WO2024010686A2 - Dosages de vaccins dans des tissus - Google Patents

Dosages de vaccins dans des tissus Download PDF

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WO2024010686A2
WO2024010686A2 PCT/US2023/025705 US2023025705W WO2024010686A2 WO 2024010686 A2 WO2024010686 A2 WO 2024010686A2 US 2023025705 W US2023025705 W US 2023025705W WO 2024010686 A2 WO2024010686 A2 WO 2024010686A2
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vaccine
tissue
cell
cells
immune
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PCT/US2023/025705
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WO2024010686A3 (fr
WO2024010686A9 (fr
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Peter Alan Sims
Donna Lynn FARBER
Alex George
Julia DAVIS-PORADA
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The Trustees Of Columbia University In The City Of New York
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • 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
    • A61K39/12—Viral antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/12—Antivirals
    • A61P31/14—Antivirals for RNA viruses
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5044—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving specific cell types
    • G01N33/5047—Cells of the immune system
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5082—Supracellular entities, e.g. tissue, organisms
    • G01N33/5088—Supracellular entities, e.g. tissue, organisms of vertebrates
    • 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
    • A61K2039/545—Medicinal preparations containing antigens or antibodies characterised by the dose, timing or administration schedule
    • 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
    • A61K2039/57—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2
    • A61K2039/575—Medicinal preparations containing antigens or antibodies characterised by the type of response, e.g. Th1, Th2 humoral response
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
    • C12N2760/00011—Details
    • C12N2760/18011—Paramyxoviridae
    • C12N2760/18411—Morbillivirus, e.g. Measles virus, canine distemper
    • C12N2760/18434—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
    • C12N2760/00011—Details
    • C12N2760/18011—Paramyxoviridae
    • C12N2760/18711—Rubulavirus, e.g. mumps virus, parainfluenza 2,4
    • C12N2760/18734—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/36011—Togaviridae
    • C12N2770/36211—Rubivirus, e.g. rubella virus
    • C12N2770/36234—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6841—In situ hybridisation

Definitions

  • kits for testing immune responses, safety, and efficacy of vaccines.
  • the methods, compositions, systems and kits of the present invention test immune responses, duration of the immune responses, dose responses and age dependencies in cellular components of lymph nodes, other lymphoid tissues, mucosal tissues, barrier tissues, intestinal tissues, pulmonary tissues, and other solid tissues to vaccines after exposure in cell culture and tissue slices.
  • lymph nodes lymph nodes
  • DC dendritic cells
  • the vaccine induces a SARS-CoV-2 Spike (S) protein-specific neutralizing antibody response that is protective (Baden, L.R., et al. Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine. N Engl J Med (2020); Thompson, M.G., et al. Prevention and Attenuation of Covid-19 with the BNT162b2 and mRNA-1273 Vaccines. N Engl J Med (2021); Widge, AT, et al. Durability of Responses after SARS-CoV-2 mRNA-1273 Vaccination.
  • S SARS-CoV-2 Spike
  • kits for testing immune responses, safety, and efficacy of vaccines.
  • the methods, compositions, systems and kits of the present invention test immune responses, duration of the immune responses, dose responses and age dependencies in cellular components of lymph nodes, other lymphoid tissues, mucosal tissues, barrier tissues, intestinal tissues, pulmonary tissues, and other solid tissues to vaccines after exposure in cell culture and tissue slices.
  • lymph nodes and other lymphoid, mucosal, and barrier tissues The nature of the innate and adaptive immune response that is initiated in tissue sites including lymph nodes and other lymphoid, mucosal, and barrier tissues is unaccounted for using conventional technologies.
  • the cellular composition of human lymphoid sites changes with age from predominantly naive T cells in early life and childhood, to increased frequencies of memory T cells in adults, and predominantly memory T cells in the elderly that affect the ability to respond to newly introduced antigens. Lymphoid sites such as lymph nodes also undergo age- associated changes in morphology, composition and function of myeloid cells.
  • compositions, systems, and kits to test immune responses to vaccines in humans and other mammals that target a diversity of antigens in lymph nodes and a diversity of other lymphoid, mucosal, barrier and solid tissues.
  • the present invention provides compositions and methods to test a vaccine comprising: exposing tissue or cells from lymph node tissue, other lymphoid tissue, mucosal tissue, barrier tissue, intestinal tissue, and /or pulmonary tissue to a vaccine and evaluating the vaccine.
  • the evaluation may include one or more of: the nature of the immune response generated, the establishment of immune memory, the efficacy of the vaccine for subject that provided the tissue or a category of subject to which the tissue donor belongs (e.g., based on age, health status, drugs or other agents taken (e.g., immunomodulatory drugs), etc.), and the identification of biomarkers that provide an indication of the efficacy of the vaccine and/or the duration of the immune response.
  • vaccine evaluation is performed using intact tissue, which preserves the intercellular interactions and structural features of the tissue that are important for immune memory formation.
  • the invention analyzes the early cellular and molecular immune responses to vaccination directly in animal (e.g., human) lymph node tissue, or in cultures of total mononuclear cells from animal (e.g., human) lymph nodes.
  • Adaptive immune responses to vaccination are initiated in lymph nodes; T and B cells become activated and interact to promote antibody production, and where the cellular stores of immune memory to vaccines likely reside.
  • Conventional serological measures of vaccine responses simply assess the amount of antibody produced in response to vaccination that is present in peripheral blood, and do not provide any information on the early immune response to vaccination, nor on the cells that produce the antibodies or maintain long-term immune memory.
  • the invention has the advantage of measuring immune responses directly at the tissue site that orchestrates immune memory formation and directly assess the functional responses of lymph node cells which is where vaccine responses are initiated in vivo.
  • the present invention provides a method to test a vaccine, comprising: exposing a vaccine to a tissue sample comprising one or more of a lymph node tissue, other lymphoid tissue, mucosal tissue, barrier tissue, intestinal tissue, and/or pulmonary tissue, or cells derived therefrom, and assessing one or more characteristics of the vaccine.
  • the present invention provides a method to test a vaccine, comprising: digesting one or more solid tissues to an immune cell suspension; generating one or more cell cultures from the immune cell suspension; and applying the vaccine to the one or more cell cultures.
  • the vaccine is an attenuated live vaccine, an inactivated vaccine, a toxoid and/or toxin vaccine, a subunit vaccine, a conjugate vaccine, an outer membrane vesicle vaccine, a heterologous vaccine, a DNA vaccine, an RNA vaccine, a viral vector vaccine, a lipid nanoparticle vaccine, a dendritic cell vaccine, a recombinant vector vaccine, a T-cell receptor vaccine, a killed bacteria vaccine, and existing pathogen vaccine, and emerging pathogen vaccine, a bacterial vector vaccine, a plasmid vector vaccine, or an antigen-presenting cell vaccine.
  • the vaccine is a mRNA vaccine.
  • the mRNA vaccine is a SARS-CoV-2 mRNA vaccine.
  • the solid tissue is a lymph node tissue, other lymphoid tissue, mucosal tissue, barrier tissue, intestinal tissue, and/or pulmonary tissue. In some embodiments, the solid tissue is a tissue slice sample, a biopsy sample, or a needle aspirate sample.
  • the method comprises assessing the cell culture for an immune response.
  • the assessing comprises supernatant testing for one or more activation marker concentrations, co-stimulatory marker concentrations, cytokine concentrations, chemokine concentrations, secreted factor concentrations, and/or cell free nucleic acid sequences and modifications.
  • the assessing comprises cell testing for high parameter flow cytometry, T-cell activation and proliferation, B-cell activation, myeloid cell activation, and/or cell-type specific and/or single cell nucleic acid sequences and modifications.
  • assessing is performed serially at hourly, daily, weekly and/or monthly intervals.
  • the assessing comprises identification of at least one biomarker of immune response duration.
  • two or more vaccines with different durations of pathogen protection differ in at least one biomarker of immune response duration.
  • the one or more cell cultures comprises two or more cell cultures from two or more solid tissues from an individual or from two or more individuals.
  • the assessing comprises assessing two or more immune responses from the two or more cell cultures.
  • the present invention provides a method to test an immunomodulatory agent, comprising: digesting one or more solid tissues to an immune cell suspension; generating one or more cell cultures from the immune cell suspension; and applying the immunomodulatory agent to the one or more cell cultures.
  • the immunomodulatory agent is an antibody, a cytokine, an immunomodulating drug, an immunostimulating drug, an immunosuppressive drug, a receptor antagonist, an immunoglobulin, a cytotoxic agent, an antimetabolite, a checkpoint inhibitor, a cytokine, an adjuvant or a small molecule.
  • the method comprises applying an immunomodulatory agent and a vaccine to the one or more cell cultures.
  • the present invention provides a method to test a vaccine or immunomodulatory agent comprising: obtaining a tissue slice from a solid tissue; generating a tissue culture from the tissue slice; applying the vaccine or immunomodulatory agent to the tissue culture; and assessing one or more characteristics of the vaccine or immunomodulatory agent.
  • the tissue culture is a cultured tissue slice.
  • the method comprises digesting the tissue culture before the applying.
  • the solid tissue comprises one or more of a lymph node tissue, other lymphoid tissue, mucosal tissue, barrier tissue, intestinal tissue, and/or pulmonary tissue.
  • the solid tissue is fresh-frozen tissue and/or formalin-fixed paraffin-embedded (FFPE) tissue.
  • the assessing comprises one or more of microscopy, histology, spatial profiling, immunohistochemistry, immunofluorescence, RNA-FISH, RNA-ISH, spatial transcriptomics, and highly multiplexed RNA-FISH.
  • the present invention provides a method to test a vaccine or immunomodulatory agent comprising: applying the vaccine or immunomodulatory agent to a tissue sample comprising one or more of a lymph node tissue, other lymphoid tissue, mucosal tissue, barrier tissue, intestinal tissue, and/or pulmonary tissue, or cells derived therefrom; digesting the tissue sample to generate an immune cell suspension; generating one or more cell cultures from the immune cell suspension; and assessing one or more characteristics of the vaccine or immunomodulatory agent.
  • Figure 1 shows a schematic workflow comprising a comparison of lymph node (LN) suspension and lymph node slice culture.
  • LN lymph node
  • corresponding liquid and slice cultures are generated from an organ donor from a LN.
  • T cells in cultures are stimulated with reagents.
  • scRNA-seq with cell surface proteomics Cellular Indexing of Transcriptomes and Epitopes or CITE-seq is performed on liquid and slice culture after dissociation to single cell suspension.
  • FIG. 2 shows a schematic diagram of 2 stimulation reagents used in liquid and slice LN culture.
  • Anti CD3/28 antibody encodes signal 1 and 2 respectively to activate T cells and is independent of antigen presenting cells (APCs).
  • a superantigen mimicking bispecific antibody brings APCs in contact with T cells by bridging major histocompatibility complex (MHC) Class II and T cell receptor (TCR) thereby providing signal 1), and proximity of APCs to T cells provides costimulatory signals 2 and paracrine signal 3 to facilitate T cell activation.
  • MHC major histocompatibility complex
  • TCR T cell receptor
  • Figure 3 shows a schematic diagram of slice culture generation workflow. Gross dissection of lymph node is performed to attenuate the collagen rich capsule and subcutaneous fat to facilitate tissue slicing downstream. Dissected and/or cleaned nodes are embedded in low melting point agarose (6% v/w) at 37 degrees C. LNs embedded in agarose are cut into blocks and glued onto a stage of a tissue chopper. Slices are generated (500 pM) and placed in complete culture media (IMDM, 5% FBS, IX penicillin/streptomycin/glutamine - PSQ). 2-3 slices are placed on each transwell insert (in, for example, a 6 well plate well). 1.5 mL of media is placed on the bottom under the transwell insert.
  • IMDM complete culture media
  • Slices are moved to the periphery of a “reagent pool” to prevent slices from floating in the media pool and to establish contact with the transwell on the bottom of the slice, while facilitating gas exchange and contact with complete media pool or treatment at the level of the transwell insert.
  • Slices may be cultured for 18-24 hours or longer. If cultured > 24 hours, 1.5 mL of media under the transwell is replaced every 24 hours.
  • Figure 4. shows % viability of LN slice culture after dissociation to a single cell suspension in 7 distinct organ donors.
  • Donor 1 was cultured for 96 hours and Donors 2-7 for 21 hours.
  • Figure 5. shows a schematic diagram of steps to assess lymphocyte activation dynamics in corresponding slice and liquid cultures.
  • Figure 6. shows a heatmap of z-scored average expression values from scRNA-seq of unstimulated LN liquid and slice cultures from 3 organ donors. Expression is evaluated specifically in T cells. Markers provided are associated with cytotoxic CD8 T cells and are found at higher levels in LN slice cultures compared to LN liquid cultures.
  • Figure 7 shows a heatmap of z-scored average expression values from scRNA-seq of unstimulated and stimulated LN liquid and slice cultures from 3 organ donors. T cells were identified computationally and expression of each marker was computed specifically in T cells. Markers shown are associated with T cell activation. Liquid LN cultures exhibit higher Thl responses (IFNG, IL2), particularly with anti-CD3/anti-CD28 stimulation, whereas CD8 effector memory activating markers including XCL1 and XCL2 are higher in stimulated LN slice cultures.
  • IFNG Thl responses
  • IL2 Thl responses
  • CD8 effector memory activating markers including XCL1 and XCL2 are higher in stimulated LN slice cultures.
  • Figure 8 shows the expression of activation markers as a function of measles, mumps, rubella MMR-II vaccine dose and IFN positive control stimulation in LN liquid cultures as measured by flow cytometry. Dilution values on the x-axis correspond to MMR-II dose.
  • Figure 9 shows uniform manifold approximation and projection (UMAP) embedding of CITE-seq data for MMR-II vaccine stimulated and unstimulated LN liquid and slice cultures colored by classification of major immune cell types.
  • UMAP uniform manifold approximation and projection
  • Figure 10 shows a heatmap of z-scored average expression values from scRNA-seq of unstimulated and MMR-II- stimulated LN liquid and slice cultures.
  • T cells were identified computationally and expression of each marker was computed specifically in T cells. Markers shown are generally associated with resting and activated T cells. Slice cultures exhibit higher induction of CD8 effector memory activation markers XCL1, XCL2, and CCL4 compared to liquid culture.
  • B) B cells were identified computationally and expression of each marker was computed specifically in B cells. Markers shown are associated with resting and activated B cells. Liquid cultures exhibit higher induction of B cell activation markers such as CD80 and CD 86 than slice cultures.
  • Figure 11 shows representative H&E-stained tissue section from a lymph node slice culture prepared as described in Experimental Example 11.
  • the term "about” represents an insignificant modification or variation of the numerical value such that the basic function of the item to which the numerical value relates is unchanged.
  • protein is used synonymously with “peptide,” “polypeptide,” or “peptide fragment.”
  • a “purified” polypeptide, protein, peptide, or peptide fragment is substantially free of cellular material or other contaminating proteins from the cell, tissue, or cell-free source from which the amino acid sequence is obtained, or substantially free from chemical precursors or other chemicals when chemically synthesized.
  • module means to alter, either by increasing or decreasing, the activity of a gene or protein.
  • inhibitor means to prevent or reduce the activity of gene or protein.
  • bioactivity indicates an effect on one or more cellular or extracellular process (e.g., via binding, signaling, etc.) that can impact physiological or pathophysiological processes.
  • Ranges provided herein are understood to be shorthand for all of the values within the range.
  • a range of 1 to 50 is understood to include any number, combination of numbers, or sub -range from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 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, or 50 (as well as fractions thereof unless the context clearly dictates otherwise).
  • any concentration range, percentage range, ratio range, or integer range is to be understood to include the value of any integer within the recited range and, when appropriate, fractions thereof (such as one tenth and one hundredth of an integer), unless otherwise indicated.
  • any number range recited herein relating to any physical feature, such as polymer subunits, size or thickness are to be understood to include any integer within the recited range, unless otherwise indicated.
  • cell culture refers to any in vitro culture of cells. Included within this term are continuous cell lines (e.g., with an immortal phenotype), primary cell cultures, transformed cell lines, finite cell lines (e.g., non-transformed cells), tissues, and any other cell population maintained in vitro.
  • /// vitro refers to an artificial environment and to processes or reactions that occur within an artificial environment.
  • In vitro environments can consist of, but are not limited to, test tubes and cell lysate.
  • the term “/// vivo” refers to the natural environment (e.g., an animal or a cell) and to processes or reaction that occur within a natural environment.
  • kits for testing immune responses, safety, and efficacy of vaccines.
  • the methods, compositions, systems and kits of the present invention test immune responses, duration of the immune responses, dose responses and age dependencies in cellular components of lymph nodes, other lymphoid tissues, mucosal tissues, barrier tissues, intestinal tissues, pulmonary tissues, and other solid tissues to vaccines after exposure in cell culture and tissue slices.
  • Immune cells may be referred to as “white blood cells.” But most, including more than 95% of T cells, reside and function in tissues, particularly lymphoid organs including bone marrow, spleen and lymph nodes, and in barrier surfaces including skin, gut and mucous membranes. (Kumar BV, Connors TJ, Farber DL. Human T Cell Development, Localization, and Function throughout Life. Immunity. 2018 Feb 20;48(2):202-213.) Certain immune cells are rarely found in blood. Some fail to enter the circulation. Others change their phenotypes when they do enter the circulation. For example, memory T cells, develop from activated T cells that migrate to tissues following priming in lymph nodes during infection. The tissuehoming T cells take up long-term residence in tissues and develop properties that are distinct in each.
  • RNA transcripts, protein content, DNA methylation, histone and chromatin status, genotype and gene modifications may be pinpointed even for single cells. Combined with computational analyses, these measurements allow' the simultaneous identification of immune-cell composition, lineage, and functional states.
  • the present invention provides tissue platforms comprising lymph nodes and/or other lymphoid, mucosal, and barrier tissue platforms to assay the efficacy and safety of candidate vaccines, to optimize vaccines, and to select appropriate vaccine for administration to particular subjects or groups of subjects.
  • the present invention provides methods, compositions, systems and kits that predict vaccine responses in mammals and humans, including durable immune memory and side effects.
  • Conventional technologies rely on pre-clinical studies in animal models followed by large-scale clinical trials that may take months or years to complete.
  • Prior efforts to identify predictors of vaccine efficacy directly from human immune cells have relied on peripheral blood because of its accessibility.
  • peripheral blood because of its accessibility.
  • the early-stage cellular and molecular events that orchestrate long-term protection by vaccines occur in the lymph nodes (LNs).
  • testing immunomodulatory drugs as a general class of therapeutics have relied on peripheral blood rather than LNs.
  • the present invention provides methods and compositions for procuring and culturing human lymph node slices for direct perturbation with immunomodulatory drugs, biologies and vaccines, and for analyzing cell type-specific, molecular responses with single-cell genomics.
  • the present invention provides methods, compositions, systems and kits comprising LN assays to test immunomodulatory drugs and vaccines, and for collecting and analyzing single-cell genomic data as a readout for these assays.
  • T cell responses of liquid mononuclear cell (MNC) cultures derived from human LNs were compared to directly perturbed human LN slice cultures ( Figure 1).
  • TCR T cell receptor
  • APC antigen-presenting cells
  • CytostimTM a bi-specific TCR/MHC II antibody that stimulates APC-mediated TCR signaling
  • LNs are dissected and embedded in agarose, sectioned to 500-micron slices with a tissue chopper, and cultured on transwell inserts in tissue culture plates ( Figure 3). LNs from 7 human organ donors reproducibly yielded high-viability cells after dissociation of LN slice cultures and 21-96 hours of culture ( Figure 4).
  • CITE-seq Cellular Indexing of Transcriptomes and Epitopes
  • T cell responses elicited in LN slice cultures compared to liquid cultures.
  • T cells in LN slice cultures comprise a more cytotoxic phenotype, expressing granzymes, perforin- 1, and other markers at higher levels than in liquid cultures (Figure 6).
  • T cell stimulation particularly with anti-CD3/anti-CD28, generates strong Thl responses (IFNG, IL2) in liquid culture, whereas a subset of genes associated with CD8 effector memory responses (XCL1, XCL2) are more strongly induced in slice culture (Figure 7).
  • the methods of the present invention find use in screening a candidate vaccine for immune responses, safety, and efficacy and for developing and identifying vaccine with desired characteristics.
  • the method provides a vaccine discovery method.
  • the method provides a vaccine optimization method for a vaccine function or property comprising, for example, speed of protection onset, duration of protection, concentration range of protection, breadth of protection vs. diverse species and strains, side effects and toxicity of a vaccine, interaction of a vaccine with co-existing solid tissue conditions, interaction of a vaccine with co-administered medications and compounds, combinations of two or more related or unrelated vaccines, and the like.
  • the method provides a method for precision, personalized vaccination wherein one or more functions or properties of a vaccine differ between individuals.
  • the method provides a manufacturing method.
  • the method provides a quality assurance method.
  • the method finds use in satisfying vaccine regulatory requirements.
  • Methods of the present invention are not limited to a specific pathogen, a specific candidate vaccine, or to a specific assay tissue.
  • methods of the present invention are performed in parallel with two or more sample sources, for example, a blood sample source and a lymph node tissue sample source, or two or more lymph node sources from, for example, one individual or two or more individuals.
  • the methods, compositions, reaction mixtures, systems and kits of the present invention find use in the identification of biomarkers of susceptibility, diagnosis, prognosis, response to therapy, and transmissibility of an infection or heritability of a cancer.
  • the vaccine is an attenuated vaccine, an inactivated vaccine, a toxoid vaccine, a subunit vaccine, a conjugate vaccine, an outer membrane vesicle vaccine, a heterologous vaccine, a DNA vaccine, an RNA vaccine, a viral vector vaccine, a lipid nanoparticle vaccine, a dendritic cell vaccine, a recombinant vector vaccine, a T-cell receptor vaccine, a bacterial vector vaccine, a plasmid vector vaccine, or an antigen-presenting cell vaccine.
  • the vaccine comprises an adjuvant, an excipient, and/or a preservative.
  • the vaccine is directed to infection by an adenovirus, a papovavirus, a parvovirus, a herpes virus, a poxvirus, a poliovirus, a reovirus, a rotavirus, a pircomavirus, a calicivirus, a togavirus, an arenavirus, a flavivirus, an orthomyxovirus, a paramyxovirus, a bunyavirus, a rhabdovirus, a filovirus, a coronavirus, an astrovirus, a bornavirus, an arterivirus, a hepevirus, a retrovirus, a heptavirus, a hepadnavirus or other viral pathogen.
  • the vaccine is directed to infection by Corynebacieritim diphtheriae , Clostridium letani, Bordeiella pertussis, Haemophilus influenzae type b, Streptococcus pneumoniae. Neisseria meningitidis, Salmonella typhi, Mycobacterium tuberculosis. Yersinia pestis, Bacillus anfhracis, Vibrio cholerae or other bacterial pathogen.
  • the vaccine is directed to infection by a fungal pathogen, for example, a Candida fungus, and Cryptococcus fungus, an Aspergillus fungus or other fungal pathogen.
  • the vaccine is directed to infection by a parasite, for example, a malarial parasite, a leishmaniasis parasite, a schistosomiasis parasite or other parasite infection.
  • the vaccine is directed to cancer prevention and/or to cancer therapy.
  • kits of the present invention comprise at least one tissue dissociation reagent, at least one cell culture reagent, and/or at least one detection reagent.
  • such kits may comprise, for example, two or more of a stabilizer, a buffer, instructions, positive and negative control reagents (for example, positive and negative vaccine control reagents), one or more calibrants, and ligands to identify possible sources of error and contamination.
  • a positive control vaccine achieves statistical significance indicating that the positive control experiment performs to specification.
  • a kit of the present invention comprises calibration reagents and ligands including, for example, a detection calibration reagent.
  • the kit comprises customizable options.
  • a kit of the present invention comprises frozen (e.g., prepared with glycerol for storing at -20 C degree) components and reagents, and/or desiccated reagents and components.
  • compositions and reaction mixtures comprising components of the assays described herein.
  • Such compositions and reaction mixtures may comprise, for example, two or more of a stabilizer, a buffer, positive and negative control reagents, and ligands to identify possible sources of error and contamination.
  • compositions and reaction mixtures of the present invention comprise a cell culture or tissue slice supernatant, and/or a cell culture or tissue slice living cell.
  • Tissues from human organ donors have been acquired through collaboration with organ procurement organizations (OPOs) in the New York Metropolitan area for adults of all ages, and OPOs through the entire US for tissues from infant and pediatric donors aged 0-12 years of age.
  • OPOs organ procurement organizations
  • Multiple LN are obtained, including lung- and gut-associated LN, and peripheral LN, together with spleen, bone marrow, lungs, intestines, and blood to test immune cells and vaccine responses across multiple tissues and ages.
  • Example 1 Lymph node vaccine response from donors of different ages
  • lymph nodes obtained from donors of different ages
  • total immune cells are isolated from donor LNs after tissue digestion to obtain single cell suspensions. Lymphocytes, DC, and other myeloid cells predominate in LN.
  • Total LN immune cells are cultured with scaled concentrations of a mRNA vaccine formulation for evaluation at serial intervals beginning with 12-24 hours to measure innate immune responses, and 48-96 hours to monitor adaptive immune responses. Supernatants and cells are isolated at each interval.
  • Upregulation of activation markers (e.g., HLA Class II) and co-stimulatory markers (e.g., CD80/86) by DC and myeloid-lineages cells are assessed by high parameter flow cytometry at early serial intervals, while T cell activation and proliferation to S protein are assessed at later serial intervals, with spike (S)-specific B cell activation assessed at 1 week and thereafter in culture.
  • Supernatants are analyzed for 50+plex cytokines and chemokines from both innate and adaptive cells. Lymph nodes acquired from donors aged 2-80 years are used to test whether a candidate mRNA vaccine promotes immune responses in LN obtained from donors that differ by age. The optimal mRNA vaccine dose for each age is identified in vitro by measuring responses to different doses in cultures from LN donors of different ages.
  • Parallel ex vivo cultures are prepared, and supernatants and cells are tested for immune responses in lung and intestinal tissue after exposure to a vaccine.
  • a candidate vaccine is loaded directly onto a tissue slice, for example, a lymph node tissue slice, followed by incubation, dissociation, cell culture and characterization.
  • a tissue slice for example, a lymph node tissue slice
  • Immune responses to a candidate vaccine are tested in situ by imaging, flow cytometry, genotype, single cell transcriptome profiling, methylation and/or histone status, chromatin status, immune receptor identity (for example, T-cell receptor identity and/or antibody clonal identity), and/or protein/ surf ace phenotype of cells isolated from tissue slices that have been exposed to the vaccine.
  • the present invention provides methods, compositions, systems, and kits to generate and maintain slice cultures of human lymphoid tissues with high viability (>90%) for up to ⁇ 96 hours after sectioning (Figure 3).
  • LNs from organ donors were dissected to attenuate the collagen-rich capsule and remove surrounding fat/connective tissue, embedded in 6% w/v low melting point agarose (Invitrogen, Cat: 16520100) at 37 °C, and sectioned at a thickness of 500 pM (McIlwain Tissue Chopper, Ted Pella, Cat: 10180).
  • Slice cultures (pooling all slice cultures per experimental condition) were processed to a single-cell suspension using enzymatic and mechanical dissociation.
  • a corresponding suspension culture as a comparator to slice culture for a specific donor is also generated with the following protocol: LN slices or dissected whole LN were digested with DNAse I (0.1-0.3 mg/mL, Millipore Sigma, Cat: DN25-5G) and Collagenase D (1-3 mg/mL, Millipore Sigma, Cat: 11088882001) for 30 min at 37 °C.
  • the digest was passed through a 100 pM filter (MACS smart strainer, Miltenyi) and mononuclear cells were isolated with density gradient centrifugation (Ficoll-Paque PLUS, Cytiva).
  • Slice cultures were generated (500 pM thick) together with corresponding single cell (liquid culture) suspensions from the same donor using the procedure in Experimental Example 5.
  • 5xl0 6 cells in suspension were cultured in complete media (IMDM (Thermo Fisher, Cat: 12440053), 5% FBS (Thermo Fisher, Cat: A3160401), IX Penn/Strep/Glutamine (Thermo Fisher, Cat: 10378016)) as an unstimulated control at a density of IxlO 6 cells/mL.
  • IMDM Thermo Fisher, Cat: 12440053
  • FBS Thermo Fisher, Cat: A3160401
  • IX Penn/Strep/Glutamine Thermo Fisher, Cat: 10378016
  • Liquid culture was stimulated with a-CD3/28 (ImmunocultTM, Stem Cell Technologies, Cat: 10971) in complete media for 18hrs at 25 pL of reagent per million cells at lxl0 6 cells/mL (5xl0 6 cells total).
  • Liquid culture was also stimulated with APC independent superantigen mimicking reagent (CytostimTM, Miltenyi Biotec, Cat: 130-092-172) in complete media for 18hrs as per manufacturer’s protocol (20 pL of reagent per IxlO 7 cells at IxlO 7 cells/mL, IxlO 7 cells total).
  • a subset of slice cultures was set aside as an unstimulated control (for example, 6+ slices w/ 2-3 slices on transwell insert per well in 6 well plate) in complete media with 60 uL of media added on top of slices which were moved to the periphery of the “media/reagent pool” to prevent slices from floating and to establish contact with the transwell on the bottom of the slice while facilitating gas exchange and contact with media/reagent at the level of the transwell insert.
  • Slices were stimulated with aCD3/28 for 18 hours in complete media (60 uL of Immunocult 1M aCD3/28 reagent on top of 2-3 slices per transwell as described in method above).
  • Slice culture media beneath the transwells was collected for cytokine analysis.
  • Slice cultures were pooled per stimulation/unstimulated condition, digested with DNAse I (0.1-3 mg/mL, Millipore Sigma, Cat: DN25-5G) and Collagenase D (1-3 mg/mL, Millipore Sigma, Cat: 11088882001) for 30 min at 37 °C.
  • the digest was passed through a 100 pM filter (MACS smart strainers, Miltenyi) and mononuclear cells were isolated with density gradient centrifugation (Ficoll-Paque PLUS, Cytiva).
  • Suspension cell cultures on ice and single cell suspension from slices were quantified for viability and cell counts, incubated with Fc blocking reagents (TruStain FcX, Biolegend, Cat: 422301; FcR blocking reagent human, Miltenyi Biotec, Cat: 130-059-901) for 10 min at 4 °C, incubated with barcoded antibodies for hash-tagging and cell surface proteomics (Total Seq-A human panel, Biolegend) for 30 min at 4 °C, and processed for single cell sequencing using lOx Genomics Chromium 3’ v3.1 chemistry (10X Genomics, Cat: PN-1000121). Libraries were sequenced on a NextSeq 500/550 system (Illumina).
  • Example 7 Single cell mononuclear suspensions and MMR vaccine
  • Example 4 Single cell mononuclear suspensions isolated from human lung-draining lymph nodes as described in Example 4 were thawed as described in Example 8 and plated in a 24-well flat bottom plate (1.5xl0 7 cells per well) in 1.5mL of complete media (RPMI (Corning, catalog no. 10-040-CM), 10% inactivated human AB serum (Gemini, catalog no. 507533010) and penicillin- streptomycin-glutamate (Thermo Fisher Scientific, catalog no. 10378016)), and incubated overnight at 37°C in 5% CO2. The next day, one dose of Merck Measles, Mumps, and Rubella live virus vaccine (M-M-R II; McKesson catalog no.
  • M-M-R II Merck Measles, Mumps, and Rubella live virus vaccine
  • the myeloid and lymphoid fraction samples were washed with FACS buffer (PBS (Coming, cat no. 20-030-CV) with 2% heat inactivated FBS (GeminiBio, cat no. 100-106) and ImM EDTA (Coming, cat no. 46-034-CI)) and resuspended in lOuL Human TruStain FcX (Biolegend, cat no. 422302) for 10 minutes at room temperature.
  • FACS buffer PBS (Coming, cat no. 20-030-CV) with 2% heat inactivated FBS (GeminiBio, cat no. 100-106) and ImM EDTA (Coming, cat no. 46-034-CI)
  • Fluorochrome-conjugated antibodies and fixable viability stain eFluor780 in Brilliant Stain buffer (BD Bioscience, catalog no. 566349) were added to cell suspensions for 20 minutes at room temperature protected from light, washed twice, and incubated for 10 minutes with Annexin V BUV395 (BD Bioscience, catalog no. 564871) in the recommended buffer. Cells were washed and resuspended in fixation buffer (Tonbo, catalog no. TNB-0607-KIT) for 30 minutes at room temperature. Flow cytometry data were collected using the five-laser Cytek Aurora flow cytometer and analyzed using FlowJo V10.7.1.
  • Organ donor samples in saline or University of Wisconsin solution were placed on ice, transported to the laboratory, and processed within 2 to 4 hours of procurement.
  • Single cell suspensions were obtained from blood, bone marrow, spleen, lungs, and associated lymph nodes (LN) using mechanical and enzymatic digestion as previously described (Granot et al., ibid. , ' Sathaliyawala et al., Distribution and compartmentalization of human circulating and tissueresident memory T cell subsets, Immunity 38, 187-197 (2013); Thome et al., ibid).
  • Blood and bone marrow samples were diluted with wash buffer (PBS (Coming, cat #20-030-CV) + 2mM EDTA (Corning, cat #46-034-CI) + 5% FBS (GeminiBio, cat #100-106)), and mononuclear cells were isolated by density centrifugation using Ficoll-Paque PLUS (GE Healthcare, catalog no. 17- 1440-03). Lymph nodes were isolated by dissection from the mesentery of the small and large intestine, the tracheobronchial tree of the lung, and inguinal fat. Tissue samples were first mechanically disrupted with scissors.
  • Isolated LNs and lung were then placed into digestion media (IMDM + Collagenase D Img/mL (Millipore Sigma cat# 11088882001) and + DNAse 0. Img/mL (Millipore Sigma cat# DN25-5G)) on a shaker at 37°C for 30 minutes followed by addition of 0.5M EDTA (pH 8.0). Digested LNs and lung as well as mechanically disrupted spleen were then pushed through 100pm filters and washed with buffers. The samples then underwent density centrifugation as above to isolate live leukocytes.
  • digestion media IMDM + Collagenase D Img/mL (Millipore Sigma cat# 11088882001) and + DNAse 0. Img/mL (Millipore Sigma cat# DN25-5G)
  • Frozen cryovials were incubated in a water bath at 37C for one minute.
  • ImL of warmed complete media (RMPI, 10% heat inactivated FBS, and penicillin-streptomycin-glutamate) was added dropwise to each vial and the vial contents were carefully decanted into a 50mL conical containing 25mL of complete media.
  • the sample was topped up to 50mL and the cells are pelleted by centrifugation at 400xg for 10 minutes.
  • the pellet was resuspended in lOmL of complete media with lOOuL benzonase (Millipore Sigma, catalog no. E1014-25KU) and incubated in 37C water bath for 20 minutes. The resulting sample is counted and used as required.
  • perturbation comprised of stock MMR (60 pL of MMR stock ‘pool’ on 3 slices per transwell). A total of 9 slices in three transwells were treated with this condition. Unstimulated liquid (3xl0 6 cells) and slice cultures (9 slices) were prepared and treated as in Experimental Example 5 and CITE-seq was carried out using the procedure described in Experimental Example 5.
  • FFPE formalin-fixed paraffin embedding
  • Hematoxylin and Eosin (H&E) staining was performed on the 5 micron sections (Columbia Histology Service, Molecular Pathology Core Facility, New York, NY) and images were acquired using an automated slide imaging system (Leica SCN 400).
  • Figure 11 shows a representative image of an H&E-stained tissue section from a lymph node slice culture.
  • Example 12 Spatial profiling with commercial systems
  • Human lung lymph node slice cultures (500 microns thick) are generated as described in Example 4. Three slice cultures are set aside as unstimulated controls in complete media (IMDM (Thermo Fisher, Cat: 12440053), 5% FBS (Thermo Fisher, Cat: A3160401), IX Penn/Strep/Glutamine (Thermo Fisher, Cat: 10378016)) with 60 uL of media added on top of the slices. Another three slices are cultured in the same media, but also stimulated for 24 hours with stock MMR-II vaccine (Merck - 60 uL per slice). The two sets of slice cultures are then fixed with formaldehyde, and 5 micron FFPE tissue sections are prepared from each slice culture as described in Experimental Example 11.
  • IMDM Thermo Fisher, Cat: 12440053
  • FBS Thermo Fisher, Cat: A3160401
  • IX Penn/Strep/Glutamine Thermo Fisher, Cat: 10378016
  • oligonucleotide probes from the Human Lung Gene Expression Panel are hybridized to target mRNAs at 50C overnight at a concentration of 10 nM followed by probe ligation, primer hybridization, and enzymatic amplification of the resulting padlock probes by rolling circle amplification as described previously (Janesick et al., bioRxiv, Nov. 3, 2022). After extensive washing, tissue sections are loaded into consumables for imaging with sequential fluorescence hybridization using the lOx Genomics Xenium Analyzer platform. The resulting data contain a spatial map of the lymph node slice cultures that localize -300 mRNA species to individual cells.
  • each cell is classified and the spatial location of each lymphocyte and myeloid cell subset is determined.
  • the gene expression profile of the MMR- II-stimulated cells is then compared to the corresponding control to identify gene expression responses to the vaccine.
  • a feature space comprised of the spatially adjacent neighbor cells is further defined and unsupervised clustering in this feature space is performed to further refine the immune cell subsets on the basis of the identities of their neighboring cells (e.g., cell-cell interactions).
  • unsupervised clustering in this feature space is performed to further refine the immune cell subsets on the basis of the identities of their neighboring cells (e.g., cell-cell interactions).
  • differential expression analysis between MMR-II- stimulated cells and the corresponding controls is further performed to identify gene expression-level immune responses.

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Abstract

L'invention concerne des méthodes, des compositions, des systèmes et des kits destinés à tester les réponses immunitaires, la sécurité et l'efficacité de vaccins. En particulier, les méthodes, les compositions, les systèmes et les kits de la présente invention testent les réponses immunitaires, la durée des réponses immunitaires, les réponses aux doses ainsi que les dépendances en fonction des ages dans des constituants cellulaires des noeuds lymphatiques, d'autres tissus lymphoïdes, des tissus muqueux, des tissus barrière, des tissus intestinaux, des tissus pulmonaires et d'autres tissus solides face aux vaccins après exposition en culture cellulaire et dans des tranches de tissus.
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