WO2021209775A1 - Antigen pool - Google Patents

Antigen pool Download PDF

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Publication number
WO2021209775A1
WO2021209775A1 PCT/GB2021/050940 GB2021050940W WO2021209775A1 WO 2021209775 A1 WO2021209775 A1 WO 2021209775A1 GB 2021050940 W GB2021050940 W GB 2021050940W WO 2021209775 A1 WO2021209775 A1 WO 2021209775A1
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WO
WIPO (PCT)
Prior art keywords
antigen
seq
cells
clt
cell
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/GB2021/050940
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English (en)
French (fr)
Inventor
George KASSIOTIS
George Young
Jan ATTIG
Ambrosius SNIJDERS
David Perkins
Fabio MARINO
Ray Jupp
Magdalena VON ESSEN
Peter Mason
Nicola TERNETTE
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Francis Crick Institute Ltd
Enara Bio Ltd
Original Assignee
Francis Crick Institute Ltd
Enara Bio Ltd
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Francis Crick Institute Ltd, Enara Bio Ltd filed Critical Francis Crick Institute Ltd
Priority to EP21721983.1A priority Critical patent/EP4136096A1/en
Priority to JP2022562752A priority patent/JP2023522193A/ja
Priority to CN202180029092.4A priority patent/CN115667288A/zh
Priority to CA3176754A priority patent/CA3176754A1/en
Publication of WO2021209775A1 publication Critical patent/WO2021209775A1/en
Priority to US18/046,670 priority patent/US20230302109A1/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/00119—Melanoma antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/10—Cellular immunotherapy characterised by the cell type used
    • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/515—Animal cells
    • A61K2039/5154—Antigen presenting cells [APCs], e.g. dendritic cells or macrophages
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/53—DNA (RNA) vaccination
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/555—Medicinal preparations containing antigens or antibodies characterised by a specific combination antigen/adjuvant
    • A61K2039/55511—Organic adjuvants
    • A61K2039/55555—Liposomes; Vesicles, e.g. nanoparticles; Spheres, e.g. nanospheres; Polymers
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/80—Vaccine for a specifically defined cancer
    • A61K2039/876—Skin, melanoma
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterised by the cancer treated
    • A61K2239/57—Skin; melanoma

Definitions

  • antigen pools of the invention are expected to be useful in a range of embodiments in cancer immunotherapy and prophylaxis, particularly immunotherapy and prophylaxis of melanoma, as discussed in more detail below.
  • Description of the Figures Each of Figures 1-38 shows an extracted MS/MS spectrum (with assigned fragment ions) of a peptide obtained from a tumor sample of a patient and either a bottom panel showing a rendering of the spectrum indicating the positions of the linear peptide sequences that have been mapped to the fragment ions or similar data shown in tabular form.
  • Figure 1 Spectra for the peptide of SEQ ID NO.9 obtained from a tumor sample of patient Mel-3.
  • insertions do not occur in the region of an epitope, and do not therefore have a significant impact on the immunogenic properties of the antigen.
  • One example of insertions includes a short stretch of histidine residues (e.g., 2-6 residues) to aid expression and/or purification of the antigen in question.
  • Polypeptide variants include those wherein amino acids have been deleted compared to the reference sequence, for example, such deletions may occur at 1-10 locations (such as 1-5 locations, suitably 1 or 2 locations, in particular 1 location) and may, for example, involve the deletion of 50 or fewer amino acids at each location (such as 20 or fewer, in particular 10 or fewer, especially 5 or fewer).
  • fragments of the full-length polypeptides of SEQ ID NOs.1-8 which contain at least one T-cell epitope may be immunogenic and may contribute to immunoprotection. It will be understood that in a diverse outbred population, such as humans, different HLA types mean that specific epitopes may not be recognised by all members of the population. Consequently, to maximise the level of recognition and scale of immune response to a polypeptide, it is generally desirable that an immunogenic fragment contains a plurality of the epitopes from the full-length sequence (suitably all epitopes within a CLT antigen).
  • PILEUP a reference sequence is compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted end gaps.
  • PILEUP can be obtained from the GCG sequence analysis software package, e.g., version 7.0 (Devereaux et al., 1984, Nuc. Acids Res.12:387-395).
  • Another example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., 1977, Nuc. Acids Res.25:3389-3402 and Altschul et al., 1990, J. Mol. Biol. 215:403-410, respectively.
  • the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, 1993, Proc. Nat’l. Acad. Sci. USA 90:5873-5787).
  • the fusion protein of the invention comprises eight antigenic polypeptides (a) to (h) wherein the antigenic polypeptides (a) to (h) have the amino acid sequences: (a) SEQ ID NO: 1; (b) SEQ ID NO: 2 minus the N-terminal methionine residue; (c) SEQ ID NO: 3; (d) SEQ ID NO: 4; (e) SEQ ID NO: 5 minus the N-terminal methionine residue; (f) SEQ ID NO: 6 minus the N-terminal methionine residue; (g) SEQ ID NO: 7; and (h) SEQ ID NO: 8.
  • immunogenic pharmaceutical compositions of the invention which comprise an antigen pool, comprising two or more (e.g. two) different antigens wherein each antigen is present in the form of a nucleic acid encoding said polypeptide and wherein the different antigens are present in the antigen pool as a nucleic acid encoding a fusion protein, in combination with a pharmaceutically acceptable carrier.
  • the immunogenic pharmaceutical compositions of the invention may comprise an antigen pool comprising two or more (e.g.
  • the figures show fragment spectra for indicated peptide sequences as detected in individual patient SKCM tumors by nUPLC-MS 2 (images extracted by PEAKSTM software from the inventors’ internal dataset or from Bassani-Sternberg et al. dataset stored in PRIDE). All fragments that have been detected are indicated in the peptide sequence above the spectrum and the most abundant fragment ions are assigned in each spectrum.
  • Figures 1-2, 4-6, 8-9, 11-12, 14-37 the lower panel of the figures illustrates the peptide sequences assigned to the MS/MS spectrum, whereas similar data are shown in tabular form on the right side of Figures 3, 7, 10, 13 and 19.
  • the inventors interrogated the spectra of the HLA-Class I dataset from these normal tissue samples, searching for all possible peptide sequences derived from the polypeptide sequences of CLT antigens 1, 2, 3, 4, 5, 6, 7 and 8, alongside all the polypeptides found in the human proteome (UniProt) using the PeaksTM software (V8.5 and X). No peptides derived from CLT antigen 1, 2, 3, 4, 5, 6, 7 or 8 were detected in the set of normal tissue samples (Table 3) providing additional evidence that the CLTs have cancer-specific expression.
  • Step 4 TCRseq (sequencing of the TCR-V ⁇ CDR3 sequences) was performed on all wells, and TCR-V ⁇ CDR3 sequences that were amplified in the presence of individual CLT Antigen-derived peptides (but not amplified in the presence of control peptides or in the absence of peptide stimulation) were identified. The presence of amplified TCR- V ⁇ CDR3 sequences in individual wells of the assay thus identifies CLT Antigen- derived peptides that elicited an immune response in the melanoma patient.
  • Figure 62 shows significant CD8 T-cell responses from a normal blood donor to an HLA-A*02:01-restricted peptide from CLT Antigen 8 (CLT008 in the Figure).
  • Figure 63 shows a lack of response to HLA-B*0702 restricted peptides from CLT Antigens 1 and 4 (CLT001 and CLT004 in the figure) in memory CD45RO-positive CD8 T-cells (panels A and C).
  • Na ⁇ ve CD45RO-negative CD8 T-cells from the same donor respond significantly to peptides from both CLT001 and CLT004 ( Figure 63, panels B and D).
  • ISH in situ In situ hybridisation
  • DCs can be generated by methods such as positive isolation via CD14 capture (for example, anti-CD14 antibodies conjugated to magnetic beads, where CD14-positive cells are labelled with the beads and captured on a magnetic column) or isolation via their adhesive properties, for example, adherence to tissue culture plastics by incubation of peripheral blood mononuclear cells (PBMCs) with cell culture dishes for a period of 4-48 hr to allow adherence of monocytes.
  • PBMCs peripheral blood mononuclear cells
  • DCs can be generated from the CD14-positive or adherent immune cell fractions by well- described methods utilising cytokines such as, but not limited to: GM-CSF, IL-4, TNF ⁇ , IL-1 ⁇ , IL-6, Prostaglandin E2.
  • autologous CD3+ isolated T cells would be co-cultured with the APCs at a ratio of excess T cell to APC, for example 10 T cells per 1 APC (10:1), in cytokine-containing medium (such as IL-6 and IL-12 or other cytokines supplemented in the basal media used).
  • cytokine-containing medium such as IL-6 and IL-12 or other cytokines supplemented in the basal media used.
  • the cells would be co-cultured for as little as overnight or up to 1 week to stimulate T cells, but typically 18 – 48 hours, after which the T cells could be subjected to enrichment prior to expansion, if required.

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Animal Behavior & Ethology (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Organic Chemistry (AREA)
  • Epidemiology (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Immunology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Toxicology (AREA)
  • Zoology (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Microbiology (AREA)
  • Mycology (AREA)
  • Oncology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)
  • Peptides Or Proteins (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Medicinal Preparation (AREA)
PCT/GB2021/050940 2020-04-17 2021-04-19 Antigen pool Ceased WO2021209775A1 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
EP21721983.1A EP4136096A1 (en) 2020-04-17 2021-04-19 Antigen pool
JP2022562752A JP2023522193A (ja) 2020-04-17 2021-04-19 抗原プール
CN202180029092.4A CN115667288A (zh) 2020-04-17 2021-04-19 抗原池
CA3176754A CA3176754A1 (en) 2020-04-17 2021-04-19 Antigen pool
US18/046,670 US20230302109A1 (en) 2020-04-17 2022-10-14 Antigen pool

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EP20170255.2 2020-04-17
EP20170255 2020-04-17

Related Child Applications (1)

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US18/046,670 Continuation US20230302109A1 (en) 2020-04-17 2022-10-14 Antigen pool

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WO2021209775A1 true WO2021209775A1 (en) 2021-10-21

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PCT/GB2021/050940 Ceased WO2021209775A1 (en) 2020-04-17 2021-04-19 Antigen pool

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US (1) US20230302109A1 (https=)
EP (1) EP4136096A1 (https=)
JP (1) JP2023522193A (https=)
CN (1) CN115667288A (https=)
CA (1) CA3176754A1 (https=)
WO (1) WO2021209775A1 (https=)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2025202937A1 (en) 2024-03-26 2025-10-02 BioNTech SE Cancer vaccines

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WO2005099750A1 (en) 2004-04-16 2005-10-27 Georg-August-Universität Göttingen Stiftung Öffentlichen Rechts Vaccination against malignant melanoma using bcg and/or vaccinia
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Publication number Priority date Publication date Assignee Title
CN116057067A (zh) * 2020-04-17 2023-05-02 弗朗西斯·克里克研究所有限公司 用于治疗黑素瘤的ctl抗原的融合蛋白

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