope is expressed in a respective tumor cell of the subject according to exome, transcriptome, or whole genome nucleotide sequencing data obtained from the subject; (ii) each MHC neoepitope comprises at least one alteration that makes the MHC neoepitope distinct from a corresponding wild-type peptide expressed in a normal cell of the subject according to the exome, transcriptome, or whole genome nucleotide sequencing data obtained from the subject; and (iii) each MHC neoepitope is predicted to be presented by a respective MHC allele on the surface of the tumor cell of the subject according to a deep-learning presentation model trained on peptide-MHC binding data.

4. The adenovirus vector of claim 1, wherein the one or more MHC neoepitope-encoding nucleic acid sequence encodes between 10-20 MHC neoepitope-encoding nucleic acid sequences each encoding a respective MHC neoepitope, wherein each MHC neoepitope is characterized by each of the following characteristics: (i) each MHC neoepitope is expressed in a respective tumor cell of the subject according to exome, transcriptome, or whole genome nucleotide sequencing data obtained from the subject; (ii) each MHC neoepitope comprises at least one alteration that makes the MHC neoepitope distinct from a corresponding wild-type peptide expressed in a normal cell of the subject according to the exome, transcriptome, or whole genome nucleotide sequencing data obtained from the subject; and (iii) each MHC neoepitope is predicted to be presented by a respective MHC allele on the surface of the tumor cell of the subject according to a deep-learning presentation model trained on peptide-MHC binding data.

5. The adenovirus vector of claim 1, wherein each MHC neoepitope-encoding nucleic acid sequence comprises: (a) a 5' linker sequence that encodes a native N-terminal amino acid sequence of the respective MHC neoepitope, wherein the 5' linker sequence encodes a peptide that is between 2-20 amino acids in length, and wherein the 5' linker sequence is directly 5' of the polynucleotide sequence encoding the respective MHC neoepitope; and (b) a 3' linker sequence that encodes a native C-terminal amino acid sequence of the respective MHC neoepitope, wherein the 3' linker sequence encodes a peptide that is between 2-20 amino acids in length, and wherein the 3' linker sequence is directly 3' of the polynucleotide sequence encoding the respective MHC neoepitope, and wherein each MHC neoepitope-encoding nucleic acid sequence is linked directly to one another such that adjacent native N-terminal and C-terminal amino acid sequences are directly linked.

6. The adenovirus vector of claim 1, wherein an ordered sequence of each element of the neoantigen cassette is described in a formula, from 5' to 3', comprising:         Pa-(L5b-Nc-L3d)X-(G5e-Uf)Y-G3g-Ah wherein P comprises a promoter sequence operably linked to the MHC neoepitope-encoding nucleic acid sequence, where a = 1, N comprises the MHC neoepitope-encoding nucleic acid sequence, where c = 1, L5 comprises a 5' linker sequence, where b = 0 or 1, L3 comprises a 3' linker sequence, where d = 0 or 1, G5 comprises a GPGPG-encoding linker sequences, where e = 0 or 1, G3 comprises a GPGPG-encoding linker sequences, where g = 0 or 1, U comprises at least one MHC class II antigen-encoding nucleic acid sequence, where f = 0 or 1, A comprises a polyadenylation sequence, where h = 0 or 1, X = 1 to 400, and Y = 0-2, where for each Y the corresponding Uf is a distinct MHC class II antigen-encoding nucleic acid sequence.

7. The adenovirus vector of claim 6, wherein: b = 1, d = 1, e = 1, g = 1, h = 1, X = 10-20, Y = 2, P is a CMV promoter sequence, each N encodes an MHC class I epitope 7-15 amino acids in length, L5 is a 5' linker sequence that encodes a native N-terminal amino acid sequence of the respective MHC neoepitope N, wherein the 5' linker sequence encodes a peptide that is between 2-20 amino acids in length, L3 is 3' linker sequence that encodes a native C-terminal amino acid sequence of the respective MHC neoepitope N, wherein the 3' linker sequence encodes a peptide that is between 2-20 amino acids in length, the adenovirus vector comprises a chimpanzee adenovirus vector comprising an E1 deletion and an E3 deletion, and the neoantigen cassette is inserted within the E1 deletion or the E3 deletion.

8. The adenovirus vector of claim 1, wherein the MHC neoepitope is predicted to have an increased likelihood of presentation by the MHC allele relative to the corresponding wild-type peptide.

9. The adenovirus vector of claim 1, wherein the MHC neoepitope is a MHC class I neoepitope between 8 and 15 amino acids in length.

10. The adenovirus vector of claim 6, wherein: f = 1 and the at least one MHC class II antigen-encoding nucleic acid sequence comprises at least one universal MHC class II antigen-encoding nucleic acid sequence, optionally wherein the at least one universal sequence comprises at least one sequence from at least one of Tetanus toxoid and PADRE; or wherein P comprises an inducible promoter.

11. The adenovirus vector of claim 1, wherein: the adenovirus vector comprises a chimpanzee adenovirus vector, optionally wherein the chimpanzee adenovirus vector comprises a ChAdV68 vector; or the neoantigen cassette is inserted in the vector at a deleted adenovirus region that allows incorporation of the neoantigen cassette, optionally wherein the deleted adenovirus region is an E1 region or a E3 region; or the adenovirus vector comprises the sequence of SEQ ID NO: 1 except for a deletion between base pair number 577 and 3403 of the sequence shown in SEQ ID NO:1 and / or a deletion between base pair 27,125 and 31,825 of the sequence shown in SEQ ID NO:1.

12. The adenovirus vector of claim 3, wherein each MHC neoepitope-encoding nucleic acid sequence is linked directly to one another in the neoantigen cassette, and wherein the neoantigen cassette comprises junctional epitope sequences formed by adjacent MHC neoepitopes-encoding nucleic acid sequences in the neoantigen cassette, wherein at least one or each junctional epitope sequence has an affinity of greater than 500 nM for MHC, optionally wherein each junctional epitope sequence is non-self.

13. A pharmaceutical composition comprising the adenovirus vector of claim 1 and a pharmaceutically acceptable carrier, optionally wherein the composition further comprises an adjuvant.

14. A method of manufacturing the adenovirus vector of claim 1, the method comprising: one or both of: (i) transfecting a plasmid sequence comprising the adenovirus vector into a host cell, and (ii) infecting a host cell with an adenovirus comprising the adenovirus vector; and isolating the adenovirus vector from the one or more host cells, optionally wherein isolating comprises: lysing the host cell to obtain a cell lysate comprising the vector, and optionally purifying the adenovirus vector from the cell lysate.

15. An adenovirus vector comprising a neoantigen cassette according to claim 1, for use in a method of inducing an immune response in a subject in need thereof, optionally a tumor-specific immune response in a subject with a tumor.

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