US20230181757A1 - Uses of extracellular vesicle comprising a fusion protein having fc binding capacity - Google Patents

Uses of extracellular vesicle comprising a fusion protein having fc binding capacity Download PDF

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US20230181757A1
US20230181757A1 US16/319,087 US201716319087A US2023181757A1 US 20230181757 A1 US20230181757 A1 US 20230181757A1 US 201716319087 A US201716319087 A US 201716319087A US 2023181757 A1 US2023181757 A1 US 2023181757A1
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evs
detection
protein
polypeptide
containing protein
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André GÖRGENS
Dhanu GUPTA
Oscar WIKLANDER
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Evox Therapeutics Ltd
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Evox Therapeutics Ltd
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    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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    • C07K14/31—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F) from Staphylococcus (G)
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    • C07—ORGANIC CHEMISTRY
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    • C—CHEMISTRY; METALLURGY
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    • C07K—PEPTIDES
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    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
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    • G01—MEASURING; TESTING
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    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
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    • C07K2319/70—Fusion polypeptide containing domain for protein-protein interaction
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Definitions

  • the present invention pertains to extracellular vesicles engineered to function as research and diagnostics tools for e.g. standardization and evaluation of assays for EV characterization, in diagnostics of various diseases, and as biological reference material (RM) for e.g. flow cytometry.
  • RM biological reference material
  • Extracellular vesicles are nano-sized vesicles that are released by EV-producing cells into the extracellular environment.
  • EVs and in particular exosomes have been shown to be able to transport protein biologics, such as antibodies and decoy receptors, enabling an entirely novel form of advanced biological therapeutics harnessing the properties of EVs in combination with the specificity of recombinant proteins.
  • protein biologics such as antibodies and decoy receptors
  • EVs smaller than 300 nm constitute the majority of EV population (Aatonen et al., 2014). Typical size distributions of EVs start at ⁇ 30 nm, exhibiting a peak at a diameter ⁇ 100 nm, and follow a decreasing power-law function or exponential function for diameters>100 nm (van der Pol et al., 2016). With the exception of transmission electron microscopy (TEM), none of the current analytical methods are able to detect the entire population of EVs (van der Pol et al., 2016). The inability to detect the smallest EVs leads to both differences and underestimation of the determined concentration. Consequently, the reported number of EVs in normal human plasma ranges from 10 4 to 10 12 mL-1 (van der Pol et al., 2014a). These 8 orders of magnitude difference in EV concentration highlights the need for standardization.
  • a lower size gate set with 200 nm polystyrene beads which scatter the same amount of light as EVs of ⁇ 500 nm (Chandler et al., 2011), leads to the exclusion of EVs between 200 and 500 nm (van der Pol et al., 2014b). Since the concentration of EVs decreases with increasing diameter, a polystyrene size gate generally leads to an underestimation of the actual EV concentration.
  • NTA nanoparticle tracking analysis
  • Submicron particles with physical and biochemical properties similar to EVs can be isolated from naturally occurring sources, and may include 1) isolated EV populations from, e.g. cell cultures, 2) plasma lipoproteins, plant and marine viruses, and 3) small spherically shaped (coccoid) bacteria, or picoplankton.
  • Potential EV sources are in vitro cell cultures, therapeutic clinical grade erythrocyte and platelet concentrates, urine, and outer membrane vesicles produced by bacteria.
  • the specific advantage is that the obtained RM have enhanced physical and biochemical similarities, including the molecular contents, with actual EVs.
  • Lipoproteins and viral particles from plant and marine sources are suitable as EV-RM because they have a size distribution overlapping with the bulk of EVs and they do have a relatively small variation in size.
  • a major drawback of lipoproteins and viral particles is that the RI of these particles is higher than the RI of EVs, due to their high protein content, a prominent problem especially of protein-enveloped viruses.
  • Another issue of using viral particles is their biosafety, which could be circumvented by producing virus-like particles, i.e. particles lacking the viral genome.
  • Biological RM can further be produced by disrupting cells to produce small vesicles from the fragments yielding particles with varying diameters.
  • the main advantage of using such materials is that the physical and biochemical properties of the obtained RM would better resemble EVs compared to synthetic RM.
  • Erythrocytes are theoretically ideal materials to use, since their cell membrane composition is well-characterized and they are devoid of intracellular membranes. Additionally, erythrocytes are structurally stable during extended storage and are an easily accessible material. For these reasons, erythrocytes from clinical surplus concentrates have been used to produce an RM for testing and evaluation and different methods for erythrocyte disruption have also been compared.
  • Biological RM can also be obtained from lipid constructs such as liposomes that are extensively used as delivery vehicles and their production methods are well known.
  • Liposomes of a desired size can be prepared by ultrasonication or extrusion of the starting material through e.g. polycarbonate filters of a set pore size.
  • An advantage of liposomes is that their RI can be manipulated during the production.
  • lyophilized exosome are used as standardized positive controls for immunocapture performance evaluation. Lyophilization is a commonly applied technique for preserving the long-term stability of various types of biological samples, and lyophilized exosomes can be purchased as control standards for multiple applications including flow cytometry (FACS), Western blotting (WB), ELISA and as calibration standards for quantitation of exosome-derived markers from biological samples.
  • FACS flow cytometry
  • WB Western blotting
  • ELISA as calibration standards for quantitation of exosome-derived markers from biological samples.
  • lyophilization considerably affects the biophysical and biological properties of EVs, and as such this method for generating biological RM is not suitable for powerful analytical methods where the similarity to EVs in their natural form is required.
  • the present invention aims to satisfy other existing needs within the art, for instance to enable using EVs as a predictable and specific positive control, as a compensation control or as a biological RM for any kind of assay that uses e.g. antibodies, fluorescent probes, and/or various biomolecules to detect, enumerate, size or phenotype EVs, for research or diagnostics.
  • the present invention also aims to provide for novel important uses of EVs as research tools in preclinical, clinical, and diagnostics settings, for instance in combination with immunohistochemistry, microscopy, radiolabeling, etc.
  • the unique delivery properties of engineered EVs are in the present application harnessed to address several obstacles within the broad field of biomedical research.
  • the present invention achieves these and other objectives by utilizing Fc binding polypeptides (herein often referred to as Fc binders) of human and/or non-human origin to engineer the content and characteristics of EVs.
  • Fc binding polypeptides (herein often referred to as Fc binders) of human and/or non-human origin to engineer the content and characteristics of EVs.
  • Fc binding polypeptides are fused to exosomal polypeptide to enhance loading of EVs with the Fc binding polypeptides.
  • the EVs comprising Fc binding polypeptides may then be allowed to bind to the Fc domains present on antibodies, other proteins natively comprising Fc domains, and/or proteins that have been modified to comprise Fc domains for the purpose of the present invention.
  • the present invention provides for a biological RM, comprising an EV comprising at least one Fc binding polypeptide, which optionally forms part of a fusion protein together with an exosomal polypeptide.
  • a biological RM comprising an EV comprising at least one Fc binding polypeptide, which optionally forms part of a fusion protein together with an exosomal polypeptide.
  • the Fc domain of an Fc containing protein (such as an antibody, which may be tagged with a detection moiety) is bound by the Fc binding polypeptide of the EV, thereby generating a coated EV with broad utility as RM, diagnostic tool, imaging tool, and for essentially any research purpose.
  • the invention provides the use of an EV comprising at least one Fc binding polypeptide, as a research tool, a diagnostic tool, imaging tool, in a detection kit, as a biological RM, as an experimental control and/or an experimental standard.
  • the present invention relates to an in vitro, in vivo and/or ex vivo method for delivery of an Fc containing protein to a target cell.
  • the method comprises the steps of (i) providing an EV comprising at least one Fc binding polypeptide, (ii) allowing the Fc binding polypeptide to bind the Fc containing protein, and (iii) putting the EV having attached to its Fc binding polypeptide the Fc containing protein in contact with a target cell, to enable intracellular, extracellular, and/or intramembrane delivery of the Fc containing protein in question.
  • the present invention provides a detection kit comprising an EV, wherein the EV comprises a fusion protein comprising at least one Fc binding polypeptide and at least one exosomal polypeptide.
  • the Fc binding polypeptide may be bound (attached) to at least one Fc containing protein, such as an antibody.
  • the detection kit may be used for various purposes, for instance detection of an intracellular, intramembrane, or extracellular antigen which can be achieved by delivering e.g. a labelled antibody against the antigen in question.
  • the instant invention relates to a kit of parts comprising (i) an EV comprising at least one Fc binding polypeptide, and (ii) at least one Fc containing protein.
  • the Fc binding polypeptide may be fused to at least one exosomal polypeptide to increase the number of Fc binders in or on the EV.
  • the present invention relates to a nanoparticle complex between (i) an EV comprising at least one Fc binding polypeptide and (ii) at least one Fc containing protein.
  • the at least one Fc containing protein may be several copies of one type of Fc containing proteins (e.g. multiple copies of an antibody targeting an intracellular oncogenic protein) or more than one type of Fc containing protein (for instance multiple copies of an antibody against one intracellular target and multiple copies of another antibody against a membrane target).
  • the nanoparticle complex formed between EVs as per the present invention and Fc containing proteins can be used broadly across various research, diagnostic and therapeutic areas, for instance within flow cytometry, electron microscopy, confocal and/or fluorescence microscopy, in vitro, in vivo and/or ex vivo diagnostics, imaging and/or treatment of target cells, and for numerous other purposes.
  • the present invention pertains to methods for producing EVs capable of binding to proteins comprising an Fc domain.
  • Such methods may comprise the steps of: (i) introducing into an EV source cell a polynucleotide construct encoding a fusion protein comprising at least one Fc binder polypeptide and at least one exosomal polypeptide, and (ii) harvesting EVs which are secreted from the EV source cell, said EVs comprising the fusion protein of interest.
  • the present invention relates to methods for coating EVs with at least one protein comprising an Fc domain, comprising the steps of (i) providing an EV comprising a fusion protein comprising at least one Fc binder and at least one exosomal polypeptide, and (ii) allowing the Fc binder of the fusion protein to bind the Fc domain of at least one protein comprising an Fc domain.
  • the present invention also relates to fusion proteins comprising at least one Fc binding polypeptide and at least one exosomal polypeptide, and polynucleotide constructs encoding for such fusion proteins, as well as vectors, EVs and cells comprising such constructs.
  • FIG. 1 Schematic illustration of an EV comprising a fusion protein comprising an exosomal protein fused to an Fc binding polypeptide (i.e. the Fc binder domain).
  • the Fc binder is capable of binding e.g. an antibody and/or any other protein comprising an Fc domain, thereby turning the EV into a multivalent delivery vehicle for protein therapeutics.
  • FIG. 2 Electron microscopy pictures of EVs comprising Fc binding polypeptides (A) are decorated with nanogold labeled antibodies (i.e. Fc containing proteins), whereas control EVs (B), which lack Fc binding polypeptides, do not have any antibodies bound to their surfaces.
  • A Fc binding polypeptides
  • B control EVs
  • FIG. 3 Flow cytometry data showing that the EVs comprising Fc binding polypeptides bind Fc containing proteins of interest (human IgG). The binding is very efficient to all bead populations included in the kit, including the unspecific/Isotype/negative control bead populations
  • FIG. 4 Anti-HER2 antibody increases uptake of antibody-decorated EVs as compared to isotype control-decorated and wild type EVs only in HER2 high-expressing cell line MDA-MB-361, but not in HER2 low-expressing cell line MDA-MB-231.
  • FIG. 5 Signals of fluorescently labelled antibodies are clearly present in cells treated with Fc-binding EVs having attached to their surfaces antibodies comprising Fc domains, while fluorescence signals are absent in untreated (1) or control EV treated (2) cells, measured by fluorescence microscopy (A) and flow cytometry (B).
  • Fc containing proteins such as antibodies can be delivered intracellularly by Fc binding EVs, and that binding to EVs dramatically increases uptake of antibodies into cells.
  • FIG. 6 Successful inhibition of NFkB-mediated intracellular signals when an anti-NFkB antibody is delivered into cells by Fc-binding EVs (i.e. EVs comprising at least one Fc binding polypeptide fused to at least one exosomal polypeptide).
  • Fc-binding EVs i.e. EVs comprising at least one Fc binding polypeptide fused to at least one exosomal polypeptide.
  • the present invention relates to EVs comprising at least one Fc binding polypeptide for use across a large number of research, diagnostic, and therapeutic applications.
  • the at least one Fc binding polypeptide is comprised in a fusion protein with an EV polypeptide, in order to increase the numbers of Fc binding polypeptides in each EV.
  • the Fc domain of an Fc containing protein (such as an antibody, which may be tagged with a detection moiety) is bound by the Fc binding polypeptide of the EV, thereby generating an EV having attached to its surface the Fc containing protein, resulting in a nanoparticle with broad utility techniques such as flow cytometry, nanoparticle tracking analysis, microscopy and electron microscopy, as a diagnostic tool, as an imaging tool, and for essentially any research, imaging, diagnostic, and therapeutic purpose.
  • Fc binding polypeptides described herein in connection with the EVs comprising fusion proteins comprising such Fc binding polypeptides are to be understood to be disclosed, relevant, and compatible with all other aspects, teachings and embodiments herein, for instance aspects and/or embodiments relating to the methods for producing or coating the EVs, or relating to the polynucleotide and polypeptide constructs described herein.
  • EVs comprising Fc binding polypeptides having attached to the EV a plurality of Fc containing proteins, as described in relation to their use as biological RM
  • EVs may naturally also be relevant in connection with other aspects and/or embodiments, for instance embodiments pertaining to the use of EVs as diagnostic tools and/or imaging tools in e.g. pathology and/or immuno-histochemistry.
  • all polypeptides and proteins identified herein can be freely combined in fusion proteins using conventional strategies for fusing polypeptides.
  • all Fc binding polypeptides described herein may be freely combined in any combination with one or more exosomal polypeptides.
  • Fc binding polypeptides may be combined with each other to generate constructs comprising more than one Fc binding polypeptide.
  • any and all features for instance any and all members of a Markush group
  • any and all other features for instance any and all members of any other Markush group
  • any Fc binding protein may be combined with any Fc containing protein such as any antibody
  • any exosomal polypeptide may be combined with any Fc binding polypeptide.
  • teachings herein refer to EVs (and/or the EV-anchored fusion protein—Fc containing protein complexes) in singular and/or to EVs as discrete natural nanoparticle-like vesicles it should be understood that all such teachings are equally relevant for and applicable to a plurality of EVs and populations of EVs and the EVs coated with Fc containing proteins.
  • the Fc binding polypeptides, the Fc containing proteins such as the antibodies, the EV-producing cell sources, the exosomal polypeptides, and all other aspects, embodiments, and alternatives in accordance with the present invention may be freely combined in any and all possible combinations without deviating from the scope and the gist of the invention.
  • any polypeptide or polynucleotide or any polypeptide or polynucleotide sequences (amino acid sequences or nucleotide sequences, respectively) of the present invention may deviate considerably from the original polypeptides, polynucleotides and sequences as long as any given molecule retains the ability to carry out the desired technical effect associated therewith.
  • the polypeptide and/or polynucleotide sequences according to the present application may deviate with as much as 50% (calculated using for instance BLAST or ClustalW) as compared to the native sequence, although a sequence identity that is as high as possible is preferable (for instance 60%, 70%, 80%, or e.g. 90% or higher).
  • the combination (fusion) of e.g. at least one Fc binding polypeptide and at least one exosomal protein implies that certain segments of the respective polypeptides may be replaced and/or modified and/or that the sequences may be interrupted by insertion of other amino acid stretches, meaning that the deviation from the native sequence may be considerable as long as the key properties (e.g. Fc binding properties, trafficking to the surface of exosomes, binding affinity, etc.) are conserved. Similar reasoning thus naturally applies to the polynucleotide sequences encoding for such polypeptides.
  • accession numbers and SEQ ID NOs mentioned herein in connection with peptides, polypeptides and proteins shall only be seen as examples and for information only, and all peptides, polypeptides and proteins shall be given their ordinary meaning as the skilled person would understand them.
  • the skilled person will also understand that the present invention encompasses not merely the specific SEQ ID NOs or the accession numbers referred to herein but also variants and derivatives thereof.
  • all accession numbers referred to herein are UniProtKB accession numbers as per the 22 Jun. 2017 version of the database, and all proteins, polypeptides, peptides, nucleotides and polynucleotides mentioned herein are to be construed according to their conventional meaning as understood by a skilled person.
  • extracellular vesicle or “EV” or “exosome” are used interchangeably herein and shall be understood to relate to any type of vesicle that is obtainable from a cell in any form, for instance a microvesicle (e.g. any vesicle shed from the plasma membrane of a cell), an exosome (e.g. any vesicle derived from the endo-lysosomal pathway), an apoptotic body (e.g. obtainable from apoptotic cells), a microparticle (which may be derived from e.g. platelets), an ectosome (derivable from e.g. neutrophils and monocytes in serum), prostatosome (e.g.
  • a microvesicle e.g. any vesicle shed from the plasma membrane of a cell
  • an exosome e.g. any vesicle derived from the endo-lysosomal pathway
  • an apoptotic body
  • EVs may vary considerably but an EV typically has a nano-sized hydrodynamic radius, i.e. a radius below 1000 nm.
  • EVs may be derived from any cell type, both in vivo, ex vivo, and in vitro.
  • the said terms shall also be understood to relate to extracellular vesicle mimics, cell membrane-based vesicles obtained through for instance membrane extrusion, sonication, or other techniques, etc.
  • the present invention normally relates to a plurality of EVs, i.e. a population of EVs which may comprise thousands, millions, billions or even trillions of EVs.
  • EVs may be present in concentrations such as 10 5 , 10 8 , 10 10 , 10 11 , 10 12 , 10 13 , 10 14 , 10 15 , 10 18 , 10 25 10 30 EVs (often termed “particles”) per unit of volume (for instance per ml), or any other number larger, smaller or anywhere in between.
  • the term “population”, which may e.g. relate to an EV comprising a certain fusion protein between an exosomal polypeptide and an Fc binding polypeptide which in turn may be bound to an Fc containing protein of interest, shall be understood to encompass a plurality of entities constituting such a population.
  • individual EVs when present in a plurality constitute an EV population.
  • the present invention pertains both to individual EVs and populations comprising EVs, as will be clear to the skilled person.
  • the EVs of the present invention may also comprise additional therapeutic and/or diagnostic agents, in addition to the Fc containing proteins which may be bound to the EV surfaces.
  • the EV may comprise diagnostic and tracing agents such as fluorophores, radioactive compounds, tracers, inorganic and organic compounds, imaging agents, etc.
  • the additional therapeutic agent may be at least one therapeutic small molecule drug.
  • the therapeutic small molecule drug may be selected from the group consisting of DNA damaging agents, agents that inhibit DNA synthesis, microtubule and tubulin binding agents, anti-metabolites, inducers of oxidative damage, anti-angiogenics, endocrine therapies, anti-estrogens, immuno-modulators such as Toll-like receptor agonists or antagonists, histone deacetylase inhibitors, inhibitors of signal transduction such as inhibitors of kinases, inhibitors of heat shock proteins, retinoids, inhibitors of growth factor receptors, anti-mitotic compounds, anti-inflammatories, cell cycle regulators, transcription factor inhibitors, and apoptosis inducers, and any combination thereof.
  • the additional agent may be a therapeutic and/or diagnostic and/or imaging nucleic acid-based agent.
  • nucleic acid-based therapeutic agents may be selected from the group comprising single-stranded RNA or DNA, double-stranded RNA or DNA, oligonucleotides such as siRNA, splice-switching RNA, CRISPR guide strands, short hairpin RNA (shRNA), miRNA, antisense oligonucleotides, polynucleotides such as mRNA, plasmids, or any other RNA or DNA vector.
  • nucleic acid-based agents which are chemically synthesized and/or which comprise chemically modified nucleotides such as 2′-O-Me, 2′-O-Allyl, 2′-O-MOE, 2′-F, 2′-CE, 2′-EA 2′-FANA, LNA, CLNA, ENA, PNA, phosphorothioates, tricyclo-DNA, etc.
  • the EVs as per the present invention may comprise additional therapeutic and/or diagnostic agents which may be protein and/or peptides.
  • Such proteins and/or peptides may be present inside of the EVs, inserted into the EV membrane or in association with the EV membrane, or may be protruding from the EV into the extravesicular environment.
  • Such protein and/or peptide agents may be selected from a group of non-limiting examples including: antibodies, intrabodies, single chain variable fragments (scFv), affibodies, bi- and multispecific antibodies or binders, affibodies, darpins, receptors, ligands, enzymes for e.g.
  • enzyme replacement therapy or gene editing tumor suppressors, viral or bacterial inhibitors, cell component proteins, DNA and/or RNA binding proteins, DNA repair inhibitors, nucleases, proteinases, integrases, transcription factors, growth factors, apoptosis inhibitors and inducers, toxins (for instance pseudomonas exotoxins), structural proteins, neurotrophic factors such as NT3/4, brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF) and its individual subunits such as the 2.5S beta subunit, ion channels, membrane transporters, proteostasis factors, proteins involved in cellular signaling, translation- and transcription related proteins, nucleotide binding proteins, protein binding proteins, lipid binding proteins, glycosaminoglycans (GAGs) and GAG-binding proteins, metabolic proteins, cellular stress regulating proteins, inflammation and immune system regulating proteins, mitochondrial proteins, and heat shock proteins, etc.
  • toxins for instance pseudomonas exotoxins
  • structural proteins neurotrophic factors such as NT3/
  • the therapeutic agent may be a CRISPR-associated (Cas) polypeptide (such as Cas9 (as a non-limiting example the accession number Q99ZW2)) with intact nuclease activity which is associated with (i.e. carries with it) an RNA strand that enables the Cas polypeptide to carry out its nuclease activity in a target cell once delivered by the EV.
  • Cas polypeptide may be catalytically inactive, to enable targeted genetic engineering.
  • Yet another alternative may be any other type of CRISPR effector such as the single RNA-guided endonuclease Cpf1 (from species such as Acidaminococcus or Lachnospiraceae) (as a non-limiting example the accession number U2UMQ6 and A0Q7Q2).
  • Cpf1 from species such as Acidaminococcus or Lachnospiraceae
  • accession number U2UMQ6 and A0Q7Q2 accession number
  • Additional preferred embodiments include therapeutic proteins selected from the group comprising enzymes for lysosomal storage disorders, for instance glucocerebrosidases such as imiglucerase, alpha-galactosidase, alpha-L-iduronidase, iduronate-2-sulfatase and idursulfase, arylsulfatase, galsulfase, acid-alpha glucosidase, sphingomyelinase, galactocerebrosidase, galactosylceramidase, glucosylceramidase (as a non-limiting example the accession number P04062) ceramidase, alpha-N-acetylgalactosaminidase, beta-galactosidase, lysosomal acid lipase, acid sphingomyelinase, NPC1 (as a non-limiting example the accession number 015118
  • the therapeutic protein may be e.g. an intracellular protein that modifies inflammatory responses, for instance epigenetic proteins such as methylases and bromodomains, or an intracellular protein that modifies muscle function, e.g. transcription factors such as MyoD (as a non-limiting example the accession number P15172) or Myf5, proteins regulating muscle contractility e.g.
  • an intracellular protein that modifies inflammatory responses for instance epigenetic proteins such as methylases and bromodomains
  • an intracellular protein that modifies muscle function e.g. transcription factors such as MyoD (as a non-limiting example the accession number P15172) or Myf5, proteins regulating muscle contractility e.g.
  • all of the above-mentioned therapeutic proteins may be engineered to contain an Fc domain, in order to enable binding to the Fc binding polypeptide present on the EVs.
  • Another non-limiting example is the fusion of an Fc domain onto the enzyme NPC1 for subsequent delivery into a target cell.
  • Yet another non-limiting example which may be utilized to improve intracellular bioactivity of EV-delivered Fc containing proteins (for instance Fc-Cas9 or antibodies) is to fuse an Fc domain to an endosomal escape peptide or protein, such as HA2, cell-penetrating peptides (CPPs) such as the TAT peptide, transportan, peneratin, poly-lysine, or gp41, cholera toxin, Shiga toxin, saporin, diphtheria toxin peptides, etc. Displaying such endosomal escape domains on the surface of an EV may enhance both internalization into target cells and subsequent endosomal escape.
  • endosomal escape peptide or protein such as HA2, cell-penetrating peptides (CPPs) such as the TAT peptide, transportan, peneratin
  • an Fc domain can be fused onto a protein of interest is the fusion of an Fc domain onto Cas9, Cpf1, non-cleaving Cas variants, or any other type of gene editing protein or ribonucleoprotein (RNP) for EV-mediated delivery into a target cell.
  • an Fc domain is fused either N-terminally or C-terminally to Cas9, which has been pre-loaded in vitro or ex vivo with the single guide RNA (sgRNA) strand (Cas pre-loaded with RNA forms a so called ribonucleoprotein (RNP) complex).
  • sgRNA single guide RNA
  • RNP ribonucleoprotein
  • the resulting Fc domain-containing RNP complex thus formed is then allowed to be bound by the Fc binding polypeptides of a suitable EV to attached them to the EV surface, followed by delivery into target cells.
  • Creation of the RNP complex can be achieved in different ways and with different RNA components, such as conventional single guide RNA, a synthetic guide RNA comprising both the crRNA and the tracrRNA optionally combined with a hairpin loop, crRNA, tracrRNA, and various combinations thereof.
  • Repair templates for homology-directed recombination or non-homologous end-joining or any other repair or replacement mechanism may also be included in a pre-formed RNP which can then be attached to EVs using the Fc domain—Fc binding polypeptide linkage.
  • an antibody refers to a glycoprotein comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, or an antigen binding-portion thereof.
  • Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as V H ) and a heavy chain constant region.
  • Each light chain is comprised of a light chain variable region (abbreviated herein as V L ) and a light chain constant region.
  • the variable regions of the heavy and light chains contain a binding domain that interacts with an antigen.
  • V H and V L regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR).
  • CDR complementarity determining regions
  • FR framework regions
  • an antibody of interest preferably has an Fc domain or a derivative thereof to which the Fc binding polypeptides of the present invention can bind, in order to enable coating of the EV surface.
  • Antibodies of use in the invention may be monoclonal antibodies (mAbs) or polyclonal antibodies, preferably mAbs.
  • Antibodies of particular utility in the invention may be chimeric antibodies, CDR-grafted antibodies, nanobodies, human or humanised antibodies or any derivative thereof as long as it can be bound by the Fc binding polypeptide, which are typically comprised in the fusion proteins as per the present invention.
  • the production of antibodies is outside of the scope of the present invention but typically both monoclonal and polyclonal antibodies are raised experimental non-human mammals such as goat, rabbit, llama, camelids, rat or mouse, but suitable antibodies may also be the result of other production methodologies, e.g. the standard somatic cell hybridization technique of Kohler and Milstein. Hybridoma production in e.g. the mouse is a very well-established procedure and can be achieved using techniques well known in the art.
  • an antibody of use in the invention may be a human antibody, humanized antibody, and/or any type of chimeric antibody.
  • the term “human antibody”, as used herein, is intended to include antibodies having variable regions in which both the framework and CDR regions are derived from human germline immunoglobulin sequences.
  • the human antibodies of use in the invention may include amino acid residues not encoded by human germline immunoglobulin sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo).
  • antibody derivatives refers to any modified form of an antibody, e.g.
  • humanized antibody refers to antibodies in which CDR sequences derived from another mammalian species, such as a mouse, camelid, llama, etc., have been grafted onto human framework sequences. Additional framework region modifications may be made within the human framework sequences.
  • Antibodies in accordance with the present invention may include all isotypes and subtypes such as IgG (for instance IgG1, IgG2, IgG3, IgG4, IgG2a, IgG2d, and IgG2c), IgA, IgM, IgM, IgD, etc., and monomers, dimers, and oligomers thereof.
  • IgG for instance IgG1, IgG2, IgG3, IgG4, IgG2a, IgG2d, and IgG2c
  • IgA for instance IgG1, IgG2, IgG3, IgG4, IgG2a, IgG2d, and IgG2c
  • IgA IgA
  • IgM IgM
  • IgD IgD
  • monomers, dimers, and oligomers thereof monomers, dimers, and oligomers thereof.
  • antibodies as per the present invention may have several functions when displayed on EVs: (1) antibodies may target specific cell types, tissues, and/or organs, (2) diagnostic and/or therapeutic antibodies that interact with a target antigen of interest can be efficiently delivered to tissues of interest using EVs, (3) multiplexed antibodies on the surface of EVs may be significantly better at binding target antigens, (4) antibody-drug conjugates (ADCs) may be multiplexed on EVs to enhance the potency of e.g.
  • ADCs antibody-drug conjugates
  • antibodies bound by Fc binding polypeptide may have higher affinity for the target because of the binding between Fc binding polypeptide and the antibody Fc domain
  • antibodies coated onto EVs as per the present invention may be delivered intracellularly for diagnostic and/or therapeutic and/or imaging and/or research purposes.
  • antibodies and other Fc containing proteins as per the present invention are advantageously labelled with some form of detection moiety.
  • a detection moiety such as a fluorophore, a radioactive substance, a PET tracer, MRI agents, or any other type of detection moiety
  • a detection moiety such as a fluorophore, a radioactive substance, a PET tracer, MRI agents, or any other type of detection moiety
  • PET scans confocal microscopy and fluorescence microscopy
  • electron microscopy electron microscopy
  • X-ray scans CAT scans
  • flow cytometry nanoparticle tracking analysis, etc.
  • Fc containing protein and “protein comprising an Fc domain” and “Fc domain-containing protein” and “Fc domain containing protein” and “Fc domain protein” and similar terms are used interchangeably herein and shall be understood to relate to any protein, polypeptide, or peptide (i.e. any molecule comprising a sequence of amino acids) which comprises at least one Fc domain, either naturally or as a result of engineering of the protein in question to introduce an Fc domain.
  • Fc stands for “fragment crystallizable”, which is the name of the tail regions of antibodies. Fc domains can however also be created and used on other proteins, not only antibodies.
  • Fc domain-containing proteins include antibodies and antibody derivatives, Fc-modified decoy receptors and/or signal transducers such as interleukin decoy receptors for IL1, IL2, IL3, IL4, IL5, IL6 (such as the signal transducer gp130 (as a non-limiting example the accession number P40189)), IL7, IL8, IL9, IL10, IL11, IL12, IL13, IL14, IL15, IL17 (such as IL17R, with as a non-limiting example the accession number Q96F46), IL23 (such as IL23R, as a non-limiting example the accession number Q5VWK5), etc., Fc domain-containing bi- and multispecific binders, any type of Fc domain-containing receptors or ligands, Fc domain-modified enzymes for e.g.
  • Suitable Fc domains that may be fused with a protein of interest natively lacking an Fc domain include the following non-limiting examples: human IGHM (as a non-limiting example the accession number P01871), human IGHA1 (as a non-limiting example the accession number P01876), human IGHA2 (as a non-limiting example the accession number P01877), human IGKC (as a non-limiting example the accession number P01834), human IGHG1 (as a non-limiting example the accession number P01857), human IGHG2 (as a non-limiting example the accession number P01859), human IGHG3 (as a non-limiting example the accession number P01860), human IGHG4 (as a non-limiting example the accession number P0186
  • any protein of interest may be modified to incorporate an Fc domain.
  • proteins onto which an Fc domain can be introduced include for instance tumor suppressors, viral or bacterial inhibitors, cell component proteins, DNA and/or RNA binding proteins, DNA repair inhibitors, nucleases, proteinases, integrases, transcription factors, growth factors, apoptosis inhibitors and inducers, toxins (for instance pseudomonas exotoxins), structural proteins, neurotrophic factors such as NT3/4, brain-derived neurotrophic factor (BDNF) and nerve growth factor (NGF) and its individual subunits such as the 2.5S beta subunit, ion channels, membrane transporters, proteostasis factors, proteins involved in cellular signaling, translation- and transcription related proteins, nucleotide binding proteins, protein binding proteins, lipid binding proteins, glycosaminoglycans (GAGs) and GAG-binding proteins, metabolic proteins, cellular stress regulating proteins, inflammation and immune system regulating proteins, mitochondrial proteins, and heat shock proteins,
  • proteins of interest is not exhaustive and other proteins may also be relevant, as long as the protein either comprises an Fc domain or as long as it is possible to engineer the protein in question to comprise an Fc domain.
  • One non-limiting example of such engineering of a protein to introduce an Fc domain includes adding an Fc domain to a decoy receptor, e.g. adding an Fc domain onto the Cas9 enzyme for bioactive delivery into target cells to enable gene editing.
  • Another non-limiting example of such engineering of a protein to introduce an Fc domain includes adding an Fc domain onto an enzyme for enzyme replacement therapy (for instance Fc domain-glucocerebrosidase or Fc domain- ⁇ -galactosidase or Fc domain-NPC1).
  • Fc domain-containing proteins as per the present invention may be essentially any protein of interest that contains an Fc domain, either naturally or as a result of introduction thereof.
  • all Fc domain containing proteins may be modified to incorporate a detection moiety, in order to enable detection and tracing of the molecule in question and/or of the EV in question.
  • Fc binding polypeptide and “Fc binding protein” and “Fc binder” and “Fc-binding protein” and “binder” are used interchangeably herein and shall be understood to relate to any protein, polypeptide, or peptide (i.e. any molecule comprising a sequence of amino acids) which can bind an Fc domain of any protein of interest.
  • the Fc binding polypeptides of the present invention are derived from various sources that are either human or non-human (e.g.
  • mammal sources, bacteria, etc. they have high affinity for Fc domains of various antibody isotypes, subtypes, and species (for instance IgG (and more specifically IgG1, IgG2, IgG3, IgG4, IgG2a, IgG2d, and/or IgG2c), IgA, IgM, IgM, IgD, etc.), and they can be fused to EV proteins.
  • IgG and more specifically IgG1, IgG2, IgG3, IgG4, IgG2a, IgG2d, and/or IgG2c
  • IgA IgM
  • IgM IgM
  • IgD IgD
  • Non-limiting examples of Fc binding polypeptides in accordance with the present invention include, in addition to other Fc binding polypeptides mentioned through the present application, Protein A (as a non-limiting example the SEQ ID NO 77), Protein G (as a non-limiting example the SEQ ID NO 78), Protein A/G (as a non-limiting example the SEQ ID NO 72), Z domain (as a non-limiting example the SEQ ID NO 73), ZZ domain (two operably linked copies of as a non-limiting example the SEQ ID NO 73, i.e.
  • the Fc containing proteins are often described herein as being “attached to” an EV and/or to an Fc binding polypeptide.
  • EVs are sometimes referred to as being “coated by” Fc containing proteins, or as having “bound to their surface” or “attached to their surface” the Fc containing proteins.
  • the EV which comprises the Fc binding polypeptide therefore has attached to it, by virtue of the chemical bond, the Fc domain of the Fc containing protein.
  • an EV may consequently have a plurality of such Fc containing proteins bound (attached) to it, resulting in a form of coating when the binding is taking place on the EV surface.
  • EV protein and “EV polypeptide” and “exosomal polypeptide” and “exosomal protein” are used interchangeably herein and shall be understood to relate to any polypeptide that can be utilized to transport a polypeptide construct (which typically comprises, in addition to the EV protein, at least one Fc binding polypeptide and optionally additional polypeptides and/or linkers) to a suitable vesicular structure, i.e. to a suitable EV. More specifically, these terms shall be understood as comprising any polypeptide that enables transporting, trafficking or shuttling of a fusion protein construct to a vesicular structure, such as an EV.
  • exosomal polypeptides are for instance CD9 (as a non-limiting example the SEQ ID NO 1), CD53 (as a non-limiting example the SEQ ID NO 2), CD63 (as a non-limiting example the SEQ ID NO 3), CD81 (as a non-limiting example the SEQ ID NO 4), CD54 (as a non-limiting example the SEQ ID NO 5), CD50 (as a non-limiting example the SEQ ID NO 6), FLOT1 (as a non-limiting example the SEQ ID NO 7), FLOT2 (as a non-limiting example the SEQ ID NO 8), CD49d (as a non-limiting example the SEQ ID NO 9), CD71 (also known as the transferrin receptor) (as a non-limiting example the SEQ ID NO 10) and its endosomal sorting domain, i.e.
  • the transferrin receptor endosomal sorting domain (as a non-limiting example the SEQ ID NO 23), CD133 (as a non-limiting example the SEQ ID NO 11), CD138 (syndecan-1) (as a non-limiting example the SEQ ID NO 12), CD235a (as a non-limiting example the SEQ ID NO 13), ALIX (as a non-limiting example the SEQ ID NO 14), Syntenin-1 (as a non-limiting example the SEQ ID NO 15), Syntenin-2 (as a non-limiting example the SEQ ID NO 16), Lamp2b (as a non-limiting example the SEQ ID NO 17), syndecan-2 (as a non-limiting example the SEQ ID NO 20), syndecan-3 (as a non-limiting example the SEQ ID NO 21), syndecan-4 (as a non-limiting example the SEQ ID NO 22), TSPAN8, TSPAN14, CD37, CD82, CD151, CD231, CD102, NOT
  • At least one exosomal polypeptide is fused to at least one Fc binding polypeptide, in order to form a fusion protein present in an EV.
  • fusion proteins may also comprise various other components to optimize their function(s), including linkers, transmembrane domains, cytosolic domains, multimerization domains, etc.
  • Source cell or “EV source cell” or “parental cell” or “cell source” or “EV-producing cell” or any other similar terminology shall be understood to relate to any type of cell that is capable of producing EVs under suitable conditions, for instance in suspension culture or in adherent culture or any in other type of culturing system.
  • Source cells as per the present invention may also include cells producing exosomes in vivo.
  • the source cells per the present invention may be select from a wide range of cells and cell lines, for instance mesenchymal stem or stromal cells or fibroblasts (obtainable from e.g.
  • amnion cells and more specifically amnion epithelial cells optionally expressing various early markers, myeloid suppressor cells, M2 polarized macrophages, adipocytes, endothelial cells, fibroblasts, etc.
  • EVs may be derived from essentially any cell source, be it a primary cell source or an immortalized cell line.
  • the EV source cells may be any embryonic, fetal, and adult somatic stem cell types, including induced pluripotent stem cells (iPSCs) and other stem cells derived by any method.
  • iPSCs induced pluripotent stem cells
  • the source cell may be either allogeneic, autologous, or even xenogeneic in nature to the patient to be treated, i.e. the cells may be from the patient himself or from an unrelated, matched or unmatched donor.
  • allogeneic cells may be preferable from a medical standpoint, as they could provide immuno-modulatory effects that may not be obtainable from autologous cells of a patient suffering from a certain indication.
  • allogeneic MSCs may be preferable as EVs obtainable from such cells may enable immuno-modulation via e.g. macrophage and/or neutrophil phenotypic switching (from pro-inflammatory M1 or N1 phenotypes to anti-inflammatory M2 or N2 phenotypes, respectively).
  • the present invention relates to the use of EVs comprising at least one Fc binding polypeptide as a research tool.
  • Non-limiting uses of relevance include the use of the Fc binding EVs in a detection kit, as a biological RM, as a control and/or a standard in flow cytometry, imaging flow cytometry, nanoparticle tracking analysis, nanoimaging, confocal microscopy, fluorescence microscopy, dynamic light scattering, electron microscopy, luminescence-based detection, fluorescence correlation spectroscopy, fluorescence resonance energy transfer (FRET)-based techniques, positive or negative selection techniques based on magnetic, fluorescent, and/or buoyancy-based labelling, positive or negative selection techniques based on particle density, charge or size, or in essentially any other technique or method wherein an EV with the ability to bind to Fc domain containing proteins (such as antibodies) can be useful.
  • the at least one Fc binding polypeptide which is comprised in the EV forms part of a fusion
  • the EVs as per the present invention are highly advantageous for various research, diagnostic, imaging, and therapeutic uses in particular when the Fc binding polypeptide of the EV binds to a protein comprising an Fc domain.
  • the binding between the Fc binding polypeptide of the EVs and an Fc containing protein results in the formation of a nano-sized EV-Fc protein complex, with extraordinary utility in e.g. flow cytometry, as a transport vehicle for Fc containing proteins such as antibodies, in nanoparticle tracking analysis, in dynamic light scattering, in electron microscopy, and/or in various other types techniques.
  • the use of the EVs as per the present invention includes attaching an antibody to the at least one Fc binding polypeptide, and in even more preferred embodiments the antibody is labelled with some form of detection moiety.
  • Suitable detection moieties and/or agents which may be attached the antibodies (or to any other Fc containing protein) are fluorophores, radioactive labels, PET ligands, MRI agents, nanoparticles, inorganic and/or compounds, enzymes, or any other suitable detection moiety adapted to the method in which the EVs are used.
  • the present invention provides for a vesicular reference material (RM) based on the EVs disclosed herein.
  • RM can mean any material that can be used for the purpose of standardization, positive control, calibration control, and/or compensation control or any other type of reference control, in any kind of assay, method or application.
  • the optimal RM would be a biologically derived vesicle, which is why the Fc binding polypeptide-containing EVs of the present are optimally suited for this purpose.
  • the present invention relates to an RM comprising a population of EVs as described herein, i.e.
  • EVs comprising an Fc binding polypeptide, which optionally is comprised in a fusion protein with at least one EV protein.
  • the Fc binding polypeptides bind to an Fc containing protein (such as an antibody), which adds an additional layer of information and functionality to the RM.
  • the RM may be present in any physical form, such as in a liquid, in a powder, in an aerosol, as a freeze-dried material, etc.
  • biologically relevant RMs are highly sought after not only within the EV field but also more broadly across the sciences and the engineered EVs of the present invention represent an almost perfect RM for many applications from flow cytometry and nanoparticle tracking analysis to fluorescence microscopy and electron microscopy.
  • the at least one Fc binding polypeptide comprised in the EV forms part of a fusion protein together with at least one exosomal polypeptide.
  • the fusion with at least one EV protein normally enhances the trafficking to EVs and subsequently the incorporation and/or display of the Fc binding polypeptide.
  • the Fc binding polypeptide present in and/or on the EV is clearly intended to bind to, and thereby attach to the EV, proteins containing Fc domains, such as antibodies and/or proteins onto which an Fc domain has been fused. The binding naturally takes place between the Fc binding polypeptide of the EV and the Fc domain of the protein of interest, typically via a conventional non-covalent interaction.
  • the biological RM has attached to it an Fc containing protein in the form of an antibody.
  • Fc containing protein has attached to it at least one fluorophore, at least one radioactive label, at least one PET ligand, at least one MRI agent, or any other detection moiety, in order to enable detection, tracing and imaging of the RM in vitro, in vivo, ex vivo, or in any research setting.
  • the research settings in which the biological RM may be used include the following non-limiting examples: flow cytometry, imaging flow cytometry, nanoparticle tracking analysis, nanoimaging, confocal microscopy, fluorescence microscopy, dynamic light scattering, electron microscopy, luminescence-based detection, fluorescence correlation spectroscopy, fluorescence resonance energy transfer (FRET)-based techniques, positive or negative selection techniques based on magnetic, fluorescent, and/or buoyancy-based labelling, positive or negative selection techniques based on particle density, charge or size, or any combination thereof.
  • flow cytometry imaging flow cytometry
  • nanoparticle tracking analysis nanoimaging
  • confocal microscopy fluorescence microscopy
  • dynamic light scattering electron microscopy
  • luminescence-based detection luminescence-based detection
  • fluorescence correlation spectroscopy fluorescence correlation spectroscopy
  • FRET fluorescence resonance energy transfer
  • the present invention relates to an in vitro, in vivo and/or ex vivo method for delivery of at least one type of Fc containing protein into a target cell, comprising (i) providing an EV comprising at least one Fc binding polypeptide, (ii) allowing the Fc binding polypeptide to bind the Fc containing protein, and (iii) contacting a target cell with the EV having attached to its Fc binding polypeptide the Fc containing protein.
  • the at least one Fc binding polypeptide may form part of a fusion protein together with at least one exosomal polypeptide, and optionally with various other polypeptides (such as linkers, multimerization domains, cytokine receptors and signal transducers, etc.).
  • the Fc containing protein is an antibody.
  • the Fc containing protein is attached to at least one fluorophore, at least one radioactive label, at least one PET ligand, or any other detection moiety.
  • the present invention relates to a detection kit comprising an EV, wherein the EV comprises at least one Fc binding polypeptide (fused to at least one exosomal polypeptide), wherein the Fc binding polypeptide is optionally bound to at least one an Fc containing protein.
  • Antibodies are clearly particularly suited for detection of various target antigens and with the aid of the EVs as per the present invention not only extracellular but also intracellular targets can be probed.
  • the Fc containing protein e.g. at least one type of antibody
  • detection moiety is completely dependent on the detection method being applied but suitable detection moieties may be select from for instance the following non-limiting examples: a fluorophore, a radioactive label, a PET ligand, an MRI agent, an enzyme for enzymatic detection, a colorimetric detection moiety, a bioluminescence and/or chemiluminescence detection moiety, inorganic or organic compounds, metals, quantum dots, nanoparticles (for instance gold nanoparticles), or any other detection moiety dependent on the detection method one intends to applied.
  • suitable detection moieties may be select from for instance the following non-limiting examples: a fluorophore, a radioactive label, a PET ligand, an MRI agent, an enzyme for enzymatic detection, a colorimetric detection moiety, a bioluminescence and/or chemiluminescence detection moiety, inorganic or organic compounds, metals, quantum dots, nanoparticles (for instance gold nanoparticles), or any other detection moiety dependent on
  • the present invention allows for detection both inside and outside target cells, and also in the cell membrane, meaning that extracellular, membrane-associated and/or intracellular biomolecules can be probed using the EV-based detection kit of the present invention.
  • the detection of a particular biomolecule may take place in vitro, in vivo and/or ex vivo.
  • the sample (such as an animal, tissue, organ, cell, subcellular organelle, body fluid, etc.) may be visualize and/or imaged either alive or dead, e.g. frozen, preserved, fixed or conserved for e.g. immuno-histochemistry, or on slides and grids for microscopy and electron microscopy.
  • the detection kit as per the present invention may be utilized in flow cytometry, nanoparticle tracking analysis, nanoimaging, confocal microscopy, fluorescence microscopy, dynamic light scattering, electron microscopy, luminescence-based detection, fluorescence correlation spectroscopy, fluorescence resonance energy transfer (FRET)-based techniques, positive or negative selection techniques based on magnetic, fluorescent, and/or buoyancy-based labelling, positive or negative selection techniques based on density, charge or size, or any combination of such methods.
  • the detection kit would be designed or formulated to enable the bond between the Fc binding polypeptide-containing EVs and the Fc containing protein to remain intact under various conditions, and occasionally to release the Fc containing proteins under other conditions.
  • the complex between the EVs and the Fc containing proteins may be present in various physical and chemical states, e.g. in solution, in a gel, in an emulsion, in a suitable buffer, in lyophilized form, in nebulized form, in particulate form, in a hydrogel, in a liposomal formulation, in a polymer formulation, etc.
  • the present invention relates to a kit of parts comprising (i) an EV comprising at least one Fc binding polypeptide, and (ii) at least one Fc containing protein.
  • the at least one Fc binding polypeptide may be comprised in a fusion protein together with at least one exosomal polypeptide and optionally other polypeptides and domains thereof.
  • the components (i) and (ii) may be present e.g. in different containers, or in the same container, depending on e.g. how the kit is to be used, stored, sold, and shipped.
  • the components (i) and (ii) may be mixed immediately prior to use or they may be pre-mixed and shipped as a nanoparticle complex between the EVs and the Fc containing protein.
  • the present invention pertains to a nanoparticle complex between (i) an EV comprising at least one Fc binding polypeptide and (ii) an Fc containing protein.
  • the at least one Fc binding polypeptide may form part of a fusion protein together with at least one exosomal polypeptide, in order to increase its incorporation into the EV and/or the display of the Fc binding polypeptide on the surface of an EV.
  • the nanoparticle complex formed between the engineered EV and the Fc containing protein can be schematically described as a nanoparticle coated with the Fc containing protein (as an example, multiple copies of an antibody).
  • Antibodies constitute a particularly preferred embodiment of the present invention, as they exhibit high target specificity, are easy to develop, can be modified to incorporate detection moieties and, with the aid of the EVs of the present invention, can be delivered into target cells.
  • the nanoparticle complexes of the present invention have broad utility across research, diagnostics, imaging, analytics and therapy, and may be used as biological RM, as a research tool, as a diagnostic tool, an imaging tool, a detection kit, and/or for in vitro, in vivo and/or ex vivo delivery of different types of Fc containing proteins.
  • the EVs themselves comprise a detection moiety, which may optionally be combined with a detection moiety attached to the Fc containing protein (such as a fluorescently labelled antibody).
  • a detection moiety attached to the Fc containing protein (such as a fluorescently labelled antibody).
  • detection moieties may be used, for instance fluorophores, dyes, fluorescent proteins such as green fluorescent protein, red fluorescent protein, yellow fluorescent protein, and any fluorescent protein; firefly or renilla luciferase, NanoLuciferase and other types of enzymes producing bioluminescence signals; radioactive agents; PET and MRI agents and tracers; nanoparticles, inorganic compounds, metals and metal ions, either solubilized or in various complexes, etc.
  • An advantageous embodiment is EVs comprising GFP and/or luciferase/NanoLuciferase, combined with e.g. fluorescently labelled antibodies (or any other Fc containing protein) attached to the Fc binding polypeptides of the EVs.
  • fluorescently labelled antibodies or any other Fc containing protein attached to the Fc binding polypeptides of the EVs.
  • adding any other type of detection moiety to the EV as such provides for detection through more than one means which may be highly useful in e.g. microscopy, flow cytometry, nanoparticle tracking analysis, dynamic light scattering, and in various other techniques.
  • the Fc binding polypeptides of the present invention may be of non-human origin or of human origin.
  • the Fc binders may be obtained e.g. from bacteria, viruses, or non-human mammals. In another embodiment, the Fc binders are of human or mammal origin.
  • the at least one Fc binding polypeptide may be selected from the group comprising Protein A (as a non-limiting example the SEQ ID NO 77), Protein G (as a non-limiting example the SEQ ID NO 78), Protein A/G (as a non-limiting example the SEQ ID NO 72), Z domain (as a non-limiting example the SEQ ID NO 73), ZZ domain (as a non-limiting example the SEQ ID NO 74), Protein L (as a non-limiting example the pdb id no 1HEZ), Protein LG, human FCGRI (as a non-limiting example the SEQ ID NO 31), human FCGR2A (as a non-limiting example the accession number P12318), human FCGR2B (as a non-limiting example the accession number P31994), human FCGR2C (as a non-limiting example the accession number P31994), human FCGR3A (as a non-limiting example the accession number P08
  • Fc binding polypeptides which have been obtained from e.g. phage display screening and via bioinformatics, include the Fc binding peptides SPH (as a non-limiting example the SEQ ID NO 57), SPA (as a non-limiting example the SEQ ID NO 58), SPG2 (as a non-limiting example the SEQ ID NO 59), SpA mimic 1 (as a non-limiting example the SEQ ID NO 60), SpA mimic 2 (as a non-limiting example the SEQ ID NO 61), SpA mimic 3 (as a non-limiting example the SEQ ID NO 62), SpA mimic 4 (as a non-limiting example the SEQ ID NO 63), SpA mimic 5 (as a non-limiting example the SEQ ID NO 64), SpA mimic 6 (as a non-limiting example the SEQ ID NO 65), SpA mimic 7 (as a non-limiting example the SEQ ID NO 66), SpA mimic 8 (as a non--
  • Protein A/G is a recombinant genetically engineered protein comprised of 7 Fc-binding domains EDABC-C1C3, with the Protein A part being obtained from Staphylococcus aureus segments E, D, A, B and C, and the Protein G part from Streptococcus segments C1 and C3.
  • Protein A/G (as a non-limiting example the SEQ ID NO 72) has a broader binding capacity than either Protein A (as a non-limiting example the SEQ ID NO 77) or Protein G (as a non-limiting example the SEQ ID NO 78) alone and it has a broad binding affinity for antibodies from various species.
  • Protein A/G binds to various human, mouse and rat IgG subclasses such as the human IgG1, IgG2, IgG3, IgG4; mouse IgG2a, IgG2b, IgG3 and rat IgG2a, IgG2c.
  • Protein A/G binds to total IgG from cow, goat, sheep, horse, rabbit, guinea pig, pig, dog and cat.
  • Protein A/G has been engineered to remove the cell wall-binding region, the cell membrane-binding region and albumin-binding region to enable strong binding to the Fc domain of a protein of interest, such as an antibody.
  • the Fc binder comprises more than one Fc binding region, as is the case with Protein A, Protein G, and Protein A/G, in order to enable binding a wide range of antibodies.
  • the Fc binder may be multiplied in order to enable binding to more than one copy of an antibody of interest.
  • the short Z domain Fc binder may be included in the fusion protein in more than one copy, through an operational linkage allowing for binding to more than one Fc domain. This way it is possible to multiplex antibodies and other Fc domain-containing proteins not only between separate fusion proteins but also within one single fusion protein, which thus may bind more than one antibody.
  • Fc binding polypeptides are introduced into EV proteins belonging to the tetraspanin family (such as CD63) it may be advantageous to insert one Fc binder on one loop and another Fc binder (which can be the same or different) on another loop of the protein.
  • the Fc binder can be placed on inward-facing and/or outward-facing loops, depending on whether the Fc containing protein is meant to be loaded into the lumen of the EV or onto the surface of the EV.
  • the fusion proteins comprising the exosomal polypeptide and the Fc binding polypeptide may also contain additional polypeptides, polypeptide domains or sequences.
  • additional polypeptide domains may exert various functions, for instance such domains may (i) contribute to enhancing the EV surface display of the fusion protein, (ii) lead to clustering of the fusion proteins thereby increasing the avidity of the Fc binding polypeptides, (iii) function as linkers to optimize the interaction between the exosomal polypeptides and the Fc binding polypeptide, and/or (iv) improve anchoring in the EV membrane, as well as various other functions.
  • transmembrane domains of these additional polypeptides may be highly useful to optimize the insertion into the EV membrane and the display of the Fc binding polypeptide.
  • TNFR1 tumor necrosis factor receptor 1
  • the transmembrane domains of these additional polypeptides may be highly useful to optimize the insertion into the EV membrane and the display of the Fc binding polypeptide.
  • various transmembrane domains may be highly advantageous as additional domains in the fusion proteins.
  • an additional polypeptide domain such as the transmembrane domain of TNFR or the transmembrane domain of gp130, for instance between syntenin and the Fc binding polypeptide of the fusion protein.
  • Further additional domains may include multimerization domains such as fold-on domains, leucine zipper domains and/or trimerization domains, in order to increase surface display and/or avidity. A non-limiting schematic example of this is shown below:
  • the exosomal polypeptide may be selected from the group comprising CD9, CD53, CD63, CD81, CD54, CD50, FLOT1, FLOT2, CD49d, CD71, CD133, CD138, CD235a, ALIX, Syntenin-1, Syntenin-2, Lamp2b, TSPAN8, syndecan-1, syndecan-2, syndecan-3, syndecan-4, TSPAN14, CD37, CD82 (as a non-limiting example the SEQ ID NO 24), CD151, CD231, CD102, NOTCH1, NOTCH2, NOTCH3, NOTCH4, DLL1, DLL4, JAG1, JAG2, CD49d/ITGA4, ITGB5, ITGB6, ITGB7, CD11a, CD11b, CD11c, CD18/ITGB2, CD41, CD49b, CD49c, CD49e, CD51, CD61, CD104, Fc receptors, interleukin receptors, immunoglobulins, MHC-I or MHC-II components, CD2,
  • Particularly advantageous fusion proteins as per the present invention may comprise the human exosomal proteins CD63, CD81, CD9, CD71 (transferrin receptor), Lamp2, and syntenin, fused to at least one copy of the following Fc binding polypeptides: Z domain, Protein A, Protein G, Protein A/G, FCGRI, human FCGR2A, human FCGR2B, human FCGR2C, human FCGR3A, human FCGR3B, human FCGR3C, human FCAMR, human FCAR, and human FCERA.
  • Fc binding polypeptides Z domain, Protein A, Protein G, Protein A/G, FCGRI, human FCGR2A, human FCGR2B, human FCGR2C, human FCGR3A, human FCGR3B, human FCGR3C, human FCAMR, human FCAR, and human FCERA.
  • fusion of two Z domains to the EV protein CD63 results in a highly potent Fc binder which is displayed in high quantities on the surface of EVs, as a consequence of the small size of the Z domain and the high EV surface expression of CD63.
  • Display of the Fc binder on the outer surface of EVs is naturally preferable in order to enable exogenous binding of Fc domain-containing proteins of interest.
  • Z domains may be inserted into the first and second loop of CD63, to enable display on the outer EV surface after anchoring of CD63 into the EV membrane.
  • suitable additional polypeptides and polypeptide domains and linkers may also be included in the fusion proteins, which normally comprises an exosomal polypeptide and an Fc binding polypeptide.
  • additional polypeptides include domains from various cytokine receptors such as TNFR1 and TNFR2, the IL6 signal transducer gp130, and various other cytokines and cytokine-related polypeptides.
  • cytokines and cytokine-related polypeptides may alone be able to transport Fc binding polypeptides to EVs.
  • Linkers of particular utility are multiples and/or combinations of small and flexible amino acids such as glycine (G) and serine (S), typically denoted GS, for instance 2XGS or 4XGS. His tags for simplifying purification and assaying may also be added, both C terminally and N terminally, and so may various fluorescent proteins such as GFP.
  • G glycine
  • S serine
  • His tags for simplifying purification and assaying may also be added, both C terminally and N terminally, and so may various fluorescent proteins such as GFP.
  • the following are particularly advantageous non-limiting examples of fusion proteins comprising at least one exosomal polypeptide and at least one Fc binding polypeptide, often connected via linkers and optionally including an additional polypeptide or polypeptide domain:
  • fusion proteins are merely examples of the many engineering possibilities the present invention allows for and as such they are merely non-limiting embodiments of the present invention. All components of the fusion proteins as per the present invention may be freely combined, e.g. the fusion proteins may contain one or several exosomal polypeptides which may be placed C terminally, N terminally, or both, or anywhere in the fusion protein. Further, the fusion proteins may also contain one or several Fc binding polypeptides, which may be placed C terminally, N terminally, or both, or on one or more of any loops of e.g. transmembrane parts, or anywhere in the fusion protein.
  • exosomal polypeptide and more than one type of Fc binding polypeptide may be comprised in a single construct.
  • additional stretches of amino acids such as linkers (often comprising the amino acids glycine and serine) and His tags may be included to simplify purification, assaying and visualization.
  • linkers often comprising the amino acids glycine and serine
  • His tags may be included to simplify purification, assaying and visualization.
  • other peptides and polypeptide domains may also be included anywhere in the fusion protein sequence. For instance, various domains and regions from various cytokine receptors may advantageously be included, for instance various domains of TNFR1, TNFR2, IL17R, IL23R, gp130, IL6R, etc.
  • the Fc binding polypeptides may as above-mentioned bind to any protein comprising an Fc domain, not only antibodies but also other proteins comprising Fc domains, both naturally occurring and engineered Fc domain-containing proteins, such as the ones mentioned in several instances above.
  • the present invention results in EVs coated with a plurality of proteins comprising an Fc domain, through interaction between the Fc binding polypeptide and at least one Fc containing protein.
  • the interaction between the Fc binder and the Fc containing protein is normally based on non-covalent bonds between the Fc binding polypeptide and the Fc domain of the Fc containing protein.
  • one single EV may be coated with more than one type of Fc domain-containing protein.
  • the Fc binding EVs are coated with one antibody targeting a suitable target along the PD1 axis, whereas another antibody is targeting a suitable target along the CTLA4 axis.
  • the Fc binding EVs are coated with an antibody targeting an intracellular oncoprotein and a tumor suppressor fused to an Fc domain.
  • One single EV may also, as is typically the case, comprise a substantial plurality of one single type of Fc domain-containing protein, such as one type of monoclonal antibody.
  • ADCs antibody-drug conjugates
  • the EVs according to the present invention are coated with a plurality of proteins comprising an Fc domain.
  • a highly expressed EV protein such as CD63 or CD81 or syntenin one can achieve very dense coating of the surface of EVs via the interaction between the Fc binding polypeptide and the Fc domains of the Fc containing proteins.
  • the present invention may be coated with at least 10 proteins comprising an Fc domain, preferably at least 20 proteins comprising an Fc domain, even more preferably at least 30 proteins comprising an Fc domain.
  • Such proteins may be copies of the same protein (e.g. 50 antibodies targeting an intracellular protein attached on one single EV, by way of example) or more than one protein (e.g.
  • an intracellular protein and 40 Fc domain containing tumor suppressor proteins for instance.
  • an optimal combination of EV protein and Fc binder it may be possibly to increase the display further, in certain cases it may be possible to coat an EV with more than 50 proteins comprising an Fc domain, or even more than approximately 75 proteins comprising an Fc domain, or in certain instances even more than 100 Fc containing proteins per EV.
  • the present invention relates to methods for producing EVs capable of binding to proteins comprising an Fc domain, such as antibodies and proteins engineered to comprise Fc domains.
  • Such methods typically comprise the steps of (i) introducing into an EV source cell a polynucleotide construct which encodes at least one Fc binding polypeptide and optionally at least one exosomal polypeptide, and (ii) collecting EVs that have been secreted by the EV-producing source cells, wherein the EVs comprise the Fc binding polypeptide (optionally comprised in a fusion protein) which has been expressed from the polynucleotide construct.
  • the EVs comprising the Fc binding polypeptide may be purified using a suitable purification technique, followed by being exposed to an Fc domain-containing protein, such as an antibody, to enable binding of the Fc containing protein through interaction between the Fc binding polypeptide and the Fc domain of the protein of interest.
  • step (i) may also include expressing the Fc containing protein of interest from a polynucleotide construct in the same EV source cell, thereby achieving endogenous loading of the EV.
  • the Fc binding polypeptide (optionally comprised in a fusion protein with at least one exosomal polypeptide) and the Fc containing protein may be expressed from the same or from different polynucleotide construct, depending on the construct design.
  • the present invention relates to method for coating EVs with at least one protein comprising an Fc domain, such as an antibody. Such methods comprise the steps of (i) providing an EV comprising at least one Fc binding polypeptide comprising at least one Fc binding protein, optionally fused to at least one exosomal polypeptide, and (ii) allowing the Fc binding polypeptide to bind the Fc domain of at least one protein comprising an Fc domain.
  • the EV source cells used for production of EVs comprising the Fc binding polypeptides may be either stably or transiently transfected with the polynucleotide construct needed to generate the EVs carrying the Fc binding polypeptide-Fc containing protein complex.
  • Stable transfection is advantageous as it enables creation of master cell banks (MCBs) and working cell banks (WCBs).
  • transient transfection is also advantageous in certain instances, for example when assessing different constructs or e.g. when rapidly creating an autologous therapy comprising EVs obtained from a patient's own EV-producing cells. These methods may be followed by additional steps to optimize the EVs and the Fc containing proteins for application in research, diagnostics, imaging and therapy.
  • the EVs comprising Fc binding polypeptides may be formulated in a liquid formulation in a suitable vessel for storage and use.
  • a liquid formulation may be frozen, lyophilized, formulated in a lipid or protein formulation, and/or handled in any suitable way depending on the application in question.
  • the Fc containing protein may also be formulated as a liquid formulation but alternatively can also be formulated in another physical form, for instance as a lyophilized powder.
  • the different components of the detection kits and the kits of parts shall be designed and produced with the end application in mind, be it flow cytometry, fluorescence microscopy, electron microscopy, in vitro, in vivo, and/or ex vivo delivery methods, etc.
  • the present invention pertains to the use of EVs as delivery vehicles for antibodies and other Fc domain containing proteins of interest, in vitro, ex vivo and/or in vivo. Furthermore, the present invention also provides for the use of EVs attached to Fc containing proteins as delivery vehicles for other diagnostic, imaging, and/or therapeutic agents of interest. As a non-limiting example, EVs having attached to their surface a targeting antibody may also contain additional diagnostic and/or therapeutic agents which may be present either inside the EV and/or in the EV membrane.
  • an antibody-coated EV may be used to deliver an RNA therapeutics cargo (such as an mRNA, an siRNA, an oligonucleotide, etc.) to a target cell, tissue and/or organ.
  • RNA therapeutics cargo such as an mRNA, an siRNA, an oligonucleotide, etc.
  • EVs having attached to their surface an Fc containing targeting protein such as a scFv which have been engineered to contain an Fc domain
  • a therapeutic protein such as Cas9 for gene editing, optionally together with a CRISPR RNA guide strand.
  • the methods of the present invention may also comprise exposing the EV source cells to serum starvation, hypoxia, bafilomycin, or cytokines such as TNF-alpha and/or IFN-gamma, in order to influence the yield or properties of the resulting EVs.
  • the EV production scale and timeline will be heavily dependent on the EV-producing cell or cell line and may thus be adapted accordingly by a person skilled in the art.
  • the methods as per the present invention may further comprise an EV purification step, which may be carried out prior to co-incubating the EVs comprising the Fc binding polypeptide with the Fc domain-containing protein (such as an antibody) to be attached to the EVs.
  • EVs may be purified through a procedure selected from a group of techniques comprising liquid chromatography (LC), high-performance liquid chromatography (HPLC), bead-eluate chromatography, spin filtration, tangential flow filtration (TFF), hollow fiber filtration, centrifugation, immunoprecipitation, flow field fractionation, dialysis, microfluidic-based separation, etc., or any combination thereof.
  • the purification of the EVs is carried out using a sequential combination of filtration (preferably ultrafiltration (UF), tangential flow filtration or hollow fiber filtration) and size exclusion liquid chromatography (LC) or bead-eluate chromatography.
  • UF ultrafiltration
  • LC size exclusion liquid chromatography
  • the present invention pertains to pharmaceutical, diagnostic, and/or imaging compositions comprising EVs, normally in the form of populations of EVs, as per the present invention.
  • the compositions as per the present invention comprise one type of EVs (i.e. a population of EVs comprising a certain type of Fc binding protein and having attached to it one or more types of Fc containing proteins, such as antibodies) formulated with at least one acceptable excipient.
  • more than one type of EV population may naturally be comprised in a single composition, for instance in cases where a combination of antibodies is desirable.
  • a single EV or a single population of EVs may comprise more than one Fc-containing protein (e.g.
  • excipients may be selected from the group comprising any pharmaceutically acceptable and/or research grade material, composition or vehicle, for instance a solid or liquid filler, a diluent, an excipient, a carrier, a solvent or an encapsulating material, which may be involved in e.g. suspending, maintaining the activity of or carrying or transporting the EV population.
  • the present invention relates to EVs as per the present invention for use in medicine, for instance in imaging, diagnostics, and/or therapy or theranostics.
  • the EVs as per the present invention are used in medicine, it is in fact normally a population of EVs that is being used.
  • the dose of EVs administered to a patient will depend on the number of e.g. Fc containing proteins of interest that has been coated on the EV surface, the disease or the symptoms to be detected, diagnosed, treated or alleviated, the administration route, the mechanism of action of the any additional diagnostic, imaging and/or therapeutic agent itself, the inherent properties of the EVs, the presence of any targeting antibodies or other targeting entities, as well as various other parameters of relevance known to a skilled person.
  • the EVs of the present invention carrying the Fc containing proteins may be used for several different diagnostic, imaging, and/or therapeutic aspects.
  • the EVs are covered with antibodies or other Fc containing proteins that target a specific cell type, tissue, and/or organ. This is a highly powerful way of targeting EVs, which may comprise other imaging agents or pharmaceutical agents in addition to the Fc containing protein, to tissues of interest, and could represent a step chance in theranostics, diagnostics, imaging, and drug delivery.
  • antibodies or other Fc domain-containing proteins that interact with a target antigen of interest can be efficiently delivered to tissues of interest that are typically hard to reach, using EVs with ability to cross biological barriers.
  • coating of EVs with Fc containing proteins is a way of multiplexing the Fc containing protein of interest, in order to enhance or influence its target avidity or the conformation of its binding to a target of interest in vitro, ex vivo and in vivo.
  • the EVs as per the present invention enable improved delivery and efficacy of antibody-drug conjugates (ADCs) or receptor-drug conjugates, as multiplexing of ADCs may significantly enhance their therapeutic activity and their presence on EVs means they can also enter target cells.
  • ADCs antibody-drug conjugates
  • receptor-drug conjugates as multiplexing of ADCs may significantly enhance their therapeutic activity and their presence on EVs means they can also enter target cells.
  • the ability of EVs to enter target cells means that the EVs of the present invention opens up the entire intracellular space and make it druggable by essentially any protein comprising an Fc domain and/or any protein onto which an Fc domain can be fused (such as an enzyme for enzyme replacement therapy, nuclease such as Cas9, or a tumor suppressor such as any one of p53, pVHL, APC, CD95, ST5, YPEL3, ST7, and ST14).
  • any protein comprising an Fc domain and/or any protein onto which an Fc domain can be fused
  • nuclease such as Cas9
  • a tumor suppressor such as any one of p53, pVHL, APC, CD95, ST5, YPEL3, ST7, and ST14.
  • the EVs and the EV populations thereof as per the present invention may thus be used for diagnostic, imaging, research, prophylactic and/or therapeutic purposes, e.g. for use in the diagnosis, imaging, evaluation, prophylaxis and/or treatment and/or alleviation of various diseases and disorders.
  • a non-limiting sample of diseases wherein the EVs as per the present invention may be applied comprises Crohn's disease, ulcerative colitis, ankylosing spondylitis, rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, sarcoidosis, idiopathic pulmonary fibrosis, psoriasis, tumor necrosis factor (TNF) receptor-associated periodic syndrome (TRAPS), deficiency of the interleukin-1 receptor antagonist (DIRA), endometriosis, autoimmune hepatitis, scleroderma, myositis, stroke, acute spinal cord injury, vasculitis, Guillain-Barré syndrome, acute myocardial infarction, ARDS, sepsis, meningitis, encephalitis, liver failure, non-alcoholic steatohepatitis (NASH), non-alcoholic fatty liver disease (NAFLD), kidney failure, heart failure or any acute or chronic organ failure and
  • Acute lymphoblastic leukemia ALL
  • Acute myeloid leukemia Adrenocortical carcinoma
  • AIDS-related cancers AIDS-related lymphoma
  • Anal cancer Appendix cancer
  • Astrocytoma cerebellar or cerebral
  • Basal-cell carcinoma Bile duct cancer
  • Bladder cancer Bone tumor, Brainstem glioma, Brain cancer, Brain tumor (cerebellar astrocytoma, cerebral astrocytoma/malignant glioma, ependymoma, medulloblastoma, supratentorial primitive neuroectodermal tumors, visual pathway and hypothalamic glioma),
  • Breast cancer Bronchial adenomas/carcinoids, Burkitt's lymphoma, Carcinoid tumor (childhood, gastrointestinal), Carcinoma of unknown primary, Central nervous system lymphoma, Cerebellar astrocyto
  • the EVs as per the present invention may be administered to a human or animal subject via various different administration routes, for instance auricular (otic), buccal, conjunctival, cutaneous, dental, electro-osmosis, endocervical, endosinusial, endotracheal, enteral, epidural, extra-amniotic, extracorporeal, hemodialysis, infiltration, interstitial, intra-abdominal, intra-amniotic, intra-arterial, intra-articular, intrabiliary, intrabronchial, intrabursal, intracardiac, intracartilaginous, intracaudal, intracavernous, intracavitary, intracerebral, intracisternal, intracorneal, intracoronal (dental), intracoronary, intracorporus cavernosum, intradermal, intradiscal, intraductal, intraduodenal, intradural, intraepidermal, intraesophageal, intragastric, intraging
  • Suitable targeting antibodies in accordance with the present invention may target antigens deriving from e.g. tumors, solid organs, bodily structures, cell or tissue types.
  • Non-limiting examples of the origin of antigens that may be targeted by targeting antibodies include liver, lung, kidney, heart, pancreas, adrenal glands, thyroid glands, parathyroid glands, brain including all brain regions (for instance thalamus, hypothalamus, striatum, etc.), the blood-brain-barrier, the CNS, the PNS, bone marrow, the skin, the vascular system, the lymphatic system including the spleen, joints, eyes, muscle tissues, sites of inflammation, sites of injury, and cell types such as adipocytes, muscle cells (myoblasts and myotubes), satellite cells, cardiac cells, endothelial cells, fibroblasts, hepatocytes, renal cells, pericytes, neurons, glia cells, astrocytes, oligodendrocytes, macrophages, DC-
  • Non-limiting examples of antigens relevant for targeting cancer includes adenocarcinoma antigen, alpha-fetoprotein, BAFF, C242 antigen, CA-125, carbonic anhydrase 9 (CA-IX), disialoganglioside (GD2), 4-IBB, 5T4, CD22, CD221, CD23 (IgE receptor), CD28, CD30 (TNFRSF8), CD33, CD4, CD40, CD44 v6, CD51, CD52, CD56, CD74, CD80, CEA, CNT0888, CTLA-4, DR5, EGFR, EpCAM, CD3, FAP, fibronectin extra domain-B, folate receptor 1, GD2, GD3 ganglioside, glycoprotein 75, GPNMB, HER2/neu, HGF, human scatter factor receptor kinase, IGF-1 receptor, IGF-I, IgGI, LI-CAM, IL-13, IL-6, insulin-like growth factor I receptor, integrin ⁇ 5 ⁇ 1, integrin
  • suitable non-limiting examples of antibodies in accordance with the present invention may be any one or more of Abagovomab, Abciximab, Actoxumab, Adalimumab, Adecatumumab, Adotrastuzumab emtansine, Aducanumab, Afelimomab, Afutuzumab, Alacizumab Alemtuzumab, Alirocumab, Altumomab pentetate, Amatuximab, Anatumomab mafenatox, Anifrolumab, Anrukinzumab, Apolizumab, Arcitumomab, Aselizumab, Atezolizumab, Atinumab, Atlizumab, Atorolimuma, Avelumab, Bapineuzumab, Basiliximab, Bavituximab, Bectumomab, Belimuma
  • the present invention provides for the delivery of any antibody, regardless of whether its target is intracellular and/or extracellular.
  • the ability of the EVs of the present invention to efficiently internalize antibodies represent a step-change in monoclonal antibody development and may enable targeting antigens and targets across the entire intracellular compartment of target cells.
  • antibodies and Fc containing proteins as per the present invention may advantageously be labelled for detection and imaging purposes, for instance using fluorophores, MRI agents, PET agents, radioactive agents, enzymes, nanoparticles, metals, organic and inorganic compounds, etc.
  • Construct design and cloning Various protein constructs comprising at least one Fc binding polypeptide and optionally at least one exosomal polypeptide have been constructed, cloned into vectors and produced in several different EV-producing cell sources.
  • ORFs were typically generated by synthesis and cloned into the mammalian expression vector pSF-CAG-Amp. Briefly, synthesized DNA and vector plasmid were digested with enzymes Notl and Sall as per manufacturers instruction (NEB). Restricted, purified DNA fragments were ligated together using T4 ligase as per manufacturers instruction (NEB). Successful ligation events were selected for by bacterial transformation on ampicillin-supplemented plates. Plasmid for transfection was generated by ‘maxi-prep’, as per manufacturers instruction.
  • ORF sequences were purchased (Origene Technologies, Inc.) and amplified and cloned into the MSC A site of pIRES bicistronic expression vector (Clonetech, Laboratories Inc.) such that upon translation the optional exosomal polypeptide was fused to the Fc binding polypeptide in one construct, whereas the Fc containing protein of interest was translated separately (from a separate construct or from the same construct) and transported into the EV to be formed in the EV-producing cell source.
  • the pIRES vector enables bicistronic expression of both transgenes simultaneously, ensuring EV-producing cells would express both the Fc binding polypeptide (optionally as a fusion protein) and the Fc containing protein of interest simultaneously.
  • Plasmids were transformed into the NEB 5-alpha Competent E. coli cells (NEB, Inc.) and grown overnight in a shaking incubator according to manufacturer's recommendations. Plasm ids were isolated and purified using the ‘maxi-prep plasmid DNA purification kit’ (Qiagen), as per manufacturer's instruction.
  • non-viral transient transfection and exosome production was carried out in conventional 2D cell culture, whereas in other cases virus-mediated transduction was employed to create stable cell lines, which were typically cultured in bioreactors of different type.
  • virus-mediated transduction was employed to create stable cell lines, which were typically cultured in bioreactors of different type.
  • HEK293T cells were typically seeded into 15 cm dishes (9 ⁇ 10 6 cells per dish) and left overnight in serum-containing DMEM as recommended by ATCC. The following day the cells were transiently transfected with lipoplexed DNA added directly onto cells. Briefly, DNA and polyethyleneimine (PEI) were separately incubated in OptiMEM for 5 minutes before combining together for 20 minutes at room temperature. Lipoplexed DNA and cells were co-incubated for 6 hours following which conditioned culture media was changed to OptiMEM for 48 hours.
  • PEI polyethyleneimine
  • BM-MSCs bone marrow-derived mesenchymal stromal cells
  • WJ-MSCs Wharton's jelly-derived MSCs
  • amnion cells fibroblasts
  • fibroblasts various endothelial and epithelial cells
  • immune cells and cell lines included bone marrow-derived mesenchymal stromal cells (BM-MSCs) and Wharton's jelly-derived MSCs (WJ-MSCs), amnion cells, fibroblasts, various endothelial and epithelial cells, as well as various immune cells and cell lines.
  • cell sources such as BM-MSCs, WJ-MSC, fibroblasts, amnion cells, fibroblasts, various endothelial and epithelial cells, were virus-transduced, typically using lentivirus (LV).
  • LV lentivirus
  • 100.000 cells e.g. fibroblasts, MSCs, etc.
  • 200.000 cells e.g. HEK293T
  • Stable cells were cultured in either 2D culture or in bioreactors, typically hollow-fiber bioreactors or stir-rank bioreactors, and conditioned media was subsequently harvested for exosome preparation.
  • Various preparation and purification steps were carried out.
  • the standard workflow comprises the steps of pre-clearing of the supernatant, filtration-based concentration, chromatography-based removal of protein contaminants, and optional formulation of the resultant exosome composition in a suitable buffer for in vitro, ex vivo and/or in vivo assays.
  • Western blot is a highly convenient analytical method to evaluate the enrichment of fusion proteins in EVs. Briefly, SDS-PAGE was performed according to manufacturer's instruction (Invitrogen, Novex PAGE 4-12% gels), whereby 1 ⁇ 10 10 exosomes and 20 ug cell lysate were loaded per well. Proteins from the SDS-PAGE gel were transferred to PVDF membrane according to manufacturer's instruction (Immobilon, Invitrogen). Membranes were blocked in Odyssey blocking buffer (Licor) and probed with antibodies against the Fc binding polypeptide and/or the exosomal protein according to supplier's instruction (Primary antibodies—Abcam, Secondary antibodies—Licor). Molecular probes visualized at 680 and 800 nm wavelengths.
  • nanoparticle tracking analysis was performed with a NanoSight instrument equipped with analytical software.
  • NTA nanoparticle tracking analysis
  • Electron microscopy and fluorescence microscopy were frequently used to understand intracellular location and release and to quantitate and analyze EVs and EVs coated with labelled Fc containing proteins, e.g. antibodies.
  • EVs were isolated and purified using a variety of methods, typically a combination of filtration such as TFF and LC, in particular bead-elute LC. Typically, EV-containing media was collected and subjected to a low speed spin at 300 g for 5 minutes, followed by 2000 g spin for 10 minutes to remove larger particles and cell debris. The supernatant was then filtered with a 0.22 ⁇ m syringe filter and subjected to different purification steps.
  • the sample was collected according to the UV absorbance chromatogram and concentrated using an Amicon Ultra-15 10 kDa molecular weight cut-off spin-filter (Millipore) to a final volume of 100 ⁇ l and stored at ⁇ 80° C. for further downstream analysis.
  • Amicon Ultra-15 10 kDa molecular weight cut-off spin-filter (Millipore) to a final volume of 100 ⁇ l and stored at ⁇ 80° C.
  • media was concentrated and diafiltrated with KR2i TFF system using 100 kDa and 300 kDa hollow fibre filters and a sample analysed on a Tricorn 10/300 Sepharose 4 Fast Flow (S4FF) column (GE Healthcare Life Sciences).
  • Example 1 Binding of IgG to EVs Comprising Fc Binding Polypeptides (Fc-Binding EVs)
  • EVs were isolated from the conditioned medium from engineered HEK293T cells (control versus Fc-binding construct that stably express Gp130 Extracellular domain-2XGGGGS linker-Z domain-Gp130 transmembrane domain-Leucine Zipper-N terminal syntenin-His tag) using tangential flow filtration with 300 kd hollow fiber columns, followed by ultrafiltration using 10 kd spin filters for concentration. The binding capacity for IgG by the Fc-binding EVs were then assessed using electron microscopy and flow cytometry.
  • FIG. 3 respective left dotplots show hard-dyed capture bead populations using B1-A (Excitation: 488 nm, Emission Filter: 500-550 nm; Area) versus B2-A (Excitation: 488 nm, Emission Filter: 565-605 nm, Area) parameters.
  • Respective right plots show R1-A (Excitation: 635 nm, Emission Filter: 655-730 nm, Area) versus B2-A parameters, demonstrating binding of AlexaFluor647 labeled Fc-Fragments to EVs which have bound to the capture beads only in (C).
  • FIG. 3 shows that the Fc-binding EVs bind both to AlexaFluor647-labelled Fc fragments (human IgG) and very efficiently also to the Fc domains of all 39 different antibodies which are coated on all capture bead populations by the manufacturer included in the kit, including the two negative control bead populations.
  • Fc-binding EVs can be used for the purpose of standardization, positive control, calibration control or compensation control in any kind of assay, method or application that comprises the binding of antibodies or Fc containing proteins or probes to EVs.
  • the antibodies or Fc containing proteins will be labelled with a fluorophore or other kind of detection moiety. Since the signals expected from the Fc-mediated binding of antibodies or Fc containing proteins normally will be at least as high as a signal that would be expected from the specific complementary determining region (CDR)-mediated binding of an antibody to an EV, these Fc-binding EVs will represent a suitable positive control for any kind of assay, e.g.
  • CDR complementary determining region
  • flow cytometry based phenotyping of EVs and are also compatible with any kind of antibody that might be used in flow cytometry or for that matter for any other type of technique or assay (such as fluorescence microscopy, nanoimaging, nanoparticle tracking analysis, dynamic light scattering, electron microscopy using antibodies attached to a e.g. a gold nanoparticle, etc.).
  • technique or assay such as fluorescence microscopy, nanoimaging, nanoparticle tracking analysis, dynamic light scattering, electron microscopy using antibodies attached to a e.g. a gold nanoparticle, etc.
  • an EV entity that binds a given antibody or Fc-containing probe will also be suitable to monitor variation and to validate the complete setup over time, e.g. as a stable source of calibration in a diagnostics test or laboratory setting.
  • EVs were isolated from HEK293T cells (either stably expressing FCGR1A Extracellular domain-4XGSlinker-Lamp2b, the Fc binder FCGR1A alone, or their wild type controls) using ultrafiltration and size exclusion chromatography. EVs were labelled with PKH26 red fluorescent dye, and decorated with anti-HER2 antibody or its isotype control by co-incubating EVs and antibody for 1 h at 37° C. Unbound antibody was removed by size exclusion chromatography. Uptake of antibody decorated EVs was characterized in HER2 low-expressing cell line MDA-MB-231 and in HER2 high-expressing cell line MDA-MB-361 using flow cytometry. FIG.
  • EVs were isolated from the conditioned medium of Wharton's jelly-derived MSCs (either stably expressing TNFR Extracellular domain-2XGGGGS linker-Z domain-TNFR transmembrane domain-foldon-N terminal syntenin fusion proteins or control) using ultrafiltration and size exclusion chromatography.
  • Fc-binding EVs were employed for intracellular delivery of Abs, 4 ⁇ 10 ⁇ circumflex over ( ) ⁇ 11 EVs were incubated in 400 ⁇ l for 16 hours (overnight) with total 3 ⁇ g AlexaFluor488-labelled anti-Lamin B2 IgGs [abcam ab200426, Rabbit monocolonal EPR9701(B)].
  • Huh7 cells were plated in 48 well plates at 30,000 cells per well and incubated for 16 hours before 0.675 ⁇ 10 ⁇ circumflex over ( ) ⁇ 11 antibody-labelled EVs were added. Cells were incubated for 2 hours at 37° C. and 5% CO 2 in a humidified atmosphere before they were trypsinized and analyzed by fluorescence microscopy (A) and flow cytometry (B) as shown in FIG. 5 ; A) show green fluorescence signals merged with phase contrast images. Histograms in B) show the green fluorescence intensity on a logarithmic scale on the x-axis and the normalized frequency on the y-axis. 1: HuH7 cells not treated with any antibody or EVs.
  • FIG. 5 shows that signals of fluorescent antibodies are clearly present in cells treated with Fc-binding EVs plus antibody, while fluorescence signals are absent in untreated (1) or control EV treated (2). This demonstrates that antibodies can be delivered intracellularly via Fc-binding EVs, and that binding to EVs dramatically increases uptake of antibodies into cells.
  • anti-NFkB antibodies (anti-NFkB-Ab) were incubated with respective EVs for 1 h at 37° C.
  • a reporter cell line HEK cells stably expressing NFkB-luciferase, were treated with 5 ng/ml hTNF-alpha and the EV-Ab-mix. After 6 hours of treatment the luciferase activity was measured.
  • FIG. 6 shows successful inhibition when the anti-NFkB-ab is delivered by Fc-binding EVs.

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SG11201811152YA (en) 2019-01-30

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