Patent Application
20230310650
The invention provides an invasive recombinant bacterium for use in prevention and/or treatment of an immune-related disorder; said bacterial cell comprising one or more recombinant nucleic acid molecule(s) encoding one or more therapeutic agent(s) for use in prevention and/or treatment of said immune-related disease in a mammal in need thereof.
The cells of the mammalian immune system can be categorized as lymphocytes (T-cells, B-cells, and natural killer (NK) cells), granulocytes (Eosinophils, neutrophils, and basophils), and monocytes (macrophages and dendritic cells); which together provide resistance to infection, toxins and cancer. T-cells, B-cells, NK-cells together with basophil cells, are non-phagocytic, and comprise the main cells of the adaptive immune response, which includes the production of cytokines, antibodies, and complement proteins.
A wide range of diseases are attributable to the immune system. For example, when the immune system fails to distinguish self- from nonself-antigens, this results in a wide range of chronic autoimmune diseases (AIDs), whereby a self-reactive immune response, mediated by B-cell auto-antibodies and self-reactive T-cells, destroys the body's own tissues. Additionally, various types of cancer incapacitate the immune system, of itself, specifically blood cancers such as leukaemia, Non-Hodgkin lymphoma, Hodgkin lymphoma, B cell acute lymphocyte leukemia (ALL), refractory B cell lymphoma, or multiple myeloma. While the immune system plays a key role in preventing other cancers in its early stages, this protection is limited, since genetic changes amongst the cancer cells enable them to escape the immune system.
Targeted treatment of immune-related disorders is recognized as being essential, in order to avoid off-target serious adverse events, whether it be to restore immune tolerance in autoimmune diseases or to detect and eliminate pathogens or cancers. Genome editing (e.g. CRISPR-Cas9 system) and adoptive immunotherapy are among the tools that facilitate new strategies for targeted therapy, and potentially provide long term disease control. By way of example, T-cells derived from a patient can be engineered ex vivo with a retroviral vector to express a chromosomally encoded chimeric antigen receptor (CAR) that recognizes unique surface antigens expressed by tumor cells. Once re-introduced into the patient, the CAR T-cells bind with their engineered receptors to antigens on the tumor cells which initiate various signaling cascades that activate the CAR T-cells. The activated CAR T-cells then exert a cytotoxic response to recognized cancer cells and attract other immune cells to the site. As the CAR construct is introduced into the T-cell chromosome, proliferating activated CAR T-cells pass on their CAR constructs to daughter cells and therefore mount a sustained treatment effect from potentially a single treatment dose.
The use of adoptive cellular therapy for cancer treatment can be extended to other immune-related disorders. In the case of AIDs, the CAR-T cells are modified to target specific autoantigens or antibodies expressed on a pathogenic cell surface. More specifically, chimeric autoantibody receptor T (CAAR-T) cells are engineered to express a specific antigen that recognizes and binds to cognate autoantibodies expressed by the self-reactive antibody-producing B cells, leading to their elimination. Alternatively, regulatory T-cells (Treg) can be modified ex-vivo into CAR-Tregs having antigen specificity and used to treat AIDs by a pathogenic mechanism (Chen Y et al., 2019). Among the many diseases of the immune system whose treatment employs autologous gene therapy are various forms of immunodeficiency. For example, mutations in the Adenosine deaminase (ADA) gene results in autosomal recessive severe combined immunodeficiency (SCID), where absent or impaired ADA function causes the accumulation of the toxic metabolites adenosine, 2′deoxyadenosine and deoxyadenosine triphosphate (dATP), leading to severe lymphocytopaenia affecting T- and B-lymphocytes and NK cells. Gene therapy treatments rely on ex vivo gene engineering using retroviral vectors.
A common feature for the numerous current cell therapies of immune-related disorders is the need to engineer the target immune cells ex vivo using viral vectors, which adds both to the risks associated with the treatment (e.g.: toxicity of chemo/radio therapy during cell re-introduction, fear of mutating oncogenic viral vectors, etc.) and the technical complexity (e.g.: production bottlenecks of viral vectors, high loads of re-introduced engineered cells leading to excessive anti-/pro-inflammatory responses, lengthy and cumbersome treatment preparation, high treatment cost, etc.). The disadvantages related to current therapy give rise to a need to provide alternative tools and methods that would facilitate genome engineering and/or cellular regulation of cells of a patient's immune system in vivo or ex vivo.
An invasive recombinant bacterial cell for use in prevention and/or treatment of an immune-related disorder; said bacterial cell comprising one or more recombinant nucleic acid molecule(s) encoding one or more therapeutic agent(s) for use in prevention and/or treatment of said immune-related disorder in a mammal; wherein said bacterial cell comprises one or more recombinant invasive gene(s) that facilitates invasion and release of said one or more recombinant nucleic acid molecule(s) or said one or more therapeutic agent(s) in a mammalian non-phagocytic immune cell and thereby functions as a bacteria-mediated delivery vector for in vivo or ex vivo delivery of said one or more recombinant nucleic acid molecule(s) or said one or more therapeutic agent(s) to the mammalian non-phagocytic immune cell, and wherein the immune-related disorder preferably is selected from the group: an autoimmune disorder, cancer, and a lymphoproliferative disorder.
In a further aspect thereof, the invasive recombinant bacterial cell for use in prevention and/or treatment of an immune-related disorder, is a cell comprising one or more recombinant invasive gene(s) for expressing protein(s) for invasion of non-phagocytic immune cells, said protein(s) selected from the group:
In a further aspect thereof, said mammalian non-phagocytic immune cell is a T-lymphocyte, B-lymphocyte, Natural Killer cell, or basophil.
In a further aspect thereof, said mammalian non-phagocytic immune cell is a member of the group consisting of a primate, bovine, ovine, porcine, feline, buffalo, canine, goat, equine, donkey, and camel cell.
In a further aspect thereof, said therapeutic agent is a recombinant or native DNA, RNA, or protein agent, or a combination thereof. Said agent may be selected from the group: a Chimeric Antigen Receptor; a small interfering RNA; a protein inhibitor of any one of T cell activation; T cell suppression; T cell proliferation and T cell cell death; a protein inducer of any one of T cell activation; T cell suppression; T cell proliferation and T cell cell death; a cytotoxin; a cytokine; a chemokine, and a CRISPR-Cas system.
In a further aspect thereof, said immune-related disorder is selected from the group: autoimmune disorder(s), cancer(s), and lymphoproliferative disorder(s).
In a second aspect the invention provides a method for prevention and/or treatment of an immune-related disorder in a mammal, the method comprising administering to a mammal diagnosed with said immune-related disorder, an invasive recombinant bacterial cell comprising one or more recombinant nucleic acid molecule(s) encoding one or more therapeutic agent(s); wherein said bacterial cell is capable, or engineered, to deliver said recombinant nucleic acid molecule(s) or said therapeutic agent(s) to a mammalian non-phagocytic immune cell. Delivery to said mammalian non-phagocytic immune cell may take place in-vivo, or ex-vivo followed by the step of re-introducing s the immune cell into the mammalian subject from which it was derived.
Disorder/Disease: A disease is a pathophysiological response to internal or external factors; while a disorder is a disruption to regular bodily structure and function. For the purpose of the present application the term “disorder” is to be understood to be an umbrella term that encompasses both a disease and a disorder in a mammalian subject that may be treated by the invasive recombinant bacterial cells of the present invention.
EMOPEC: “Empirical model and Oligos for Protein Expression Changes” used to predict Ribosomal Binding Site (RBS) strength (Bonde M T et al., 2016; http://emopec.biosustain.dtu.dk/).
Immune-related disorders are any diseases or disorders that can be treated, prevented or ameliorated by modulating at least one component of the host immune system; including autoimmune disorder(s); cancer(s); infectious disease(s), lymphoproliferative disorder(s), neurological and neurodegenerative diseases, and genetic disorder(s), and optionally somatic genetic disorder(s); and for which the invasive recombinant bacterial cells of the invention may be used as a bacteria-mediated delivery vector for providing said treatment, prevention or amelioration.
Invasive recombinant bacterial cell is a bacterial cell comprising invasive gene(s) or recombinant invasive gene(s) conferring the cell with the capability of ex-vivo and/or in vivo delivery of one or more recombinant nucleic acid molecules or therapeutic agent(s) comprised in said bacterial cell to a mammalian non-phagocytic immune cell.
Non-phagocytic immune cells: as defined herein are non-phagocytic T-cells, B-cells, natural killer cells, and basophils that are components of the mammalian adaptive immune system.
RT: Room temperature
TNP-KLM: 2,4,6, Trinitrophenyl hapten (TNP) conjugated to Keyhole Limpet Hemocyanin protein (KLM) via amide bonds to lysine.
The invasive recombinant bacterial cell of the invention comprises one or more recombinant nucleic acid molecules encoding one or more therapeutic agent(s) for use in the prevention and/or treatment of an immune-related disorder in a subject in need thereof. The recombinant bacterial cell functions as a bacteria-mediated delivery vector for in vivo or ex-vivo delivery of said one or more recombinant nucleic acid molecules or said one or more therapeutic agent(s) encoded by said one or more recombinant nucleic acid molecules to a mammalian non-phagocytic immune cell for use in prevention and/or treatment of an immune-related disorder in a subject.
I. A Bacteria-Mediated Delivery Vector
In one aspect, the invasive recombinant bacterial cell is engineered to express one or more genes that enable the cell to both invade and release its therapeutic payload in a non-phagocytic immune cell. Expression of the one or more genes enables the recombinant bacterial cell to both invade the non-phagocytic immune cell, where it is typically internalized in primary vesicles (such as phagosomes); and to then escape into the cytosol due to induced permeabilization of the primary vesicles. Once the recombinant bacterial cell has escaped, it is genetically adapted to undergo lysis and thereby release its therapeutic payload into the cytosol, such that the therapeutic payload can bring about a therapeutic effect on, or by means of, said non-phagocytic immune cell. Examples of recombinant bacterial cells engineered for this purpose are detailed below:
In one example, the invasive recombinant bacterial cell of the invention comprises genes encoding a first protein belonging to the 1.B.54 family of Intimin/Invasin (Int/Inv) or Autotransporter-3 (AT-3) proteins; and a second protein belonging to the 1.C.12.1.7 family of thiol-activated cholesterol-dependent cytolysin (cdc) proteins, where the expression of said first and second proteins confers on the cell the ability to act as a bacteria-mediated delivery vector for delivery of the therapeutic agent to a mammalian non-phagocytic immune cell.
The first protein, belonging to the 1.B.54 family of homologous proteins, is an outer membrane (OM) protein found in strains of Yersinia spp. (Inv), pathogenic E. coli (Int), and Citrobacter spp (Int) [Example 1]. Expression of the first protein by the recombinant bacterial cell mediates its attachment to, and invasion of, the mammalian non-phagocytic immune cell. A suitable first protein includes an invasin belonging to the 1.B.54.1.2 sub-family, such as an invasin derivable from pathogen Yersinia pseudotuberculosis.
Expression of Y. pseudotuberculosis invasin by the recombinant bacterial cell, as shown herein [Example 3], both mediates invasion of an immune cell, and its subsequent uptake into the immune cell's phagolysosome. While not bound by theory, said invasion may occur when the outer membrane invasin binds to an integrin on the surface of the target non-phagocytic immune cell, such as an integrin belonging to one or more of subtypes α3β1, α4β1, α5β1, and α6β1 integrin.
In one aspect, when the first protein is an invasin, the primary amino acid sequence of said protein may be one having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 2. Alternatively, the amino acid sequence of said protein is modified, by the substitution of its signal peptide sequence with the sequence of a signal peptide native to the recombinant bacterium in which the first protein is expressed [Example 3]. For example, where the recombinant bacterium is a strain of E. coli, then the primary amino acid sequence of the invasin comprising a substitute E. coli signal peptide is one having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 4.
The second protein, belonging to the 1.C.12.1.7 family of homologous proteins, is a cytolysin found in strains of Listeria monocytogenes. Following invasion of a non-phagocytic immune cell and its inclusion in a primary vesicle (e.g. phagocyte), the cytolysin, expressed and secreted by the recombinant bacterial cell, causes the formation of pores in the primary vesicle membrane of the immune cell, allowing escape of the bacterial cell into the cytosol. A suitable second protein includes a Listeriolysin O derivable from Listeria monocytogenes serovar 1/2a. Expression of a combination of the L. monocytogenes Listeriolysin O and the Y. pseudotuberculosis invasin by the recombinant bacterial cell, as shown herein [Example 3], both mediates invasion of an immune cell, and its subsequent release from the immune cell's phagolysosome. While not bound by theory, the acidic conditions within the phagolysosome may induce folding and activation of pore-forming properties of the Listeriolysin O when expressed by the recombinant bacterium, while once released into the cytoplasm it is inactivated by the neutral pH.
In one aspect, when the second protein is an Listeriolysin O, the amino acid sequence of said protein may be one having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 6. Alternatively, the amino acid sequence of said protein is modified, by the substitution of its signal peptide sequence with the sequence of a signal peptide native to the recombinant bacterium in which the second protein is expressed [Example 3]. For example, where the recombinant bacterium is a strain of E. coli, then the primary amino acid sequence of the Listeriolysin O comprising a substitute E. coli signal peptide is one having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 8.
In a second example, the invasive recombinant bacterial cell of the invention comprises gene(s) encoding a first and second protein derived from a viral envelope glycoprotein complex, such as from HIV envelope glycoprotein complex proteins: gp120 and gp41 found in Human Immunodeficiency Virus 1 (HIV-1); in combination with and a third protein derived from a member of the 1.B.12.8.2 autotransporter-1 (at-1) family. These first, second and third proteins, that may be expressed as domains linked together in a fusion protein, confer on the cell the ability to act as a bacteria-mediated delivery vector for delivery of the therapeutic agent to a mammalian non-phagocytic immune cell. The recombinant bacterial cell may additionally express a fourth protein belonging to the 1.C.12.1.7 family of homologous proteins, preferably a cytolysin found in strains of Listeria monocytogenes, as described above in said first example, to ensure efficient intracellular delivery of bacterial therapeutics by phagolysosome lysis.
Suitable first and second proteins are gp120 and the gp41 ectodomain, derivable from the Transmitter/Founder (T/F) R5 strain BG505, that are modified by amino acid substitutions of all N glycosylation motifs (NXT/S), such that they are expressed as non-glycosylated proteins in the recombinant bacterial cell [Example 11]. When expressed as part of a fusion protein, the gp120 and gp41 protein domains may be connected by an amino acid linker. While not bound by theory, an envelope complex (e.g. spike protein trimer) comprising gp120 and gp41 proteins derived from (T/F) R5 strain BG505 will preferentially bind to a CD4 and a CCR5 receptor found on CD4+ CCR5+ T-cells. The gp41 ectodomain facilitates invasion by insertion of its hydrophobic N terminus into the immune cell membrane. Due to the affinity of the gp41 α-helices for both the bacterial- and immune-cell membranes, the respective membranes are pulled into sufficient juxtaposition to bring about their fusion.
The third protein, comprises protein domains derived from a member of the 1.B.12.8.2 family of homologous proteins, which facilitate anchoring of the gp120/gp41 envelope complex to the outer membrane of the recombinant bacterial cell. A suitable third protein may be derived from the signal peptide (SP) and the C-terminal portion of an autotransporter antigen 43 (FLU) protein from E. coli K12, the latter comprising an autochaperone (AC1) domain followed by a β-chain translocator domain.
When expressed as a fusion protein, the first and second gp120 and gp41 proteins are expressed as passenger domains fused between the SP and the AC1 domain of the third protein. The extended sequence of the SP ensures an export rate sufficient to sustain a secretion competent state of the passenger envelope complex. The C-terminal translocator domain anchors the fusion protein to the bacterial membrane by formation of a β-barrel outer membrane pore.
In one aspect, the amino acid sequence of said fusion protein (gp120+gp41) may be one having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 10.
In one aspect, the invention provides a recombinant bacterial cell comprising recombinant genes encoding a fusion protein comprising an N-terminal signal peptide of an autotransporter antigen 43 (FLU) protein, an HIV-1 glycoprotein 120, a first linker peptide, an HIV-1 glycoprotein 41, and a second linker, an autochaperone (AC1) domain and a β-chain translocator domain of said autotransporter antigen, fused in consecutive order, such as provided in example 11.
In one embodiment, said N-terminal signal peptide of the autotransporter antigen 43 (FLU) protein may be encoded by a nucleic acid sequence having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 171. In one embodiment, said N-terminal signal peptide of the autotransporter antigen 43 (FLU) protein may be having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 288.
In one embodiment, said HIV-1 glycoprotein 120, said first linker peptide, and said HIV-1 glycoprotein 41 fused in consecutive order may have at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 286.
In one embodiment, said second linker may be derived from an autotransporter antigen 43 (FLU) protein from E. coli K12 having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 179.
In one embodiment, said autochaperone (AC1) domain may be derived from an autotransporter antigen 43 (FLU) protein from E. coli K12 having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 181.
In one embodiment, said β-chain translocator domain may be derived from an autotransporter antigen 43 (FLU) protein from E. coli K12 having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 183.
In one embodiment, said second linker, autochaperone (AC1) domain and β-chain translocator domain fused in consecutive order may have at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 290.
In a preferred embodiment, the amino acid sequence of said fusion protein comprising an N-terminal signal peptide of an autotransporter antigen 43 (FLU) protein, an HIV-1 glycoprotein 120, a first linker peptide, an HIV-1 glycoprotein 41, and a second linker, an autochaperone (AC1) domain and a β-chain translocator domain of said autotransporter antigen may have at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 284. In one embodiment, said fusion protein is SEQ ID No.: 284.
In one embodiment, said recombinant genes encoding said fusion protein are located on a plasmid, such as pCOLA gp120-gp41-flu (SEQ ID NO 169).
In a third example, the invasive recombinant bacterial cell of the invention comprises genes encoding a first and second protein derived from components of the 1.C.36.3.1 Type III secretion system (T3SS), and membrane-anchoring protein(s), where the expression of said proteins confers the cell with the ability to act as a bacteria-mediated delivery vector for delivery of the therapeutic agent to a mammalian non-phagocytic immune cell.
Suitable first and second proteins are the invasin IpaB and IpaC proteins derivable from a pathogenic bacterium such as Shigella flexneri, together with a third protein, functioning as a membrane anchoring domain [Example 2]. While not bound by theory, IpaB initiates invasion, by forming a needle tip complex and binding to the host hyaluronan receptor CD44 and α5β1 integrin of an immune cell. IpaC, when complexed with ipaB, comprises domains for secretion; actin polymerisation at, and integration into, the immune cell membrane; resulting in internalization of the recombinant bacterial cell via filopodia and phagolysosome engulfment. IpaB further facilitates escape of the bacterium from the phagolysosomal by formation of ion pores. The third protein may either be invasin IpaD or alternatively a GPI-anchored protein such as a member of the bacterial ice nucleation family (e.g. INA-K and INA-Q) derivable from Pseudomonas spp that is fused to each of the IpaB and IpaC proteins. When the recombinant bacterial cell expresses each of IpaB and IpaC as fusion proteins, fused to the C-terminus of a truncated INA protein, its glucosylphosphatidylinositol (GPI) anchor domain tethers each fusion protein to the outer cell membrane, while the INA repeat region allows complex formation between the extracellularly displayed IpaB and IpaC.
In one aspect, the amino acid sequence of the fusion proteins INA.K-IpaB-IpaC may be one having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 12.
In one aspect, the amino acid sequence of the proteins IpaB, IpaC and IpaD may be one having at least 70, 71, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 14, 16, and 18 respectively.
In a further aspect, the invasive recombinant bacterial cell of the invention is additionally genetically adapted to undergo lysis following its released from the primary vesicle (e.g. phagosome) allowing release of its therapeutic payload. For example, the bacterial cell is modified to inactivate the chromosomal DapA gene, such that the cells undergo lysis in the immune cell due to a failure to express 4-Hydroxy-tetrahydrodipicolinate synthase (DAP), essential for cell wall synthesis (Example 1).
In a further aspect, the invasive recombinant bacterial cell of the invention is a live bacterium and a species of a genus selected from among Escherichia, Bacteroides, Akkermansia, Alistipes, Prevotella, Parabacteroides, Odoribacter, Enterobacter, Klebsiella, Citrobacter, Shigella, Listeria, Yersinia, Citrobacter, Bartonella, Agrobacterium, Salmonella, Helicobacter, Bartonella, Anaplasma, Ehrlichia, Coxiella, Chlamydia, Rickettisa, Legionella, Mycobacterium, Brucella, and Pseudobutyrivibrio. In a further embodiment, the invasive recombinant bacterial cell is selected from the genus Lactobacillus or Bifidobacterium. For example, the recombinant gram-negative bacterium is E. coli, since members of this species have the added advantage of being easily engineered, and in particular it is E. coli Nissle since this is a well-characterized probiotic that is classified as a risk group I organism.
In a further aspect, the invasive recombinant bacterial cell of the invention comprises on one or more plasmids that comprise the one or more recombinant nucleic acid molecules encoding the therapeutic agent. The coding sequence for the therapeutic agent in each of the one or more recombinant nucleic acid molecules is operatively linked to a promoter, RBS, signal peptide region, terminator, and polyadenylation signal functional in either a prokaryotic or a eukaryotic cell, these being selected to provide a desired expression level and location in the recombinant bacterium of the invention or in the invaded non-phagocytic immune cell respectively.
In a further aspect, the one or more recombinant nucleic acid molecules encoding a therapeutic agent additionally comprises at least one DNA nuclear targeting sequence(s) (DTS) to facilitate efficient import into the nucleus of the non-phagocytic immune cell, in particular into non-dividing immune cells. The inclusion of DTSs increases transcription rates of the one or more nucleic acid molecules transferred into an invaded non-phagocytic immune cell. The DTS(s) are present as multiple direct repeat sequences, preferably located before the promoter sequence and after the poly A signal of the therapeutic agent coding sequence. Recombinant bacterial cells of the invention, whose one or more recombinant nucleic acid molecules comprise DTSs selected from among an SV40 enhancer (SEQ ID No.: 19); a glucocorticoid receptor binding site (SEQ ID No.: 20); and a NF-κB-binding site (SEQ ID No.: 21), are illustrated in example 4. Relative levels of nuclear import and subsequent expression of the recombinant nucleic acid molecules comprising DTSs may be detected by measuring signal strength of a co-expressed fluorescent reporter gene and the number of fluorescent cells. Suitable DTSs and their optimal number of repeats are given in Table 1; further indicating their genetic sources.
In a further aspect, the therapeutic agent encoded by the one or more recombinant nucleic acid molecules is a therapeutic protein comprising nuclear localization sequences (NLS) fused to both the C- and N-terminal end of the therapeutic protein. Suitable NLS are given in Table 2; further indicating their genetic sources.
II. Therapeutic Payload of the Bacteria-Mediated Delivery Vector
The invasive recombinant bacterial cell of the invention comprises one or more recombinant nucleic acid molecule(s) encoding one or more therapeutic agent(s) for use in prevention and/or treatment of an immune-related disorder in a subject in need thereof, wherein said agent is one or more recombinant nucleic acid molecules (RNA or DNA), or one or more proteins, or a combination thereof. In one embodiment, a wide range of therapeutic agents can be delivered, e.g. a Chimeric Antigen Receptor protein; a small interfering RNA; a protein inhibitor of any one of T cell activation, T cell suppression, T cell proliferation and T cell cell death; a protein inducer of any one of T cell activation, T cell suppression, T cell proliferation and T cell cell death; a cytotoxin; a cytokine; a chemokine, and a CRISPR-Cas9; as is further illustrated below.
In another embodiment, the therapeutic agent is a recombinant or native DNA, RNA, or protein agent selected from the group: a Chimeric Antigen Receptor, a small interfering RNA, a protein inhibitor of any one of T cell activation; T cell suppression; T cell differentiation; T cell maturation; T cell proliferation and T cell cell death; a protein s inducer of any one of T cell activation; T cell suppression; T cell differentiation; T cell maturation; T cell proliferation and T cell cell death; an oxidoreductase or an inhibitor or an activator thereof; a transferase or an inhibitor or an activator thereof; a hydrolase or an inhibitor or an activator thereof; a lyase or an inhibitor or an activator thereof; an isomerase or an inhibitor or an activator thereof; a ligase or an inhibitor or an activator thereof; a translocase or an inhibitor or an activator thereof; a cytotoxin; a cytokine; a nanobody; a monobody; an affibody; an antibody fragment; a DARPin; a nanoparticle; a growth factor; a hormone; a chemokine, and; a CRISPR-Cas system.
II.i Nucleic Acid Therapeutic Agents:
In one aspect the therapeutic payload delivered by the recombinant bacterial cell of the invention to the non-phagocytic immune cell comprises one or more recombinant nucleic acid molecules. The therapeutic effect of the payload on the immune-related disorder is mediated by the expression of proteins encoded by said one or more recombinant nucleic acid molecules in the immune cell following delivery of the payload. Expression of the encoded proteins in the immune cell is facilitated by eukaryotic expression sequences (promoter, RBS, and polyadenylation signal) operatively linked to the protein coding sequences in the recombinant nucleic acid molecules.
A first example of a protein expressed in an immune cell on delivery of the payload is a Chimeric Antigen Receptor (CAR), which is designed to confer a T cell with the ability to recognize and bind to specific epitopes of a causal agent of a given disorder.
When the causal agent is an infectious disease, the CAR may comprise an antigen recognition domain (e.g. single-chain variable fragment; receptor domain) recognizing an epitope specific to the infectious agent, such that the resulting CAR-T cells have a therapeutic effect on an infectious disease (as exemplified in Table 3).
Aspergillus fumigatus
When the causal agent is cancer, the CAR may comprise an antigen recognition domain (e.g. single-chain variable fragment; receptor domain) recognizing an epitope specific for the cancer cell, such that the resulting CAR-T cells have a therapeutic effect on the cancer. The recognized epitope on a cancer cell includes surface receptors, and by way of example a receptor may be selected from among: CD19, BCMA, CD22, CD20, CD123, CD30, CD38, CD33, CD138, CD56, CD7, CLL-1, CD10, CD34, CS1, CD16, CD4, CD5, IL-1-RAP, ITGB7, k-IgG, TACI, TRBC1, MUC1, NKG2D, PD-L1, CD133, CD117, LeY, CD70, ROR1, AFP, AXL, CD80, CD86, DLL3, DR5, FAP, FBP, LMP1, MAGE-A1, MAGE-A4, MG7, MUC16, PMEL, ROR2, VEGFR2, CD171, CLD18, EphA2, ErbB, Fra, PSCa, cMet, IL13Ra2, EPCAM, EGFR, PSMA, EGFRcIII, GPC3, CEA, HER2, GD2 and Mesothelin (MacKay et al., 2020).
II.ii RNA Interference Mediated Therapeutics:
In one aspect the therapeutic effect of the payload delivered by the recombinant bacterial cell of the invention to the non-phagocytic immune cell is mediated by small interfering RNA (siRNA) encoded by short hairpin RNA (shRNA) coding sequences comprised in said one or more recombinant nucleic acid molecules. Transcription of the siRNA in the immune cell nucleus may be facilitated by eukaryotic expression sequences (promoter and polyadenylation signal, e.g. U6 promoter and a SV40 poly A termination signal) operatively linked to the shRNA coding sequences in the recombinant nucleic acid molecules [example 6]. Alternatively, the therapeutic payload comprises one or more siRNA molecules transcribed from the one or more recombinant nucleic acid molecules in the recombinant bacterial cell, whose transcription is facilitated by prokaryotic expression sequences (promoter, RBS, and terminator, e.g. T7 prokaryotic expression sequences) operatively linked to the shRNA coding sequences in the recombinant nucleic acid molecules [example 6]. On delivery to the immune cell cytoplasm, target messenger RNA (mRNA) complementary to the siRNA and detected by RNA-induced silencing complex (RISC) is then cleaved by a nuclease under direction of the RISC.
Disorders targeted by siRNA mediated therapy include silencing: inhibitors of T-cell activation in cancer; signaling pathways that activate T-cells in inflammation; genes required for viral invasion during HIV infection (Freeley & Long, 2013); CD4 in T-cells during autoimmune disease (Lee et al., 2012); ZAP-70 to reduce T-cell activation in delayed type hypersensitivity (Gust et al., 2008); SOCS3 to reduce allergic airway response in asthma and to reduce insulin resistance in diabetes (Jorgensen et al., 2013; Moriwaki et al., 2011); Cblb to improve efficacy of tumor vaccines in melanoma (Hinterleitner et al., 2012); JAK3 in CD3+ T-cell blasts to suppress Th1-mediated inflammatory responses (Gómez-Valadés et al., 2012); SOCS-1 in CD8 T-cells to improve anti-tumor response (Dudda et al., 2013); STAT3 to decrease graft-vs-host response and increase anti-tumor response in CD4 T-cells (Pallandre et al., 2007); CD4 to prohibit HIV entry into T-cells (Novina et al., 2002); CCR5 to prohibit HIV entry into T-cells (Kumar et al., 2008), NR4A2 to decrease inflammation in multiple sclerosis (Doi et al., 2008), FOXP3 or IL10 in CCR4+ Treg cells to inhibit breast cancer metastatis into the lung (Biragyn et al., 2013); T-bet in autoreactive encephalitogenic T-cells to inhibit development of multiple sclerosis (Lovett-Racke et al., 2004); GATA-3 in TH1 cells to enhance cancer vaccine response in colorectal cancer (Tesniere et al., 2010); and CD3 to treat acute allograft rejection and graft-vs-host disease.
II.iii Protein Therapeutic Agents:
In one aspect the therapeutic payload delivered by the recombinant bacterial cell of the invention to the non-phagocytic immune cell comprises one or more proteins. The proteins are encoded by the one or more recombinant nucleic acid molecules in the recombinant bacterial cell and expressed prior to their delivery to the immune cell. Expression of the encoded proteins in the bacterial cell is facilitated by prokaryotic expression sequences (promoter, RBS, signal peptide sequence, and terminator) operatively linked to the protein coding sequences in the recombinant nucleic acid molecules.
In one example, the protein is a transcription factor that mediates a therapeutic effect on an immune-related disorder by modulating cell differentiation, activation, or proliferation on delivery to a non-phagocytic immune cell (e.g. lymphocyte) associated with a given disorder.
In one example, the protein is an inhibitor of a transcription factor that is a causal agent of pro-inflammatory downstream signaling in diseases such as lupus, rheumatoid arthritis, and type 1 diabetes.
For instance, protein therapeutic agents delivered by the recombinant bacterial cells of the invention may be selected from among: Shigella virulence factors (Mattock & Blocker, 2017); OspC3 inhibiting Caspase-4-Mediated Inflammatory Cell Death; OspF inhibiting phosphorylation of ERK1/2 [Example 8]; OspG inhibiting NFκB activation; OspI inhibiting NFκB Activation; OspZ inhibiting NFκB activation; IpaH9.8, inhibiting NFκB response; IpaH0722 inhibiting NFκB activation; IpgD activating Akt/PI3K signaling pathway; Yersinia pestis effector YopH; a phosphotyrosine phosphatase that dephosphorylates phosphotyrosine and the T-cell scaffold proteins LAT and SLP-76, which inhibits TCR signaling and T-cell activation and proliferation (Wei et al., 2012); T3SS effectors NleE and NleB, where NleE inhibits NFκB through blockage of p65 nuclear transport upon TNFα and IL-1β stimulation and further suppresses NFkB by inhibiting activation of IKKβ and therefore degradation of IκB (Nadler et al., 2010), and NleB enhances NFkB inhibition of NleE and inhibits FAS death receptor mediated extrinsic apoptosis signaling, thereby protecting affected mammalian target cells from apoptotic cell death (Pollock et al., 2017) [Example 9].
Alternatively, the protein delivered to the non-phagocytic immune cell is selected from among adenosine deaminase (ADA) for the treatment of severe combined immunodeficiency (SCID) (Flinn & Gennery, 2018); L-asparaginase for the treatment of acute lymphoblastic leukemia (Müller & Boos, 1998) (see example 10); azurin in the treatment of cancerous lymphocytes (Punj et al., 2004); cytotoxins such as colibactin, glidobactin, and luminmide in the treatment of cancerous lymphocytes (R. Li et al., 2019); pro-inflammatory cytokines/chemokines in the treatment of immunodeficiency; and anti-inflammatory cytokines/chemokines in the treatment of inflammatory diseases (Luheshi, Rothwell, & Brough, 2009).
II.iv Combinations of Protein, DNA, and RNA Therapeutic Agents:
In one aspect the therapeutic payload delivered by the recombinant bacterial cell of the invention to the non-phagocytic immune cell comprises one or more Cas endonucleases and one or more guide RNA molecules (CRISPR Cas); e.g. Cas9 and single guide RNAs (gRNA), for use in the therapeutic prevention and/or treatment of an immune-related disorder. The CRISPR Cas is encoded by the one or more recombinant nucleic acid molecules in the recombinant bacterial cell and expressed prior to its delivery to the immune cell. Expression of the encoded CRISPR Cas in the bacterial cell is facilitated by prokaryotic expression sequences (promoter, RBS, and terminator) operatively linked to their respective coding sequences in the recombinant nucleic acid molecules. An N-terminal nuclear localization signal (e.g. SV40 NLS) may be fused to the Cas endonuclease (Cas9) to improve nuclear transport of the delivered protein. Alternatively, the recombinant nucleic acid molecules encoding both the Cas endonuclease and the gRNA are delivered to the invaded mammalian non-phagocytic immune cell where they are expressed under the control of mammalian expression sequences (promoter, enhancer, and poly A tail) operatively linked to their respective coding sequences in the recombinant nucleic acid molecules. An N-terminal DTS signal may be fused to the DNA sequences encoding the Cas nuclease and the gRNA to improve nuclear localization and enhanced expression.
CRISPR Cas, delivered as the therapeutic payload to non-phagocytic immune cells, may be used for prevention and/or treatment of HIV by directing gRNA to the following target sequences: HIV provirus LTR (U3 region (Ebina et al., 2013), HIV provirus LTR (R region) (Liao et al., 2015), HIV provirus second exon of Rev (Zhu et al., 2015), HIV provirus Gag/Pol/Rev/Env (Wang et al., 2016), T cell co-receptor CCR5 (Qi et al., 2018), and T cell co-receptor CXCR4 (Hou et al., 2015).
CRISPR Cas, as the therapeutic payload, may be used in the treatment of various types of cancer by directing gRNA to oncogenes in cancerous lymphocytes or to human programmed death-1 PD-1 receptor in T-cells to counteract PD-L1 expression and subsequent immune suppression by cancer cells (Su et al., 2016).
CRISPR Cas, as the therapeutic payload, may be used to target a mutated gene by additionally co-delivering a homologous replacement DNA sequence for restoring the non-mutant gene such as: targeting loss of function mutations in the Adenosine deaminase (ADA) ada gene in ADA deficiency (Flinn & Gennery, 2018), targeting mutations in the IL2RG gene in X-linked severe combined immunodeficiency (X-SCID) (Allenspach, Rawlings, & Scharenberg, 1993).
II.v Immune-Related Disorders:
Those disorders for which the invasive recombinant bacterial cells of the invention may be used as a bacteria-mediated delivery vector for use in providing therapeutic prevention and/or treatment include: autoimmune disorder(s); lymphoproliferative disorders; and cancer(s).
When the immune-related disorder is an autoimmune disorder it may be selected from the group: Inflammatory bowel disease; Celiac disease; Severe combined immunodeficiency (SCID); Organ transplant rejection (graft vs host disease); Asthma; Crohn's disease; Myocarditis; Postmyocardial infarction syndrome; Postpericardiotomy syndrome; Subacute bacterial endocarditis (SBE); Anti-Glomerular Basement Membrane nephritis; Lupus nephritis; Interstitial cystitis; Autoimmune hepatitis; Primary biliary cholangitis (PBC); Primary sclerosing cholangitis; Antisynthetase syndrome; Alopecia Areata; Autoimmune Angioedema; Autoimmune progesterone dermatitis; Autoimmune urticaria; Bullous pemphigoid; Cicatricial pemphigoid; Dermatitis herpetiformis; Discoid lupus erythematosus; Epidermolysis bullosa acquisita; Erythema nodosum; Gestational pemphigoid; Hidradenitis suppurativa; Lichen planus; Lichen sclerosus; Linear IgA disease (LAD); Morphea; Pemphigus vulgaris; Pityriasis lichenoides et varioliformis acuta; Mucha-Habermann disease; Psoriasis; Systemic scleroderma; Autoantibodies: Anti-nuclear antibodies, anti-centromere and anti-scl70/anti-topoisomerase antibodies; Vitiligo; Addison's disease; Autoimmune polyendocrine syndrome (APS) type 1; Autoimmune polyendocrine syndrome (APS) type 2; Autoantibodies: anti-21 hydroxylase; anti-17 hydroxylase.; Autoimmune polyendocrine syndrome (APS) type 3; Autoimmune pancreatitis; Diabetes mellitus type 1; Autoimmune thyroiditis; Ord's thyroiditis; Graves' disease; Autoimmune oophoritis; Endometriosis; Autoimmune orchitis; Sjögren syndrome; Autoimmune enteropathy; Coeliac disease; Crohn's disease; Esophageal achalasia; Ulcerative colitis; Antiphospholipid syndrome; Aplastic anemia; Autoimmune hemolytic anemia; Autoimmune lymphoproliferative syndrome; Autoimmune neutropenia; Autoimmune thrombocytopenic purpura; Cold agglutinin disease; Essential mixed cryoglobulinemia; Evans syndrome; Pernicious anemia; Pure red cell aplasia; Thrombocytopenia; Adiposis dolorosa; Adult-onset Still's disease; Ankylosing spondylitis; CREST syndrome; Drug-induced lupus; Enthesitis-related arthritis; A subtype of Juvenile Rheumatoid Arthritis.; Eosinophilic fasciitis; Felty syndrome; IgG4-related disease; Juvenile arthritis; Lyme disease; Mixed connective tissue disease; Palindromic rheumatism; Parry-Romberg syndrome; Parsonage-Turner syndrome; Psoriatic arthritis; Reactive arthritis; Relapsing polychondritis; Retroperitoneal fibrosis; Rheumatic fever; Rheumatoid arthritis; Sarcoidosis; Schnitzler syndrome; Systemic lupus erythematosus; Undifferentiated connective tissue disease; Dermatomyositis; Fibromyalgia; Inclusion body myositis; Myositis; Myasthenia gravis; Neuromyotonia; Paraneoplastic cerebellar degeneration; Polymyositis; Acute disseminated encephalomyelitis; Acute motor axonal neuropathy; Anti-N-Methyl-D-Aspartate Receptor Encephalitis; Balo concentric sclerosis; Bickerstaff's encephalitis; Chronic inflammatory demyelinating polyneuropathy; Guillain-Barre syndrome; Hashimoto's encephalopathy; Idiopathic inflammatory demyelinating diseases; Lambert-Eaton myasthenic syndrome; Multiple sclerosis; Oshtoran syndrome; Pediatric Autoimmune Neuropsychiatric Disorder Associated with Streptococcus; Progressive inflammatory neuropathy; Restless legs syndrome; Stiff-person syndrome; Sydenham's chorea; Transverse myelitis; Autoimmune retinopathy; Autoimmune uveitis; Cogan syndrome; Graves' ophthalmopathy; Intermediate uveitis; Ligneous conjunctivitis; Mooren's ulcer; Neuromyelitis optica; Opsoclonus myoclonus syndrome; Optic neuritis; Scleritis; Susac's syndrome; Sympathetic ophthalmia; Tolosa-Hunt syndrome; Autoimmune inner ear disease; Meniere's disease; Behçet's disease; Rare variant: Hughes-Stovin syndrome.; Eosinophilic granulomatosis with polyangiitis; Giant cell arteritis; Granulomatosis with polyangiitis; IgA vasculitis; Kawasaki disease; Leukocytoclastic vasculitis; Lupus vasculitis; Rheumatoid vasculitis; Microscopic polyangiitis; Polyarteritis nodosa; Polymyalgia rheumatica; Urticarial vasculitis; Vasculitis; Primary immunodeficiency; Chronic fatigue syndrome; Complex regional pain syndrome; Eosinophilic esophagitis; Gastritis; Interstitial lung disease; POEMS syndrome; Raynaud's phenomenon; Primary immunodeficiency; and Pyoderma gangrenosum. The autoimmune disorder may also be allergy.
When the immune-related disorder is cancer it may be selected from the group: Acute Lymphoblastic Leukemia; Acute Myeloid Leukemia; Adrenocortical Carcinoma; AIDS-Related Cancer; AIDS-Related Lymphoma; Lymphoma; Primary CNS Lymphoma; Anal Cancer; Gastrointestinal Carcinoid Tumor; Astrocytomas; Atypical Teratoid/Rhabdoid Tumor, Brain Cancer; Basal Cell Carcinoma; Bile Duct Cancer; Bladder Cancer; Bone Cancer; Ewing Sarcoma; Osteosarcoma; Malignant Fibrous Histiocytoma; Brain Tumors; Lung Cancer; Burkitt Lymphoma; Non-Hodgkin Lymphoma; Carcinoid Tumor; Cardiac Tumor, Medulloblastoma; CNS Embryonal Tumor, Primary CNS Lymphoma; Cervical Cancer; Cholangiocarcinoma; Chordoma; Leukemia; Lymphocytic Leukemia; Myeloid Leukemia; Myelogenous Leukemia; Myeloproliferative Neoplasm; Rectal Cancer; Craniopharyngioma; Cutaneous T-Cell Lymphoma; Mycosis Fungoides; Ductal Carcinoma In Situ; Endometrial Cancer; Uterine Cancer; Ependymoma; Esophageal Cancer; Esthesioneuroblastoma; Fallopian Tube Cancer; Gallbladder Cancer; Gastric Cancer; Gastrointestinal Carcinoid Tumor; Gastrointestinal Stromal Tumor; Gestational Trophoblastic Disease; Hepatocellular Cancer; Hodgkin Lymphoma; Hypopharyngeal Cancer; Intraocular Melanoma; Islet Cell Tumor, Pancreatic Neuroendocrine Tumor; Langerhans Cell Histiocytosis; Laryngeal Cancer; Lip and Oral Cavity Cancer; Liver Cancer; Lung Cancer, Pleuropulmonary Blastoma, Tracheobronchial Tumor; Lymphoma; Melanoma; Melanoma, Intraocular cancer; Merkel Cell Carcinoma; Mesothelioma, Metastatic Squamous Neck Cancer; Midline Tract Carcinoma With NUT Gene Changes; Mouth Cancer; Multiple Endocrine Neoplasia Syndromes; Multiple Myeloma; Myelodysplastic Syndromes, Myelodysplastic/Myeloproliferative Neoplasm; Myeloproliferative Neoplasm; Nasal Cavity cancer; Paranasal Sinus Cancer; Nasopharyngeal Cancer; Non-Hodgkin Lymphoma; Non-Small Cell Lung Cancer; Pleuropulmonary Blastoma; Oropharyngeal Cancer; Osteosarcoma; Ovarian Cancer; Pancreatic Cancer; Papillomatosis; Paraganglioma; Parathyroid Cancer; Penile Cancer; Pheochromocytoma; Pituitary Tumor; Plasma Cell Neoplasm; Breast Cancer; Lymphoma; Primary Central Nervous System Lymphoma; Peritoneal Cancer; Prostate Cancer; Recurrent Cancer; Renal Cell Cancer; Retinoblastoma; Rhabdomyosarcoma, Salivary Gland Cancer; Sarcoma; Skin Cancer; Small Intestine Cancer; Soft Tissue Sarcoma; Squamous Cell Carcinoma; T-Cell Lymphoma, Testicular Cancer; Thymoma and Thymic Carcinoma; Thyroid Cancer; Urethral Cancer; Uterine Cancer, Endometrial; Uterine Sarcoma; Vaginal Cancer; Vascular Tumors; Vulvar Cancer; Chondrosarcoma; Osteosarcoma; Rhabdomyosarcoma; Heart cancer; Astrocytoma; Brainstem glioma; Pilocytic astrocytoma; Ependymoma; Primitive neuroectodermal tumor; Cerebellar astrocytoma; Cerebral astrocytoma; Glioma; Medulloblastoma; Neuroblastoma; Oligodendroglioma; Pineal astrocytoma; Pituitary adenoma; Visual pathway and hypothalamic glioma; Invasive lobular carcinoma; Tubular carcinoma; Invasive cribriform carcinoma; Medullary carcinoma; Phyllodes tumor; Multiple endocrine neoplasia syndrome; Uveal melanoma; Appendix cancer; cholangiocarcinoma; Carcinoid tumor, gastrointestinal; Colon cancer; Extrahepatic bile duct cancer; Gastrointestinal stromal tumor; Hepatocellular cancer; Pancreatic cancer; Endometrial cancer; Renal cell carcinoma; transitional cell cancer; Gestational trophoblastic tumor; Wilms tumor; Oral cancer; Paranasal sinus and nasal cavity cancer; Pharyngeal cancer; Salivary gland cancer; Acute biphenotypic leukemia; Acute eosinophilic leukemia; Acute lymphoblastic leukemia; Acute myeloid leukemia; Acute myeloid dendritic cell leukemia; AIDS-related lymphoma; Anaplastic large cell lymphoma; Angioimmunoblastic T-cell lymphoma; B-cell prolymphocytic leukemia; Burkitt's lymphoma; Chronic lymphocytic leukemia; Chronic myelogenous leukemia; Cutaneous T-cell lymphoma; Diffuse large B-cell lymphoma; Follicular lymphoma; Hepatosplenic T-cell lymphoma; Hodgkin's lymphoma; Hairy cell leukemia; Intravascular large B-cell lymphoma; Large granular lymphocytic leukemia; Lymphoplasmacytic lymphoma; Lymphomatoid granulomatosis; Mantle cell lymphoma; Marginal zone B-cell lymphoma; Mast cell leukemia; Mediastinal large B cell lymphoma; Myelodysplastic syndromes; Mucosa-associated lymphoid tissue lymphoma; Mycosis fungoides; Nodal marginal zone B cell lymphoma; Precursor B lymphoblastic leukemia; Primary central nervous system lymphoma; Primary cutaneous follicular lymphoma; Primary cutaneous immunocytoma; Primary effusion lymphoma; Plasmablastic lymphoma; Splenic marginal zone lymphoma; T-cell prolymphocytic leukemia; Skin adnexal tumors; sebaceous carcinoma; Merkel cell carcinoma; Sarcomas of primary cutaneous origin; dermatofibrosarcoma protuberans; Bronchial adenoma and carcinoid; Mesothelioma; Pleuropulmonary blastoma; Kaposi sarcoma; Epithelioid hemangioendothelioma; Desmoplastic small round cell tumor; and Liposarcoma.
When the immune-related disorder is a lymphoproliferative disorder it may be selected from the group: post-transplant lymphoproliferative disorder; autoimmune lymphoproliferative syndrome; lymphoid interstitial pneumonia; Epstein-Barr virus-associated lymphoproliferative diseases; Waldenström's macroglobulinemia; Wiskott-Aldrich syndrome; Lymphocyte-variant hypereosinophilia; Pityriasis Lichenoides; and Castleman disease.
III Administration of the Bacteria-Mediated Delivery Vector Comprising a Therapeutic Payload
The recombinant bacterial cell of the invention for use in the prevention and/or treatment of an immune-related disorder in a subject in need thereof, is suitable for administration to the subject by a mode of administration selected from the group: intravenous, intra-arterial, intraperitoneal, intralymphatic, sub-cutaneous, intradermal, intramuscular, intraosseous infusion, intra-abdominal, oral, intratumor, intravascular, intravenous bolus; and intravenous drip.
Preferably the mode of administration is either intravenous, or intralymphatic, or intraperitoneal administration.
General Methodology
Bacterial strains, plasmids, genes and cell lines used in the examples are identified in Table 4.
Escherichia coli strain TOP10 (Thermo Fischer Scientific) was used for DNA manipulations, plasmid propagations, and transfer experiments; while Escherichia coli Nissle 1917-pMUT1 (EcN), E. coli T7, or EcN Tn7::GFP, containing a chromosomally integrated GFP gene, were used for plasmid validations and transfer experiments. Bacterial strains were grown at 37° C. in Luria-Bertani (LB) broth or agar.
Jurkat clone E6-1 cells were maintained in Gibco™ RPMI 1640 Medium (ATCC modification, Fischer Scientific) supplemented with 10% Fetal Bovine Serum (FBS, RM10432, HiMedia Laboratories) and 1% Penicillin/Streptomycin/Neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/ml, P4083, Sigma Aldrich) or 500× Mycozap Plus CL (Stemcell Technologies) at 37° C. and 5% CO2. The PD-L1+ human breast cancer cell line MCF-7 was maintained in ATCC-formulated Eagle's Minimum Essential Medium (ATCC Catalog No. 30-2003) supplemented with 0.01 mg/ml human recombinant insulin, fetal bovine serum to a final concentration of 10%, and 1% Penicillin/Streptomycin/Neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/ml, P4083, Sigma Aldrich) or 500× Mycozap Plus CL (Stemcell Technologies) at 37° C. and 5% CO2. The CT26 murine colorectal carcinoma cell line (ATCC CRL-2638) was maintained in Dulbecco's modified Eagle's medium supplemented with 10% heat inactivated fetal bovine serum (FBS), and 1% Penicillin/Streptomycin/Neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/ml, P4083, Sigma Aldrich) at 37° C. and 5% CO2. The NF-κB Reporter Jurkat Cell line (Jurkat-Luc, BPS Bioscience) was maintained in Gibco™ RPMI 1640 Medium (ATCC modification, Fischer Scientific) supplemented with 10% Fetal Bovine Serum (FBS, RM10432, HiMedia Laboratories), 1 mg/ml of Geneticin, and 500× Mycozap Plus CL (Stemcell Technologies) at 37° C. and 5% CO2
Primary human T cells and human PBMCs were maintained in ImmunoCult XF T cell Expansion medium (Stemcell technologies) supplemented with Human Recombinant IL-2 (Stemcell technologies) and 1% Penicillin/Streptomycin/Neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/ml, P4083, Sigma Aldrich) or 500× Mycozap Plus CL (Stemcell Technologies) at 37° C. and 5% CO2. Primary human T cells were activated with ImmunoCult™ Human CD3/CD28 T Cell Activator (Stemcell technologies).
Statistical Analysis
Quantified results were displayed as means of technical replicates±standard error of the mean (SEM), unless otherwise stated. Data sets with more than one grouping variable were assessed for statistical differences using a two-way ANOVA test with an appropriate test for multiple comparison of experimental groups, as stated in figure legends. For data sets with only one grouping variable a one-way ANOVA was used to determine significant differences. Results were considered significant with p-values below 0.05. All statistical analyses were performed using the Prism 9 software (GraphPad).
E. coli TOP10
E. coli Nissle 1917 (EcN) cured on native plasmid MUT1
E. coli stain EcN-MUT1 deleted for dapA gene (SEQ ID
E. coli Nissle 1917 (EcN) with chromosomally integrated GFP
E. coli T7
E. coli BM2710
L. monocytogenes listeriolysin O (hly) with a W491A
monocytogenes EGDe (NC_003210.1) containing the native
Shigella flexneri phosphothreonine lyase OspF, Hygromycin
The parent bacterial strain E. coli Nissle 1917 (EcN), cured of one of its two native plasmids to create strain (EcN-pMUT1), was used for engineering gene or protein delivery vectors as described below (method). The native pMUT1 plasmid was cured using CRISPR for future reintroduction of an engineered plasmid containing the invasive phenotype (Zainuddin, Bai, & Mansell, 2019). Expression of the invasive phenotype on a native plasmid allows for plasmid maintenance without the need for antibiotic resistance genes. A deletion strain, EcN-pMUT1 ΔdapA, characterized by auxotrophy for diaminopimelic acid (DAP) due to deletion of chromosomal copies of the dapA gene encoding 4-Hydroxy-tetrahydrodipicolinate synthase, was derived from EcN-pMUT1, into which one of the alternative inv-hly expression plasmids (Table 4) were introduced. The inv-hly genes encode Yersinia pseudo tuberculosis invasin and Listeria monocytogenes listeriolysin O proteins that together provide two component system for delivery of genes or proteins into a mammalian non-phagocytic immune cell. The resulting inv-hly strains were further transformed with various reporter plasmids for monitoring transfer of a gene payload.
Methods:
Deletion of dapA gene: The dapA gene in EcN-pMUT1 was deleted by a modified CRISPR-Cas9 λ-Red recombinase genome editing strategy (Reisch and Prather, (2015)) using the plasmids: pMB-dapA containing the dapA guide RNA; pHM156 containing CRISPR Cas9 for cutting dsDNA and λ Red homologous recombination system (Gam, Beta and Exo genes), and pHM154 a template gRNA plasmid containing a guide RNA spacer for trpR. pMB-dapA, the gRNA plasmid, was generated by overlap PCR amplification with primers amplifying pHM154, whilst excluding the gRNA spacer region, using overlaps matching the 3′ end of dapA (2841684 nt-2842562 nt in EcN chromosome). The resulting fragment was assembled into a plasmid via standard Gibson assembly to create pMB-dapA. A homologous DNA fragment, OE-dapA was created for replacement of dapA. First, primers amplified 500 bp upstream and 500 bp downstream of the dapA gene. The two resulting fragments were then combined via PCR using the forward and reverse primers of the upstream and downstream fragment, respectively.
The host cell, EcN, was then transformed with the CRISPR Cas9 and λ Red system plasmid pHM156. The λ Red recombinase was induced by incubation with L-arabinose at 30° C. and the cells were electroporated with the gRNA plasmid pMB-dapA and the homologous OE-dapA flanking region DNA fragment. The CRISPR Cas9 complex introduced a double stranded cut in the dapA gene via guidance of the gRNA. The chromosomal DNA cut was fatal to the bacterial cells unless the cut was repaired via homologous recombination with the supplied DNA fragment and subsequent replacement of the dapA gene, resulting in the creation of strain EcNΔdapA. Successful knockouts were confirmed by PCR amplification and plasmids pMB-dapA and pHM156 were cured via incubation with anhydrotetracycline hydrochloride (Sigma Aldrich) at 37° C.
Cloning “Invasion-Listeriolysin O” Expression Plasmids:
Cloning Reporter Plasmids:
Cloning Protein Transfer Reporter Plasmids and Vectors:
The only protein transfer reporter that was made was the pGB3 which is also an invasive plasmid and hence described above.
Transformation of E. coli strains: The respective “invasion-listeriolysin O” (inv-hly) expression plasmids were individually transformed into E. coli strain EcN-pMUT1 ΔdapA, E. coli TOP10, E. coli Nissle-pMUT1, E. coli Tn7::GFP, E. coli Nissle-pMUT1, or E. coli BM2710 ΔdapA together with a reporter plasmid (e.g. GFP reporter plasmid (pZE3119-sfgfp) or the mCherry reporter plasmid (pshRNA-CD3d-c (HSH02212-mU6-c-CD3D)) by electroporation to create the strains listed in Table 4.
Cell line culture conditions: Jurkat cells were maintained in Gibco™ RPMI 1640 Medium (ATCC modification, Fischer Scientific) supplemented with 10% Fetal Bovine Serum (FBS, RM10432, HiMedia Laboratories) and 1% Penicillin/Streptomycin/Neomycin (5000 units penicillin, 5 mg streptomycin and 10 mg neomycin/ml, P4083, Sigma Aldrich) or 500× MycoZap Plus-CL (Lonza Bioscience) at 37° C. and 5% CO2. Primary human T cells and human PBMCs were maintained in ImmunoCult XF T cell Expansion medium (Stemcell technologies) supplemented with Human Recombinant IL-2 (Stemcell technologies) and 1% Penicillin/Streptomycin/Neomycin (5,000 units penicillin, 5 mg streptomycin and 10 mg neomycin/ml, P4083, Sigma Aldrich) or 500× Mycozap Plus CL (Stemcell Technologies) at 37° C. and 5% CO2. Primary human T cells were activated with ImmunoCult™ Human CD3/CD28 T Cell Activator (Stemcell technologies).
E. coli strains (EcN-MUT1 ΔdapA) engineered to express ipaBC-inaK fusion proteins are capable of functioning as bacteria-mediated delivery vectors of genetic material to a target non-phagocytic immune cell.
Methods:
Cloning “ipaBC-inaK” Expression Plasmid:
Primary human pan T cells were diluted to 2.67×105 cells/ml in pre-warmed ImmunoCult XF T Cell Expansion medium supplemented with 25 ng/ml of IL-2 and added to a PLO coated 96 well plate at 150 μl per well. Overnight cultures of EcN, carrying either invasive plasmid pCOLA_ipaBC_inaK and the sfGFP reporter plasmid pZE3119 or no plasmid as a negative control, were labelled with the Incucyte® pHrodo® Red Cell Labelling Kit for Phagocytosis (Essen Biosciences), following the manufacturer's instructions. pHrodo Red labelled bacteria were diluted to an MOI of 2000 or 5.33×108 cfu/ml in complete pre-warmed cell culture media and 150 μl were added to the T cell wells. As a positive control, 30 μl of labelled WT EcN were added, without cells, to separate wells containing 270 μl citrate-based buffer solution (pH<4.0). The plate was centrifuged for 10 minutes at 100×g to initiate contact between bacteria and placed into an IncucyteS3 instrument at 37° C. and 5% CO2. Using the cell-by-cell imaging software module, wells were imaged on all channels at 20× magnification every 20 minutes for a total of 2 hours. The Incucyte analysis software was used to create single cell masks to identify T cells and total mean red, as well as green, fluorescence intensity object averages were determined for each image.
Results
As shown in
On average, red fluorescence was highest for cells infected with invasive bacteria after 1 h and 50 min, compared to WT or uninfected cells. Whilst WT bacteria infected cells had a significantly higher total integrated red fluorescence per cell than uninfected cells, which indicated spontaneous uptake of the bacteria, invasive bacteria infected cells were significantly brighter than WT infected ones (
Engineered E. coli strains (EcN-MUT1 ΔdapA) containing one of the inv-hly expression plasmids (pV3 or pSQ11 (Example 1) and or a combination of the inv-hly plasmids pV3 or pSQ11 together with the reporter plasmid pZE3119-sfgfp (Example 1) were tested for their ability to infect Jurkat E6-1 cells and PBMCs, and thereby shown to function as bacteria-mediated delivery vectors of genetic material to a target non-phagocytic immune cell.
Methods:
Fluorescence microscopy analysis of invasion: Infection was performed in a flat-bottom 6-well plate, using 2.5×105-1.2×106 Jurkat E6-1 cells or PBMCs per well. The respective cells were infected with overnight cultures of E. coli EcN-pMUT1 strains comprising an inv-hly expression plasmid together with the reporter plasmid pZE3119-sfGFP or a control EcN-pMUT1 strain with only the reporter plasmid at multiplicity of infection (MOI) of either 400 or 2000 in RPMI media (see general methods) supplemented with 10% fetal bovine serum (FBS). Plates were centrifuged at 100×g for 10 min in a swinging bucket centrifuge, to initiate contact between cells of the E. coli strains and human cells, and incubated for 1 hour at 37° C. and 5% CO2. Next, well contents were transferred to individual 15 ml falcon tubes and washed once with Phosphate Buffered Saline (Gibco™ PBS, pH 7.4 at room temperature, Fischer Scientific) at 300×g for 5 min at RT. A sterilized microscope glass cover slip was placed in the wells of a new 6-well plate and the washed cells, re-suspended in PBS, were slowly added onto the cover slip. The plates were incubated at RT for 30 minutes to allow for adherence of cells to the cover slip via gravity sedimentation (Chowdhury, S. et al, 2017). Upon adherence, PBS was carefully aspirated from the wells, and the wells were gently washed three times with PBS.
The cells, adhered to cover slips, were then fixed for 15 minutes at RT with Image-iT Fixative Solution (Thermo Fischer Scientific). After subsequently washing the cover slips in PBS, cellular antigens on the slides were blocked for 30 min at 37° C. at 5% CO2 with stain buffer containing 2% fetal bovine serum (FBS) and 0.09% sodium azide (BD Biosciences).
Incucyte Live Cell Imaging Analysis of Invasion
Jurkat E6-1 cells were diluted to 3×105 cells/ml in pre-warmed RPMI+10% FCS and added to a 96 well plate at 100 μl per well. An overnight cultures of EcN Tn7::GFP containing either the invasive plasmid were diluted in complete cell culture media to MOIs ranging from 80-1280 or 2.4×107-3.8×108 cfu/ml. 100 μl of diluted bacteria were added to Jurkat cells and plates were centrifuged at 100×g for 30 sec to initiate contact between bacteria. Plates were incubated for 2 hours at 37° C. and 5% CO2. To terminate infections, cell suspensions were transferred to a 96-well V-bottom plate and centrifuged for 5 minutes at 200×g. Pellets were gently washed once with 100 μl complete cell culture medium. Cells were resuspended in 200 μl of RPMI+10% FCS+50 μg/ml Gentamicin and transferred to a new PLO coated 96-well F-bottom plates and left stationary to settle at RT for 20 minutes. The plate was then transferred to an IncucyteS3 instrument at 37° C. and 5% CO2. Using the cell-by-cell imaging software module, wells were imaged on all channels at 20× magnification every 20 minutes for a total of 4 days. The Incucyte analysis software was used to create single cell masks to identify T cells and total mean red, as well as green, fluorescence intensity object averages were determined for each image.
Results:
Jurkat E6-1 cells were infected with GFP expressing EcN-Tn7::GFP containing the invasive plasmid pV3, encoding codon-optimsed versions of the native inv-hly genes as well as containing a cytotoxicity reducing mutation in hly. Infected cells were then visualized in the Incucyte to determine green and red fluorescence. Cells exhibiting both green and red fluorescence were excluded from analysis as autofluorescent dying cells. Only cells that exclusively exhibited green fluorescence were determined to contain intracellular bacteria where green fluorescence stemmed from bacterially produced GFP and not cellular autofluorescence. As shown in
The invasive properties of the engineered E. coli EcN strains expressing the two component delivery system encoded by the Yersinia pseudotuberculosis invasin gene and the Listeria monocytogenes listeriolysin O system (inv-hly) and the reporter gene GFP, in T-cells (Jurkat E6-1) and human PBMCs infected with these strains was detected by immunofluorescence microscopy. All E. coli cells of the engineered EcN strains were identifiable and localizable by virtue of their expression of GFP and its detectable fluorescence. Those E. coli cells that remain external to the infected T-cells of PBMB cells (target cells) were detected by the combination of the primary E. coli LPS antibody and secondary anti-E. coli LPS antibody (ATTO 550) that detect E. coli surface antigens, since the antibodies are too large to enter the target cells and therefore intracellular bacteria. Subsequent detergent permeabilization of the target cells allowed detection of E. coli cells internalized within the target cells, using a combination of the primary E. coli LPS antibody and secondary anti-E. coli LPS antibody (ATTO 350). The target cells were detected and localized using anti-CD49D antibody that binds to integrin α4β1 on the mammalian cell surface. DNA staining with DAPI allows detection of the nucleus in both E. coli and target cells and their respective localization.
The target T-cells and PBMCs were infected with E. coli strains expressing two variants of the inv-hly two component delivery system encoded by genes on the plasmids pV3 and pSQ11 (Table 4). The invasin and Listeriolysin O encoded by the plasmids differed in respect to codon optimization of the expressed genes; the promoter strength and the substitution of E. coli signal peptides for the respective native signal peptide.
Infection of T-cells (Jurkat E6-1) (
When actin was detected in T-cells (Jurkat E6-1), infected with E. coli cells of the engineered EcN strain expressing the two component delivery system (inv-hly), actin polymerization was observed along points of contact with the internalized bacteria (
E. coli BM2710, containing a combination of the inv-hly expression plasmid pGB2Ωinv-hly and the mCherry reporter plasmid pshRNA-CD3d-c, was used to infect Jurkat E6-1 cells. Strong and persistent plasmid expression was shown in several infected cells and thereby the data demonstrated the use of bacteria-mediated delivery vectors of the invention for transfer and expression of genetic material to a target non-phagocytic immune cell.
Methods:
Jurkat E6-1 were diluted to 1×105 cells/ml in 6.5 ml of PBS and stained with 65 μl of the cytoplasmic labelling dye Incucyte® Cytolight Rapid Green (Essen Bioscience) for 20 minutes at 37° C., according to the manufacturer's instructions. Excess dye was diluted by addition of 40 ml RPMI+10% FCS and cell suspensions were centrifuged at 300×g for 7 minutes. Cell pellets were resuspended in complete culture medium supplemented with diaminopimelic acid (DAP) at a final concentration of 100 μg/ml. 500 μl of labelled cells were added to a 12 well plate at a density of 4×105 cells/ml. An overnight culture of E. coli BM2710 containing the invasive plasmid pGB2Ωinv-hly and the reporter plasmid pshRNA-CD3d-c was diluted to an MOI of 640 or 2.6×108 cfu/ml in complete culture medium supplemented with 10 mg/ml 2,6-Diaminopimelic acid (Sigma Aldrich) and 500 μl of bacterial suspension were added to the wells. Bacteria containing only the invasive plasmid but not the reporter plasmid served as a negative control. Co-cultures were incubated for 2 hours at 37° C. and 5% CO2. To terminate infections, well contents were pelleted, resuspended in complete cell culture medium supplemented with 50 ug/ml Gentamicin, and transferred to new PLO coated 12 well plates. The plates were transferred to an IncucyteS3 instrument and incubated at 37° C. and 5% CO2. Using the cell-by-cell imaging software module, wells were imaged on all channels at 20× magnification every 2 hours for a total of 70 hours. The Incucyte analysis software was used to create single cell masks to identify T cells and total mean red, as well as green, fluorescence intensity object averages were determined for each image. Images that were taken after plate disturbances, due to e.g.: movement of the instrument sample tray, or that contained misidentified cells were excluded from quantitative analysis.
Results:
E. coli Nissle-pMUT1 containing the inv-hly expression plasmid pV3, encoding a b-lactamase enzyme, was used to infect Jurkat E6-1 cells, to demonstrate the use of the engineered E. coli to transfer of a reporter protein to an infected T-cell.
Methods:
Jurkat E6-1 cells were diluted to 2.2×106 cells/ml in pre-warmed RPMI+10% FCS at 5 ml per flask. Overnight cultures of EcN+pV3 were diluted in complete cell culture medium at MOIs ranging from 640-1280 or 1.4×109-2.8×109 cfu/ml. WT EcN infected cells or uninfected cells served as negative controls for protein transfer. 5 ml of bacterial dilutions were added to the cells and culture flasks were incubated for 2 hours at 37° C. and 5% CO2. To terminate cell infections, flask contents were transferred to 50 ml falcon tubes (Corning) and washed once with PBS. Washed cell pellets were resuspended in complete culture medium containing 50 μg/ml Gentamicin and transferred to new 50 ml suspension culture flasks. Cell cultures were incubated for 2-24 hours at 37° C. and 5% CO2. In order to detect β-lactamase protein transfer, cultured cells were labelled with the LiveBLAzer™ FRET-B/G Loading Kit with CCF4-AM (Thermo Fischer Scientific), following the manufacturer's instructions. A modified Jurkat optimized loading protocol was used, after correspondence with Thermo Fischer Scientific. Specifically, a sort buffer consisting of Calcium- and Magnesium-free PBS, 1% glucose, 1 mM EDTA, and 1 mM HEPES was used instead of solution C from the LiveBLAzer kit. Labelled Jurkat cells were centrifuged to remove supernatants and resuspended in 1 ml of sort buffer for immediate flow cytometry analysis. Prepared cell suspensions were analysed on a Sony SH800S FACS.
Results:
As seen in
Engineered E. coli strains (EcNΔdapA) containing the inv-hly expression plasmid (pGB2) and a vector comprising a recombinant nucleic acid molecule encoding an siRNA for silencing CD3d expression are used to infect T-cells (e.g. Jurkat) in vitro. CD3d siRNA translation in the infected cells serves to demonstrate that the engineered E. coli of the invention can be used for both transfer and functional translation of CD3d siRNA in mammalian T-cells. Such T cells, silenced in their CD3d expression by the delivered siRNA, confer a therapeutic effect in mouse models exhibiting TNP-KLH induced colitis, experimental allergic encephalomyelitis (EAE), and collagen-induced arthritis.
Methods
Plasmid construction: Plasmid pshRNA-CD3d (HSH022212-mU6-a-CD3D, Genecopoeia), is a non-viral shRNA expression vector for expression in mammalian cells that encodes a siRNA against human CD3d under the mammalian U6 promoter and SV40 poly A termination signal. Plasmid psiRNA-CD3d that allows transcription of the siRNA gene in a bacterial cell, was derived from pshRNA-CD3d by replacing its mammalian U6 promoter with a T7 promoter and inserting a T7 terminator downstream of the siRNA coding sequence. Plasmid pCS6 encoded a T7 RNA polymerase under control of an L-arabinose-inducible bacterial araBAD promoter (Addgene plasmid #55752).
Cells of E. coli strain EcNΔdapA were transformed with the plasmids: pshRNA-CD3d; psiRNA-CD3d; pCS6; or CSHCTR001-mU6, in combination with the inv-hly expression plasmid pGB2 (Table 4).
In vitro RNA transfer of siRNA: Jurkat E6-1 cells were infected in 6-well plates with EcNΔdapA strains comprising plasmids: pGB2, pCS6 and psiRNA-CD3d; or pGB2 and psiRNA-CD3d as a first negative control; or pGB2 alone as a second negative control, at a range of different MOIs, as described for in vitro DNA transfer. As a positive control, Jurkat cells were electroporated with anti-CD3d siRNA and incubated without bacteria. After infection, cells were labelled with anti-CD3d antibody and DAPI nuclear stain and analysed for CD3d silencing on both a flow cytometer and a fluorescent microscope.
In vivo transfer of siRNA: In vivo bacterial transfer of anti-CD3d siRNA into T cells was performed on members of mouse models having TNP-KLH induced colitis or EAE, or collagen-induced arthritis as previously described (Kuhn & Weiner, 2016). Members of each mouse model were injected i.v. with overnight cultures of invasive EcNΔdapA (pGB2) strains in PBS comprising the anti-CD3d siRNA plasmids (psiRNA-CD3d and pCS6); or invasive EcNΔdapA (pGB2) strains without siRNA plasmids as negative controls, or a commercial anti-CD3 antibody as a positive control. Treated mice were analysed for disease model specific markers as follows: for members of the TNP-KLH induced colitis model by daily tail vein and end point blood puncture blood samples to determine bacterial load, cytokine levels, and CD3 expression on target T cells via flow cytometry, histopathological evaluation of inflamed tissues, survival, and immunohistochemistry; for members of the EAE mouse model be daily tail vein and end point blood puncture blood samples to determine bacterial load, cytokine levels, and CD3 expression on target T cells via flow cytometry, measurement of pro-inflammatory cytokines in end point samples of brain tissue and spinal cord fluid, and survival; and for members of the collagen-induced arthritis mouse model by daily tail vein and end point blood puncture blood samples to determine bacterial load, cytokine levels, C-reactive protein (CRP), and CD3 expression on target T cells via flow cytometry, measurement of paw volume or thickness over time, and erythrocyte sedimentation rate.
Engineered E. coli strains (EcNΔdapA) containing the inv-hly expression plasmid (pGB2) and a vector comprising a recombinant nucleic acid molecule encoding Cas9 and a gRNA sequence are used to infect T cells and target and knock-out the human PD-1 receptor (hPDCD1) gene on chromosome 2 Exon2, in vitro and in vivo. Knockout of hPD1 expression in the infected T cells serves to demonstrate that the engineered E. coli of the invention can be used for both transfer and functional expression of Cas9-gRNA-hPD1 in mammalian T-cells. Such T cells, modified to express Cas9-gRNA-hPD1, will confer a therapeutic effect on colorectal carcinomas in mice.
Methods
Plasmid construction: Plasmid pCas9-gRNA-hPD1, synthesised and cloned in a pUC57 backbone (Genscript), encodes a Cas9 endonuclease flanked by a SV40 Nuclear Localization Sequence (NLS) and a nucleoplasmin NLS and is operably linked to the bacterial J23105 promoter. The NLS increases the efficiency of nuclear localisation of the endonuclease protein and subsequent genome editing. The plasmid also encodes a gRNA sequence that targets the human PD-1 receptor (hPDCD1) on chromosome 2 Exon2 with the PAM sequence GGG. The gRNA is operably linked to the bacterial J23119 promoter which was modified to end with a SpeI site (Registry of Standard Biological Parts BBa_J23119). The plasmid was transformed into EcNΔdapA together with the inv-hly expression plasmid pGB2 (Table 4). As a positive control for bacterial transfer experiments, the gRNA from pCas9-gRNA-hPD1 was cloned into the gRNA backbone of plasmid pSpCas9(BB)-2A-GFP (Addgene plasmid #48138), which contains a Cas9 operably linked to a mammalian CMV promoter and enhancer control, a C-terminal fusion to EGFP, and a gRNA scaffold operably linked to a mammalian U6 promoter control, via Gibson assembly to create pCas9-GFP-gRNA-hPD1 [SEQ ID No.: 197].
In vitro CRISPR knockout of hPDCD1: Freshly isolated, primary, human T cells were activated with ImmunoCult™ Human CD3/CD28 T Cell Activator (Stemcell technologies) according to the supplier's instructions. In short, 10{circumflex over ( )}6 cells were seeded into freshly prepared ImmunoCult™-XF T Cell Expansion Medium (Stemcell technologies) containing Human Recombinant IL-2 (Stemcell technologies) and activated for 3 days at 37° C. and 5% CO2 with ImmunoCult™ Human CD3/CD28 T Cell Activator antibodies.
Bacterial transfer of the above plasmids was performed in a flat-bottom 6-well plate, seeded with 1.2×106 activated primary T cells per well. Cells were infected with overnight cultures of EcNΔdapA strains comprising plasmids: pGB2 and pCas9-gRNA-hPD1; or pCas9-gRNA-hPD1 alone as a first negative control; or pGB2 alone as a second negative control. Bacteria were added at a multiplicity of infection (MOI) of 500, 1000, or 2000 in ImmunoCult™-XF T Cell Expansion Medium media supplemented with IL-2. Additionally, primary T cells electroporated with pCas9-GFP-gRNA-hPD1 were seeded into bacteria-free wells as positive controls. Plates were centrifuged at 100×g for 10 min in a swinging bucket centrifuge, to initiate contact between cells and bacteria, and incubated for 1 hour at 37° C. and 5% CO2. Next, well contents were transferred to individual 15 ml falcon tubes and washed trice with Phosphate Buffered Saline (Gibco™ PBS, pH 7.4, Fischer Scientific) at 300×g for 5 min at RT. The pellet was re-suspended in ImmunoCult™-XF T Cell Expansion Medium supplemented with IL-2 plus gentamicin to kill extracellular bacteria and further cultured for 24 hours at 37° C. and 5% CO2 in an Incuyte S3 live imaging machine. After 24 hours, the cells were washed once in PBS at 300×g for 5 min. To determine hPD1 knockout, cells were incubated with recombinant anti-CD3d antibody (ab208514) and anti PD-1 antibody (ab52587, Abcam) and analysed on a flow cytometer. A sample aliquot was also analysed on a fluorescent microscope for visual confirmation of flow cytometer results.
To determine hPD1 knockout T cell activity, the infected activated T cells were re-suspended in ImmunoCult™-XF T Cell Expansion Medium supplemented with IL-2 and co-cultured with the PD-L1+ human breast cancer cell line MCF-7 (Y. Zheng et al., 2019) in a flat-bottom 6-well plate at a seeding density 6×105 at a ratio of 1:1. Co-cultures were incubated in the presence of IncuCyte® Cytotox Red Reagent for counting of dead cells. The co-cultures were monitored at 37° C. and 5% CO2 in an Incuyte S3 machine and analysed for an increase in red fluorescent signal as an indicator for T cell activity.
In vivo CRISPR knockout of hPDCD1: A group of CB6F1 mice were injected subcutaneously in the left and right flank with PD-L1 expressing CT26 murine colorectal carcinoma cells (ATCC CRL-2638). After 7 days, sub-groups of these mice were injected i.v. with overnight cultures of EcNΔdapA strains in PBS comprising of plasmids: pGB2 and pCas9-gRNA-hPD1; or pCas9-gRNA-hPD1 alone as a first negative control; or pGB2 alone as a second negative control, or PBS as a third negative control. An additional sub-group of mice were injected with Anti-mouse/human PD-L1 antibody (ab238697, Abcam) alone as a positive control. Body weight, temperature, survival, and food intake was measured daily to monitor signs of morbidity. Tumor size was measured daily to assess the cytotoxic activity of hPD1 knockout T cells. Tail vein blood samples were taken daily for later flow cytometric analysis of PD-1 expression of circulating lymphocytes as well as plating on LB agar plates with appropriate supplements and selection for determination of bacterial load in the blood stream. All mice were terminated after 20 days when spleens and tumors were collected for flow cytometric analysis of circulating lymphocytes and tumor cells. Heart puncture blood was assessed for cytokine/chemokine levels.
Methods
Primary human activated pan T cells were diluted to 4×105 cells/ml in pre-warmed ImmunoCult XF T Cell Expansion medium supplemented with 25 ng/ml of IL-2 and added to 96 well plates at 100 μl per flask. Overnight cultures of either TOP10, containing either the invasive plasmid pGB3 or the invasive and therapeutic plasmid pGB4, were diluted in complete cell culture medium to an MOI of 1000 or 4×108 cfu/ml. 100 μl of bacterial dilutions were added to the wells and plates were incubated for 2 hours at 37° C. and 5% CO2. Cell suspensions were then transferred to a 96 well V-bottom plate and washed once with 100 μl of PBS. Cell pellets were resuspended in 200 μl pre-warmed complete culture medium containing MycoZap Plus-CL (500×). Cells were transferred to a new 96 well F-bottom plate and incubated for up to 3 days. For sample collection, cells were pelleted in a 96 well V-bottom plate and a total of 8 wells per replicate sample were resuspended and pooled in a total volume of 100 μl of PBS. Pooled samples were pelleted, resuspended in 180 μl of PBS and 20 μl of Image-iT Fixative Solution (4%) for final dilution of 0.4% paraformaldehyde, and incubated for 7 minutes at RT. The cell suspension was centrifuged, resuspended in 200 μl of PBS and 0.5 μl eBioscience Fixable Viability Dye eFluor® 780, and incubated at 4° C. for 15 minutes. From this point onward, all steps were performed with the samples protected from light. Next, cells were pelleted and fixed in 100 ul Image-iT Fixative Solution (4%) for 7 min at RT. The fixed cells were centrifuged and permeabilized by incubation in 100 μl of ice-cold 90% methanol in PBS for 15 minutes at 4° C. Fixed and permeabilized samples were pelleted and resuspended in 100 μl stain buffer followed by incubation at 4° C. for 15 minutes. After centrifugation to remove supernatants, cells were resuspended in 93 μl stain buffer and labelled with 5 μl of Phospho-Erk1/2 (Thr202, Tyr204) PE labelled antibody (MILAN8R, Thermo Fischer Scientific) and 2 μl of Erk 1/2 AF488 labelled antibody (C-9, Santa Cruz Biotechnology). Following an overnight incubation at 4° C., labelled cells were washed trice with 100 μl stain buffer and incubated in 100 ul of PBS containing 100 μg/mL DNAse and 5 mM MgCl2 for 30 minutes at RT. Next, cells were washed once with 100 μl PBS containing 5 mM MgCl2, resuspended in 200 μl PBS containing 5 mM MgCl2 and 50 μg/mL DNAse, and analysed on a Novocyte Quanteon flow cytometer.
Results
The MAPK phosphothreonine lyase OspF is a virulence factor of Shigella flexneri that has been shown to irreversibly dephosphorylate the human transcription factor extracellular signal-regulated kinase 1/2 (Erk). Erk dephosphorylation results in reduced TCR signaling, activation, and proliferation of T cells through inhibition of the MAPK/Erk pathway (Mattock & Blocker, 2017; Wei et al., 2012). OspF dephosphorylation of Erk has therefore high therapeutic potential in Erk-deregulated cancers such as Childhood Acute Lymphoblastic Leukaemia. As OspF was of bacterial origin and the mechanism of action in T cells was well understood, it was chosen for delivery to primary T cells using the inv-hly BACTERIAL INTRACELLULAR DELIVERY VECTOR system. Primary human activated T cells were infected with E. coli TOP10 carrying the therapeutic plasmid pGB4, which contained the inv-hly system as well as the therapeutic protein OspF. Uninfected cells or cells infected with bacteria carrying the invasive plasmid without OspF (pGB3) served as negative controls. Following 2 hours of infection, cells were cultured for up to 2 days in the presence of antibiotics and labelled with a viability dye as well as antibodies for total Erk (t-Erk) and phosphorylated Erk (p-Erk). Labelled cells were analysed on a flow cytometer to determine p-Erk percentages of infected cells. The gating strategy was as follows: All events>T cells>Single cells>live cells>t-Erk>p-Erk. The t-Erk positive populations were gated based on the uninfected cell controls where the smallest t-Erk peak was excluded and the majority of cells were included in the gate (
Transfer of OspF also increased the percentage of live bacteria, shown as a stark decrease in the percentage of live cells that were t-Erk positive (
In conclusion, this experiment showed, for the first time, that a bacterium engineered to express the inv-hly system can deliver a therapeutic protein at high efficacies to human T cells.
Engineered E. coli strains (EcNΔdapA) containing the inv-hly expression plasmid (pV3) and a plasmid comprising a recombinant nucleic acid molecule encoding T3SS effectors s NleE and NleB are used to infect T-cells (e.g. NF-κB Reporter Jurkat) in vitro. Suppression of NF-kappaB activation in T-cells lines comprising an NF-κB Reporter serves to demonstrate that the engineered E. coli of the invention can transfer NleE and NleB proteins into the infected cells and interfere with the activation of selected host transcriptional regulators. Such T cells, whose host inflammatory pathways are manipulated by NleE/NleB-mediated suppression of NF-kappaB activation, confer a therapeutic effect in mouse models exhibiting TNP-KLH induced colitis, experimental allergic encephalomyelitis (EAE), and collagen-induced arthritis.
Methods
Plasmid construction: A DNA molecule comprising an operon encoding T3SS effectors NleE [SEQ ID No.: 219] and NleB [SEQ ID No.: 216] from the enteropathogenic E. coli 0127-H6 isolate EPEC E2348/69 was cloned into the pUC57-Kan plasmid (Genscript). The NleBE operon was operably linked to the strong constitutive promoter BBa_J23118 (Anderson library) and an optimised RBS sequence inserted before each gene. The predicted strength (EMOPEC) of the RBS upstream of NleE was higher than the RBS for the NleB gene to allow sufficient expression of both genes from a single promoter. The resulting plasmid, pNleBE was transformed into EcNΔdapA together with the inv-hly expression plasmid pV3 (Table 4).
In vitro NFκB inhibition: Bacterial transfer of the NleB and NleE proteins was performed in a flat-bottom 6-well plate, seeded with 1.2×106 cells/well of the NF-κB Reporter (Luc)—Jurkat Cell line (Jurkat-Luc, BPS Bioscience) which comprises a firefly luciferase gene controlled by 4 copies of NF-kB response element upstream of a TATA promoter. Cells were infected with overnight cultures of EcNΔdapA strains comprising plasmids: pV3 and pNleBE; or pNleBE alone as first negative control; or pV3 alone as a second negative control. Bacterial cells of the EcNΔdapA strains were added at a multiplicity of infection (MOI) of 500, 1000, or 2000 in RPMI media supplemented with 10% fetal bovine serum (FBS). As a positive control, Jurkat cells were treated with 0.1 nM of the glucocorticoid triamcinolone acetonide (TA) (Tsaprouni, Ito, Adcock, & Punchard, 2007) alone. Plates were centrifuged at 100×g for 10 min in a swinging bucket centrifuge, to initiate contact between cells and bacteria, and incubated for 1 hour at 37° C. and 5% CO2. Next, well contents were transferred to individual 15 ml falcon tubes and washed trice with Phosphate Buffered Saline (Gibco™ PBS, pH 7.4 at room temperature, Fischer Scientific) at 300×g for 5 min at RT. The pellet was re-suspended in complete growth medium plus gentamicin, to kill extracellular bacteria, and 10 ng/ml TNF-α was added for NFκB activation and subsequent stimulation of IL-8 production. After a 6-hour exposure to TNF-α, cells were washed thrice in RT PBS and re-suspended in complete growth medium plus gentamicin for 12 hours (overnight) at 37° C. and 5% s CO2. Next, cells were centrifuged at 300×g for 5 min to collect cell supernatants. A 500 ul sample of the supernatant was used to determine IL-8 concentrations using a commercial ELISA kit for IL-8 (ELISA, human IL-8 Duo Set; R&D Systems, Minneapolis, MN, USA), according to the manufacturer's instructions. The remaining supernatant was used to re-suspend the cell pellets in their wells. 100 μl of ONE-Step™ Luciferase Assay reagent (BPS Bioscience) was added to each well and the plates were incubated for 30 minutes at RT followed by luminescence measurement in a luminometer to determine NFκB induced luciferase production.
In vivo NFkB inhibition: In vivo bacterial transfer of NleB and NleE proteins by invasive E. coli strains expressing an NleBE operon into T cells was performed on members of mouse models having TNP-KLH induced colitis or EAE, or collagen-induced arthritis as previously described (Kuhn & Weiner, 2016). Members of each mouse model were injected i.v. with overnight cultures of EcNΔdapA strains in PBS either comprising the plasmids: pV3 and pNleBE; or pNleBE plasmid alone as first negative control; or pV3 alone as second negative control. The treated mice are analysed for each of the disease model specific markers as described in example 6.
Engineered E. coli strains (EcNΔdapA) containing the inv-hly expression plasmid (pGB2) and a plasmid comprising a recombinant nucleic acid molecule encoding L-asparaginase II (ansB) are used to infect T-cells (e.g. the human acute leukemic T-cell lymphoblast, Jurkat E6-1) in vitro. Since acute leukemic T-cells lines cannot synthesize asparagine, asparagine starvation leads to their apoptosis and cell death. Hence death of acute leukemic T cells following contact with cells of the engineered E. coli strains, serves to demonstrate that they can transfer asparaginase II into the infected cells and cause asparagine starvation. When administered to a mouse model for acute leukemia, cells of the engineered E. coli strains may confer a therapeutic effect.
Methods
Plasmid construction: The L-asparaginase II gene ansB (NCBI Reference Sequence: NP_415200.1) [SEQ ID No.: 222] was cloned into a pUC57 plasmid operatively linked to the promoter BBa_J23100, an optimised RBS sequence (98.3% EMOPEC prediction), and a transcription terminator T1 from the E. coli rrnB gene. The constructed plasmid, pUC57-ansB, was transformed into EcNΔdapA together with the inv-hly expression plasmid pGB2 (Table 4).
In vitro L-asparaginase delivery: Bacterial transfer of L-asparaginase was performed in a flat-bottom 6-well plate, seeded with 1.2×106 Jurkat E6-1 cells per well. Cells were infected with overnight cultures of EcNΔdapA strains comprising the plasmids: pGB2 and pUC57-ansB; or pUC57-ansB alone as a first negative control; or pGB2 alone as a second negative control. Bacteria cells of the EcNΔdapA strains were added at a multiplicity of infection (MOI) of 500, 1000, or 2000 in RPMI media supplemented with 10% fetal bovine serum (FBS). Additionally, Jurkat E6-1 cells were treated with commercially available L-asparaginase from Escherichia coli (Sigma Aldrich) as a positive control. Plates were centrifuged at 100×g for 10 min in a swinging bucket centrifuge, to initiate contact between cells and bacteria, and incubated for 1 hour at 37° C. and 5% CO2. Next, well contents were transferred to individual 15 ml falcon tubes and washed trice with Phosphate Buffered Saline (Gibco™ PBS, pH 7.4 at room temperature, Fischer Scientific) at 300×g for 5 min at RT. The pellet was re-suspended in complete growth medium plus gentamicin, to kill extracellular bacteria, and Incucyte® Caspase-3/7 Green Reagent and IncuCyte® Cytotox Red Reagent was added to monitor apoptosis and cell death, respectively. Cells were incubated 37° C. and 5% CO2 for 48 hours inside an Incucyte S3 live cell imaging machine.
In vivo L-asparaginase delivery: Five- to seven-week-old female NOD.Cg-Prkdcscid Il2rgtmlWjl/SzJ (NSG) mice (The Jackson Laboratory) (Mamonkin, Rouce, Tashiro, & Brenner, 2015) were intravenously injected with 3×106 firefly luciferase expressing Jurkat E6-1 cells (Jurkat-FFluc). After 3- or 6-days post engraftment, mice were intravenously injected with overnight cultures of EcNΔdapA strains comprising the plasmids: pGB2 and pUC57-ansB; or pGB2 alone as a first negative control; or PBS without bacteria as a second negative control. As a positive control, mice were injected intraperitoneally with 6 U/g L-asparaginase (Sigma Aldrich) (Takahashi et al., 2017) 3- or 6-days post-engraftment. To monitor tumor burden, mice were injected intraperitoneally with D-Luciferin (150 ug/kg) and luminescence was determined with an IVIS Imaging system (Caliper Life Sciences). Daily tail vein blood samples were taken to determine tumor load via flow cytometry and to measure cytokine levels via ELISA.
A bacteria-mediated delivery vector was engineered by transforming the deletion strain, EcN-pMUT1 ΔdapA with recombinant nucleic acid molecules encoding the envelope s glycoproteins gp120 and gp41 found in Human Immunodeficiency Virus 1 (HIV-1) and a third protein derived from a member of the 1.B.12.8.2 autotransporter-1 (at-1) family. When the three proteins are expressed as domains linked together in a fusion protein, they confer on the cell the ability to act as a bacteria-mediated delivery vector for delivery of the therapeutic agent to a mammalian non-phagocytic immune cell.
Methods:
Cloning “Gp120-Gp41-Antigen 43 (FLU)” Expression Plasmid:
The construction of a novel HIV env protein complex for bacterial expression was based on a modified protocol of Rathore et. al., In short, the sequence of HIV env protein mimic BG505 NFL.664 was chosen as a design template (Sarkar et al., 2018) due to favourable CD4 CCR5 cell targeting tropism and reduced glycosylation sites. The deleted membrane proximal external region (MPER) of the BG505 NFL.664 sequence was added back to maintain crucial membrane fusion functionality. The missing MPER sequence was added from uniprot entry Q2N0S6 which was used for annotation of the BG505 NFL.664 protein crystal structure 6B0N. In addition, the native amino acid, isoleucine, at position 559 was returned to maintain structural flexibility. To improve intracellular protein assembly and bacterial outer membrane expression, protein glycosylation was removed through mutation of asparagine (N) residues of N-linked glycosylation motifs (NXT/S) in the amino acid sequences of gp120 and gp41. The creators of the BG505 NFL.664 construct published identified glycosylation sites in their protein construct but were only able to detect glycans in the resolved crystal structure of the protein (Sarkar et al., 2018). The 6B0N protein sequence however showed stretches of sequence that contained NXS/T glycosylation motifs that lacked a secondary structure. In addition, glycosylation sites identified by the authors were described at incorrect AA positions due to incomplete numbering in the 6B0N PDB file stemming from breaks in secondary structure. Therefore, it was decided to mutate all NXS/T motifs in the sequence to further design the novel env protein complex. A total of 29 potential glycosylation sites were identified in the protein sequence, equal to the number identified in the reference HIV-1 strain HxB2. Using the NetNGlyc 1.0 Server, 21 of the 29 potential motifs were predicted to be likely glycosylated (Gupta & Brunak, 2002). After NXS/T motifs were identified, the tool HBPLUS was used to detect potential hydrogen bonds between Asn and neighbouring AA to avoid unsatisfied hydrogen bonding groups upon NXS/T mutations. AA frequencies at NXS/T motifs were identified from a multiple sequence alignment of 3978 HIV1 env sequences from a 2019 HIV-1 sequence compendium (Erk.hiv.lanl.gov) using the webtool AnalyzeAlign. The BG505 NFL.664 env AA sequence was used as a reference sequence with the following AA sequence added from the HxB2 reference sequence to the sequence beginning, to improve alignment numbering: MRVKEKYQHLWRWGWRWGTMLLGMLMICSATEK (SEQ ID NO.: 282). The ASN in the BG505 NFL.664 env sequence was then changed to the second most frequent AA at this position to remove glycosylation. The AA was changed to a less frequent AA if any unfavorable charge variations or structurally similar Ala and Gln were encountered. Using the software Chimera, the mutated sequence was computationally modelled against the original 6B0N sequence to determine any possible structural changes caused by AA mutations (Pettersen et al., 2004). Due to partially missing secondary structures, the 6B0N file was first modelled using Chimera to create a complete protein structure model. The structural similarity of the novel mutated env model with the refined 6B0N model was evaluated in Chimera based on the GA341 model score (Values higher than 0.7 generally indicate a reliable model with more than 95% probability of having the correct fold), the zDOPE normalized Discrete Optimized Protein Energy score (Negative values indicate better models), and the estimated RMSD model score (lower values indicate better models). The 2×GGGGS linker present in BG505 NFL.664 was maintained as it was previously determined to be of optimal length to allow native-like non-covalent bond formation and enable correct trimer formation (Sharma et al., 2015).
After confirming structural integrity of glycosylation site mutations, the E. coli outer membrane autotransporter Antigen 43 (flu) was added to the mutated protein sequence to enable bacterial surface expression. As the gp120 part of the env complex needed to be exposed away from the bacterial membrane and gp41 needed to be in close proximity of the bacterial membrane, anchoring could not be done through commonly used n-terminal fusion to an anchoring protein. Instead, the nucleotide sequence encoding the fused gp120-linker-gp41 domains was cloned between the coding sequences for the signal peptide and the N-terminus of the linker peptide of flu. The linker peptide ensured that the fused gp120-linker-gp41 proteins were displayed on the surface of the bacterial cell and not inside the R-barrel of the Flu protein where the Flu autochaperone C-terminus is located. The autotransporter domain serves to anchor the envelope complex to the bacterial cell membrane, and thereby performs the function of the hydrophobic transmembrane region of gp41, which was omitted from the fusion protein encoding gene construct. The resulting plasmid pCOLA_gp120-gp41-flu (SEQ ID NO 169) was transformed into E. coli TOP10. Bacteria were labelled with anti-HIV gp160 antibody (FITC conjugated, orb461521, Biorbyt) and observed on a Leica DM4000 B fluorescent microscope (Leica Microsystems) to confirm surface expression of gp160.
Results:
In this study, a novel bacterial intracellular delivery vector was constructed that exploits the natural CD4+CCR5+ cell specific targeting feature of the HIV-1 env protein complex gp120-gp41. Recombinant versions of this protein complex are termed gp140, not to be confused with the pre-cleavage complex gp160. In its native viral host, the gp120-gp41 complex initiates fusion of the viral capsid with the target cell membrane to enable virus entry into the host. In contrast to viruses and mammalian cells, gram negative bacteria contain both outer and inner membranes. Therefore, as demonstrated herein, expression of gp120-gp41 on the E. coli outer membrane surface allows for targeted delivery of periplasmic and/or cytoplasmic molecules to CD4+CCR5+ T cells in a novel manner, as illustrated in
The design strategy used for the novel gp120-gp41 construct was based on the BG505 NFL.664 env 6B0N sequence (Sarkar et al., 2018). After the mutation of 29 potential glycosylation sites and addition of several missing AA sequences, the novel construct was modelled against the reference structure 6B0N to validate that original secondary structures were maintained. Using Chimera, the novel model was confirmed to be highly similar to the reference model with GA341, zDOPE, and estimated RMSD values of 1.00, −0.13, and 7.347, respectively. Some of the predicted alpha helixes in the gp120 model were slightly shifted compared to the reference model structure. The amino acid sequence at these areas was the same and it was therefore assumed not to result in any change in protein function. After cloning of the novel BACTERIAL INTRACELLULAR DELIVERY VECTOR gp120-gp41 env construct into an expression plasmid and transformation of the resulting pCOLAgp120-gp41-flu plasmid into E. coli TOP10, surface expression of BACTERIAL INTRACELLULAR DELIVERY VECTOR gp120-gp41 was investigated using a FITC labelled anti-HIV gp160 antibody. As shown in
Methods
Primary human activated pan T cells were diluted to 5×105 cells/ml in pre-warmed ImmunoCult XF T Cell Expansion medium supplemented with 25 ng/ml of IL-2 and added to 48 well plates at 200 μl per flask. An overnight culture of either E. coli T7, carrying the invasive plasmid pCOLA-gp120-gp41 (SEQ ID NO. 169) and the periplasmic fluorescent protein reporter plasmid pSW002-Pc-TorA(sp)-mTurquoise2 (SEQ ID NO. 268), was diluted in complete cell culture medium to an MOI of 1280 or 6.4×108 cfu/ml. E. coli T7+pCOLA-gp120-gp41 without the reporter plasmid as well as uninfected T cells served as negative controls. 200 μl of bacterial dilutions were added to the wells and plates were centrifuged at 100×g for 30 seconds to initiate contact between the bacteria and human cells. The co-cultures were incubated for 2 hours at 37° C. and 5% CO2 to allow cell infections to occur. Next, cell suspensions were pelleted in 96 well V-bottom plates and resuspended in 200 μl of complete cell culture medium containing 50 μg/ml Gentamicin. Cell suspensions were transferred to new 48 well plates and incubated for a total of 6 hours. For sample collection, cells were pelleted in 2 ml Eppendord tubes and fixed in 1 ml of Image-iT Fixative Solution (4%) for 15 minutes at RT. Fixed cells were pelleted, resuspended in 100 μl PBS and transferred to a new 96 well plate for analysis on a Cytoflex S flow cytometer. 10 μl of each sample was stained with FITC conjugates anti-E. coli LPS antibody, mounted on microscopy slides and observed under a Leica DM4000 B fluorescent microscope
Results
Infected cells were analysed for mTurquoise2 expression on a fluorescence microscope for visual detection and a flow cytometer for quantification. A differential antibody staining method was used for fluorescence microscopy where an anti-E. coli LPS antibody labelled extracellular bacteria and absence or presence of mTurquoise2 fluorescence indicated successful or unsuccessful protein delivery, respectively. Flow cytometry revealed that cell numbers decreased over time for the bacterial conditions, as expected due to the cells being exposed to bacterial endotoxins and nutrient depletion in the media during infection periods (
This observation demonstrated that the majority of observed fluorescence from cells during flow cytometry analysis most likely originated from adherent bacteria and not from intracellular delivery to T cells. On the other hand, this observation also demonstrated the high efficacy of T cell binding by the gp140 protein complex. Considering the weak fluorescence of mTurquoise2 observed on microscopy images, fluorescent proteins, concentrated in the bacterial periplasm, could be highly diluted in their fluorescent signal upon release into the mammalian cell periplasm. This would likely result in a weak fluorescence signal within infected target cells which would be below the detection limit of fluorescence analysis from both microscopy and flow cytometry.
Despite this, microscopy analysis still revealed several cells with adherent bacteria that lacked mTurquoise2 fluorescence which indicated periplasmic protein transfer. The number of observed protein transfer events per cell increased over time, which indicated the high numbers of adherent cells could possibly translate into high periplasmic transfer events if infected cells were observed for more than 6 hours. Of note was an observation at the 5 hour time point where one non-adherent bacterial cell lacked mTurquoise expression (
Methods
PBMCs isolated from buffy coats were diluted to 2.2×106 cells/ml in ImmunoCult XF T Cell Expansion medium supplemented with 25 ng/ml of IL-2 and added to a 50 ml suspension culture flask (Cellstar, Greiner Bio-One) at 5 ml per flask. Overnight cultures of E. coli T7+pCOLAgp120-gp41+pUC19 were diluted in complete cell culture medium at MOIs ranging from 640-1280 or 1.4×109-2.8×109 cfu/ml. E. coli T7+pCOLAgp120-gp41 infected cells or uninfected cells served as negative controls for protein transfer. 5 ml of bacterial dilutions were added to the cells and culture flasks were incubated for 2 hours at 37° C. and 5% CO2. To terminate cell infections, flask contents were transferred to 50 ml falcon tubes (Corning) and washed once with PBS. To detach adherent PBMC, a cell scraper was used to dislodge cells. Washed cell pellets were resuspended in complete culture medium containing MycoZap Plus-CL (Lonza Bioscience) and transferred to new 50 ml suspension culture flasks. Cell cultures were incubated for 2-24 hours at 37° C. and 5% CO2. In order to detect β-lactamase protein transfer, cultured cells were labelled with the LiveBLAzer™ FRET-B/G Loading Kit with CCF4-AM (Thermo Fischer Scientific), following the manufacturer's instructions. In short, cells were centrifuged at 300×g for 7 minutes and resuspended in 6× loading solution containing CCF4-AM (solution A), solution B, and solution C/sort buffer, followed by incubation at RT for 1 hour under gentle shaking, protected from light. From this point onwards, cells were kept protected from light to avoid degradation of fluorochromes. Labelled primary cells were resuspended in 900 μl of PBS and 100 μl of Image-iT Fixative Solution (4%) for a final dilution of 0.4% paraformaldehyde. Cells were incubated for 7 minutes at RT, followed by centrifugation and resuspension in 999 μl of PBS and 1 μl of eBioscience Fixable Viability Dye eFluor® 780 (Thermo Fischer Scientific). After incubation at 4° C. for 15 minutes, cells were centrifuged and resuspended in 1 ml Image-iT Fixative Solution (4%). Following incubation at RT for 7 minutes, cells were washed once in 1 ml of PBS, resuspended in 500 μl stain buffer, and incubated for 15 minutes at 4° C. Next, cells were centrifuged and resuspended in 170 μl stain buffer and 10 μl each of anti-human CD8A SK1 APC antibody (Invitrogen, Thermo Fischer Scientific), anti-human CD3 OKT3 SB600 antibody (Invitrogen, Thermo Fischer Scientific), and anti-human CD4 OKT4 PE antibody (Invitrogen, Thermo Fischer Scientific). Cells were incubated with the antibodies overnight at 4° C. and the next day washed twice with 5 ml stain buffer. Antibodies and their dilutions are listed in table 5.
e. coli serotype o/k
e. coli serotype o/k
In an effort to remove cell aggregates in the suspension, cells were resuspended in 300 μl of PBS containing 100 μg/mL DNAse and 5 mM MgCl2 and incubated for 30 minutes at RT. Cell suspensions were washed once with 1 ml of PBS containing 5 mM MgCl2 and resuspended in 600 μl of PBS containing mM MgCl2 and 50 μg/mL DNAse. Finally, the cell suspension was gently passed through a pre-wet 70 μM reversible cell strainer (Stemcell Technologies) into 12×75 mm FACS tubes. Prepared cell suspensions were analysed on a Novocyte Quanteon flow cytometer. For compensation of fluorochrome spillover, single color control samples were prepared from cells infected with invasive bacteria carrying a β-lactamase expression plasmid. Auto-compensation was performed using the FlowLogic analysis software, where gates for positive populations as well as compensation values were manually adjusted to minimize fluorescence spillover. A compensation control for CCF4-AM was used to determine spillover into other channels from the green and blue signals as well as spillover from other fluorochromes into the detection filters for green and blue signals. As the CCF4-AM control emitted both green and blue fluorescence signals, no compensation was applied from the green signal in the blue detection filter and vice versa. The compensation matrix is shown in table 6.
Results
Cells were analysed on a flow cytometer with the CCF4-AM assay to detect protein transfer. In addition to CCF4-AM substrate loading, infected cells were also labelled with an antibody panel that allowed the identification of T and non-T cells with CD3 and further identification of cell subtypes with CD4 and CD8. A viability dye was used to exclude dead cells from analysis. After gating for live singlet lymphocytes, CD3+ and CD3− populations were assessed for their blue fluorescence and blue populations were further characterized by their distribution of CD4/CD8 positive sub populations (see
A significantly smaller fraction of CD3− lymphocytes infected with E. coli T7+pCOLA-gp140+pUC19, around 37% at 4 h p.i., also appeared to have blue cells, indicative of bacterial protein transfer
Given the highly similar distribution of CD3 cell subtypes within the blue CD3 population and the total CD3 population, one might argue that the majority of blue CD3+ cells being CD4+might not be due to specific gp140 targeting of the CD4 receptor but merely shows indiscriminate cell targeting that results in the initial cell distribution. If this argument was correct, then the percentage of CD4+ cells in the blue CD3+population should be the same as the CD4+percentage of the total CD3+population. For example, if the total CD3+population would consist of 70% CD4+ cells then the percentage of CD4+cells in the blue CD3+population should also be 70%. However, as seen in
In conclusion, the results obtained in this study showed, for the first time, that both CD3 specific targeting and protein delivery by the bacterial gp140 delivery system occurred at high efficiencies.
Methods
Two different injection routes were evaluated for potential differences in tolerance to injected invasive bacteria in mice. Animal experiments were performed in house after approval from the Danish Animal Experiments Inspectorate. A total of 8 female CB6F1 mice, 6-8 weeks old, were housed in randomized pairs of four in Type3 cages inside a ScanTainer (Scanbur), with ad libitum access to water and regular chow diet (Altromin 1314, Altromin). Acclimatized animals were injected either intravenously or intraperitoneally with 100 μl of an overnight culture of EcNΔdapA, carrying invasive plasmid pSQ11, that was washed once in sterile PBS and diluted to 1×109 cells/ml in sterile PBS. Immediately after injection, animals were closely monitored for changes in activity levels indicative of poor tolerance to bacterial injections. After 40 minutes, 4 hours and 1 week, 10 μl of blood were collected from the tail vein and stored in PBS on ice for later enumeration of viable bacterial cells. Immediately before and 7 days after bacterial injections, total body weight of the animals was measured. After 7 days, all animals were sacrificed through cervical dislocation and dissected to collect the liver, spleen, kidney, and lungs for later numeration of bacterial cells. The organs were weighted and transferred to gentleMACS C tubes (Miltenyi Biotec) containing 3 ml PBS for dissociation and generation of single cell suspensions using a gentleMACS Dissociator (Miltenyi Biotec). Dissociated liver, kidney, and lung samples were additionally passed through a 70 μm cell strainer. Single cell suspensions of prepared organs as well as tail vein blood samples were serially diluted in sterile PBS and plated on LB plates supplemented with DAP at a final concentration of 100 μg/ml and 50 μg/ml Kanamycin to enumerate live bacterial cell numbers.
Results
Only limited data exists on the safety of live EcN blood injections. Previous studies were all performed with non-auxotrophic E. coli strains which, in theory, were actively replicating after injection into the blood stream. In contrast, BACTERIAL INTRACELLULAR DELIVERY VECTORs designed in this study contained a DAP auxotrophy which inhibited growth in environments such as the bloodstream where DAP is not present. It was therefore hypothesised that higher amounts of auxotrophic bacteria could be safely injected into the bloodstream than what was deemed safe for non-auxotrophic replicating E. coli strains. It was first investigated whether a dose of 1×108 cfu of auxotrophic EcN BACTERIAL INTRACELLULAR DELIVERY VECTOR could be administered safely into healthy mice via i.v. injection. In addition to i.v. injections, the intraperitoneal (i.p.) injection route was also investigated, as it was hypothesised that bacterial cells could be better tolerated through gradual release from the intraperitoneal cavity into the blood stream. Healthy, female, 6-8 weeks old CB6F1 mice were injected either i.v. or i.p with 1×108 cfu/injection of the auxotrophic and invasive strain EcNΔdapA+pSQ11 and monitored over 1 week. Samples of tail vein blood and major organs were assessed for recovery of bacterial cells. Moreover, organ and body weights were measured to determine changes indicative of adverse reactions to BACTERIAL INTRACELLULAR DELIVERY VECTOR injections. As shown in
Methods
In an effort to determine the highest possible dose of invasive bacteria that could be injected intravenously in a safe manner, rats and mice were injected in a dose escalating manner. A total of 10 female CB6F1 mice, 6-8 weeks old, or 10 female Sprague Dawley rats, 6-8 weeks old, were housed in randomized pairs of 2 in Type3 cages inside a ScanTainer (Scanbur), with ad libitum access to water and regular chow diet (Altromin 1314, Altromin). Overnight cultures of EcNΔdapA containing the invasive plasmid pGB3 were washed once in sterile PBS and diluted in sterile PBS to MOIs of 1030-1370 or 3×1010-4×1010 cells/ml for mouse injections, or MOIs of 29-98 or 3×109-1×1010 cells/ml for rat injections. Either 100 μl or 500 μl of bacterial dilutions were injected intravenously into acclimatized mice or rats, respectively. Depending on cooperation, rats and mice were given low doses of the anaesthetic Hypnorm prior to i.v. injection. Changes in activity, measured in response to physical stimulation, were closely monitored immediately after injection as well as 30 minutes, 2 hours, 4 hours, and once daily after the first day for a total of 3 days. Total body weight was measured immediately before injections and once daily in the following days for a total of 3 days. Body temperatures were measured in triplicate, using a handheld infrared thermometer, immediately before injection as well as 30 minutes, 2 hours, 4 hours, and once daily after the first day for a total of 3 days.
Results
A range of 1×108-3×109 cfu of auxotrophic and invasive EcNΔdapA+pGB3 were injected i.v. into healthy CB6F1 mice and total body weight as well as body temperature was measured for 3 days p.i. Bacterial doses of up to 3×109 cfu were tolerated with an initial drop in body weight after 1 day before slight recovery of body weights after 2 days when no statistically significant differences were observed compared to day 0 (
In conclusion, both rats and mice tolerated high doses of i.v. injections with auxotrophic and invasive bacterial delivery vectors. While rats tolerated higher cfu/injection, mice tolerated higher MOIs. Thus, this study successfully showed for the first time that engineered bacterial delivery vectors can be safely injected into the blood stream of rodents which provides a solid foundation for further in vivo investigations into the functionality and efficacy of therapeutic molecule transfer to T cells in vivo.
Engineered E. coli strain (EcN-ΔdapA) containing a combination of an inv-hly expression plasmid (pSQ11) and a reporter plasmid (PL0017; Example 1) containing a mCherry gene encoding monomeric red fluorescent protein (mCherry) was used to infect Hela cells and shown to additionally transfer and express the mCherry reporter gene in infected Hela cells.
Methods
HeLa cells were seeded in a 6-well plate at 1×105 cells/well and allowed to attach overnight. Monolayers where then infected with cells of engineered E. coli EcNΔdapA pSQ11PL0017, or EcNΔdapA pSQ11 strains (Table 4) at an MOI of 500 for 1 hour at 37° C. and 5% CO2. After the infection, monolayers were washed trice with PBS to remove bacteria and incubated in fresh DMEM media supplemented with 10% FCS and Ciprofloxacin (10 μg/ml) inside an Incucyte live cell imager at 37° C. and 5% CO2.
Results
HeLa cells were infected with cells of engineered E. coli strains expressing the two-component delivery system (inv-hly) encoded by pSQ11, and comprising a mCherry reporter plasmid. Since mCherry gene is operably linked to a promoter and terminator functional in mammalian cells, its expression can only occur once the gene is transferred to the mammalian Hela cells by the invading E. coli and escapes into the Hela cell intracellular space. Detection of mCherry fluorescence in the infected Hela cells demonstrated that the E. coli cells invaded the Hela cells and transferred the mCherry reporter plasmid, while being absent in uninfected Hela cells or Hela cells infected with cells of E. coli strain pSQ11 plasmid (not shown). Expression of the transferred mCherry gene was first detected as fluorescence in the Hela cells after approximately 24 hours (
| Number | Date | Country | Kind |
|---|---|---|---|
| 20184439.6 | Jul 2020 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2021/068734 | 7/7/2021 | WO |
