WO2024084054A1 - Modified microorganisms - Google Patents
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- WO2024084054A1 WO2024084054A1 PCT/EP2023/079317 EP2023079317W WO2024084054A1 WO 2024084054 A1 WO2024084054 A1 WO 2024084054A1 EP 2023079317 W EP2023079317 W EP 2023079317W WO 2024084054 A1 WO2024084054 A1 WO 2024084054A1
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
- C07K14/24—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Enterobacteriaceae (F), e.g. Citrobacter, Serratia, Proteus, Providencia, Morganella, Yersinia
- C07K14/245—Escherichia (G)
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
- A61K35/66—Microorganisms or materials therefrom
- A61K35/74—Bacteria
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
- C12N1/36—Adaptation or attenuation of cells
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/74—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2319/00—Fusion polypeptide
- C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
- C07K2319/02—Fusion polypeptide containing a localisation/targetting motif containing a signal sequence
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2319/00—Fusion polypeptide
- C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
- C07K2319/036—Fusion polypeptide containing a localisation/targetting motif targeting to the medium outside of the cell, e.g. type III secretion
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12R—INDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
- C12R2001/00—Microorganisms ; Processes using microorganisms
- C12R2001/01—Bacteria or Actinomycetales ; using bacteria or Actinomycetales
- C12R2001/42—Salmonella
Definitions
- the present invention relates to live attenuated Gram-negative bacteria modified to enable delivery of a biological molecule.
- Recombinant protein secretion from bacterial chassis has been a strategy explored to deliver relevant cargo from within the cellular envelope [Freudl et al., 2018]. This can facilitate downstream purification and processing of biotechnologically relevant proteins envelope [Freudl, R., et al., 2018] or deliver actively pharmacological molecules in appropriate tissues (e.g., tumours in Immuno Oncology) in vivo [Carrier, M.J., et al., 1992; Yang, E.Y. and Shah, K., 2020; Ruano-Gallego, D., et al., 2019],
- Bacteria such as Salmonella enterica Typhi can naturally home in and establish within the tumour microenvironment (TME) [Hoffman, R.M., 2011], This can allow targeted delivery of relevant proteins and peptides in vivo to boost the initial immune response elicited by the exposure to pathogen-associated molecular patterns from Salmonella [Chen, J., et al., 2021], Salmonella can typically secrete proteins using specific pathways that rely on needle-like structures to inject protein effectors into mammalian cells [Lhocine, N., et al., 2015; Park, D., et al., 2018], After assembly of the needle and piercing of the mammalian host, a series of proteins (effectors), which contain specific signal peptides, are translocated to the host’s cytosol, where they can, for example, induce the engulfment of the bacterium [Park, D., et al., 2018], However, the fusion of recombinant proteins to recognized
- the uropathogenic strains of Escherichia coli can export a pore-forming toxin (hemolysin), involved in the lysis of erythrocytes, into the interstitial space using a specialised secretion pathway, named Type 1 Secretion System (T1SS) [Thomas, S., et al., 2014],
- T1SS Type 1 Secretion System
- HlyB and HlyD transport proteins
- HlyA Upon expression of the toxin, HlyA, and recognition of an approximately 60 base pair-long signal peptide (HlyAs) on its C- terminus end, the TolB1 D2 complex interacts with TolC, opening a pore that allows translocation of HlyA from the cytoplasm whilst the protein is still not folded.
- HlyC activates the toxicity of HlyA by transferring an acyl group into two internal lysins (Lys564 and Lys690) whilst this is still in the bacterial cytosol (/.e., before export).
- the hly genomic island is composed of four genes, hlyCABD, and one regulatory activator, hlyR [Gentschev, I., et al., 2002; Nagamatsu, K., et al., 2015; Nieto, J.M., et al., 2000; Pourhassan, N.Z., et al., 2022; Khosa, S., et al., 2018; Madrid, C., et al., 2002], Beyond the control exerted by the product of hlyR, the expression of the toxin is controlled by multiple genetic elements, such as an operator polarization sequence (ops) and RfaH binding sequence [Gentschev, I., et al., 2002; Nagamatsu, K., et al., 2015; Wang, B., M.
- TME tumour microenvironment
- hlyCABD operon shown in Figure 1
- Figure 2 the hlyCABD operon
- the present invention provides a live attenuated Gram-negative bacterium comprising a modified hlyCABD operon, wherein the modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly genes involved in secretion.
- the present invention provides a vaccine composition
- a vaccine composition comprising a live attenuated Gram-negative bacterium comprising a modified hlyCABD operon, wherein the modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly genes involved in secretion.
- the present invention provides a method of treating, preventing, inhibiting, preventing recurrence or controlling a disease in a subject, wherein the method comprises administering to a subject a live attenuated Gram-negative bacterium, said live attenuated Gram-negative bacterium comprising a modified hlyCABD operon, wherein the modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly genes involved in secretion.
- the present invention provides a method of delivering a therapeutic molecule to the interstitial space in between eukaryotic cells of the tumour microenvironment in a subject suffering from a tumour, said method comprising the steps of: i) modifying a live attenuated Gram-negative bacterium, said live attenuated Gram-negative bacteria comprising a modified hlyCABD operon, wherein the modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly genes involved in secretion and ii) administering said modified Gram-negative bacterium to the subject in need thereof.
- FIG. 1 shows a schematic representation of the hly operon which encodes the Type 1 Secretion System (T1SS).
- T1SS Type 1 Secretion System
- Figure 2 shows a schematic representation of the refactored T1SS derived from E. coli.
- the cargo region and the structural region are shown to be separated into two transcriptional units independently controlled by promoter P1 and promoter P2. Additionally, two variants of cargo region were built, one variant in which the hlyC gene was upstream of the secretable cargo, and one variant lacking the hlyC gene in order to assess the effect of the hlyC gene on cargo secretion yield.
- Figure 3 shows the secretion of reporter protein mScarlet under different configurations of the T1SS.
- Figure 3A demonstrates the impact in the export of the ratio of transcription of cargo versus structural proteins was assessed by manipulating the strength of promoter P1 and promoter P2. Analysis of protein content in the supernatant shows that increased strength of cargo promoter results in enhanced protein detected in the supernatant up to 10 times. Interestingly, increasing strengths in the promoter controlling the expression of the structural genes boosted the protein yields up to 64 times.
- Figure 3B demonstrates that when the same circuits are utilised, plus the addition of hlyC upstream of the cargo, the overall pattern previously observed was conserved, albeit at lower levels of proteins export (4 times lower). This could be due to the binding of H-NS of Hha downstream of hlyC or cell burden due to the addition of hlyC expression.
- Figure 4 shows the secretion of recombinant protein LLO (also known as ListeroLysin O) under different configurations of T1SS.
- Figure 4A shows that the reporter gene mScarlet was exchanged by hly from Listeria monocytogenes and its export into the culture supernatant was assessed under all configurations. Overall protein levels exported were lower than with reporter protein mScarlet, although the observed pattern of increased secretion with increased promoter P2 strength was conserved.
- Figure 4B demonstrates that contrary to the previous observation as shown in Figure 3, the addition of hlyC does not result in decreased export, and the pattern observed, where enhanced expression of hlyBD correlates with higher secretion, is also conserved. This suggests that the decrease previously observed in Figure 3 may be due to the protein expression burden on the cell.
- Figure 5 shows the two-plasmid system used to allow modulation of cargo export yields.
- the split of two circuits into independent plasmids supports modulation of cargo export yields by the combination of promoter strength and copy number. This allows screening for optimal experimental conditions that allow optimizing yields without over-burdening the bacterial carrier.
- the experiment evaluated the export of mScarlet in the T1SS dual-plasmid system, where mscarlet-hlyA fusion was controlled by increasingly strong promoters (2 (SEQ ID NO: 22), 4 (SEQ ID NO: 23), 6 (SEQ ID NO:24)) and hlyBD was under the control of the same increasing promoters.
- non-natural bacterium or bacteria refers to bacterial (prokaryotic) cells that have been genetically modified or “engineered” such that it is altered with respect to the naturally occurring cell.
- genetic modification may for example be the incorporation of additional genetic information into the cell, modification of existing genetic information or indeed deletion of existing genetic information. This may be achieved, for example, by way of transfection of a recombinant plasmid into the cell or modifications made directly to the bacterial genome.
- a bacterial cell may be genetically modified by way of chemical mutagenesis, for example, to achieve attenuation, the methods of which will be well known to those skilled in the art.
- non-natural bacterium or bacteria may refer to both recombinantly modified and non- recombinantly modified strains of bacteria.
- heterologous polynucleotide refers to a polynucleotide that has been introduced into the live attenuated Gram-negative bacterium, i.e., the introduction of a polynucleotide that was not previously present. Accordingly, the live attenuated Gram-negative bacteria herein disclosed is a recombinant strain of bacteria.
- the heterologous polynucleotide in the context of the present invention may be a DNA molecule or RNA molecule intended for delivery to a eukaryotic cell.
- the heterologous polynucleotide in the context of the present invention may encode for a protein or peptide intended for delivery to a eukaryotic cell.
- the heterologous polynucleotide in the context of the present invention may encode for an RNA molecule intended for delivery to a eukaryotic cell.
- the resulting RNA molecule or protein is also referred to herein as “cargo” or a “cargo molecule”.
- the DNA or RNA molecule to be encoded is a mammalian DNA or RNA molecule.
- prophylactic treatment refers to a medical procedure whose purpose is to prevent, rather than treat or cure, an infection or disease. In the present invention, this applies particularly to the vaccine composition.
- prevent as used herein is not intended to be absolute and may also include the partial prevention of the infection or disease and/or one or more symptoms of said infection or disease.
- therapeutic treatment refers to a medical procedure with the purpose of treating or curing an infection or disease or the associated symptoms thereof, as would be appreciated within the art.
- tumor refers to a cell or population of cells whose growth, proliferation or survival is greater than growth, proliferation or survival of a normal counterpart cell, e.g., a cell proliferative or differentiative disorder. Typically, the growth is uncontrolled.
- malignancy refers to invasion of nearby tissue.
- metastasis refers to spread or dissemination of a tumour, cancer or neoplasia to other sites, locations, or regions within the subject, in which the sites, locations or regions are distinct from the primary tumour or cancer.
- the cancer is malignant. In an alternative embodiment, the cancer is non-malignant.
- an effective amount refers to a sufficient amount of an agent to provide the desired biological or therapeutic result. That result can be reduction, amelioration, palliation, lessening, delaying, and/or alleviation of one or more of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system.
- an effective amount may comprise an amount sufficient to cause a tumour to shrink and/or to decrease the growth rate of the tumour (such as to suppress tumour growth) or to prevent or delay other unwanted cell proliferation.
- an effective amount is an amount sufficient to delay development or prolong survival or induce stabilisation of the cancer or tumour.
- a therapeutically effective amount is an amount sufficient to prevent or delay recurrence.
- a therapeutically effective amount can be administered in one or more administrations.
- the therapeutically effective amount of the agent or combination may result in one or more of the following: (i) reduce the number of cancer cells; (ii) reduce tumour size; (iii) inhibit, retard, slow to some extent and preferably stop cancer cell infiltration into peripheral organs; (iv) inhibit (i.e., slow to some extent and preferably stop) tumour metastasis; (v) inhibit tumour growth; (vi) prevent or delay occurrence and/or recurrence of tumour; and/or (vii) relieve to some extent one or more of the symptoms associated with the cancer.
- a "therapeutically effective dosage” may induce tumour shrinkage by at least about 5 % relative to baseline measurement, such as at least about 10 %, or about 20 %, or about 60 % or more.
- the baseline measurement may be derived from untreated subjects.
- a therapeutically effective amount of a therapeutic compound can decrease tumour size, or otherwise ameliorate symptoms in a subject.
- One of ordinary skill in the art would be able to determine such amounts based on such factors as the subject's size, the severity of the subject's symptoms, and the particular composition or route of administration selected.
- treatment refers to administering an active agent with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve, or affect a condition (e.g., a disease), the symptoms of the condition, or to prevent or delay the onset of the symptoms, complications, biochemical indicia of a disease, or otherwise arrest or inhibit further development of the disease, condition, or disorder in a statistically significant manner.
- a condition e.g., a disease
- the term "subject" is intended to include human and non-human animals. Preferred subjects include human patients in need of enhancement of an immune response.
- the methods are particularly suitable for treating human patients having a disorder that can be treated by augmenting the immune response. In a particular embodiment, the methods are particularly suitable for treatment of neoplastic disease or infectious disease in vivo.
- “about” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within 1 or more than 1 standard deviation per the practice in the art. Alternatively, “about” can mean a range of up to 20%. When particular values are provided in the application and claims, unless otherwise stated, the meaning of "about” should be assumed to be within an acceptable error range for that particular value.
- the inventors of the present invention have surprisingly found that the hlyCABD operon (shown in Figure 1) can be modified in such a way so as to enable the delivery of cargo molecules to the interstitial space between eukaryotic cells ( Figure 2).
- Figure 1 the hlyCABD operon
- Figure 2 the inventors of the present invention carried out a rational refactorisation of the hly genomic island.
- the hly operon was separated into two segments: a first segment (“cargo region”) and a second segment (“structural region”).
- the process of separating the four genes of the hlyCABD operon into two segments allows the genes involved in cargo production and/or activation (hlyC, hlyA) to be transcriptionally separated from those involved in secretion (hlyB, hlyD).
- the toxin sequence of hlyA can be replaced by a reporter gene (eg mScarlet), or indeed a heterologous nucleotide encoding any other cargo molecule, while maintaining the translocation peptide (HlyAs).
- the optimal levels of transcription of the cargo and the secretion modules were screened by manipulating the strength of the promoters upstream of each segment. The results described herein show that splitting the operon into two segments results in functional translocation, which is increased upon increasing the transcription levels of both segments. Accordingly, the present invention relates to a live attenuated Gram-negative bacterium comprising a modified hly operon.
- T1SS Type 1 Secretion System
- HlyA Escherichia coli a-hemolysin secretion system
- HlyA is a bacterial toxin and virulence factor. The secretion and activation of HlyA is determined by the hlyCABD operon.
- HlyB and HlyD are inner membrane proteins (which may be found in a HlyB-HlyD complex anchored to the inner membrane of the Gram-negative bacterial cell), whereas TolC is located on the outer membrane of the Gram-negative bacterial cell.
- HlyA carries a translocation signal sequence, known as HlyAs, on its C-terminus. Recognition of HlyAs by the HlyB-HlyD complex induces contact with TolC which forms a trans- periplasmic export channel between the inner and outer membrane. HlyC plays a role in the activation of HlyA.
- the replacement of the HlyA toxin with a heterologous nucleotide encoding a protein, or other cargo molecule enables the export of specific heterologous proteins or other molecules of interest, via the C-terminal HlyAs sequence, from a carrier bacterium to the extracellular surroundings.
- the present invention provides a live attenuated Gram-negative bacterium comprising a modified hlyCABD operon, wherein the modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly genes involved in secretion.
- the live attenuated Gram-negative bacterium of the present invention can act as an efficient and reliable method of delivering or exporting cargo molecules from the bacterial cytoplasm into the extracellular surroundings, including the interstitial space between eukaryotic cells.
- the bacterial strains herein disclosed are recombinant strains comprising a modified hlyCABD operon which comprises a heterologous polynucleotide encoding a cargo molecule.
- the heterologous polynucleotide therefore has a nucleotide-encoding structure which allows for its transcription, and, in the case where the cargo molecule is a protein, its subsequent translation into the encoded cargo molecule.
- modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter.
- the first segment (the ‘cargo region’) is envisaged to comprise the heterologous polynucleotide which encodes a cargo molecule, upstream of a hlyAs translocation sequence.
- the term “cargo” will be well known to those in the art, and refers to a specific molecule of interest which is intended to be translocated, delivered, transported, or exported from one place to another.
- a cargo molecule may be translocated from the bacterial cytoplasm to the extracellular environment surrounding eukaryotic cells.
- the cargo molecule is a protein and/or peptide.
- Cargo molecules may be heterologous proteins which do not occur naturally to the carrier bacterial cell.
- the cargo peptide and/or protein may be a therapeutic peptide and/or a therapeutic protein. While it is envisaged that the cargo molecule of the present invention may be a protein or peptide, other cargo types include DNA and RNA molecules.
- the cargo molecule is an RNA molecule.
- RNA and “ribonucleic acid” are used interchangeably, and refer to nucleic acids composed of uracil, adenine, guanine, and cytosine ribonucleic acid bases. These terms and concepts will be well known to those in the art.
- Types of RNA molecules include, for example, messenger RNA (mRNA), small interfering RNA (siRNA), short hairpin RNA (shRNA), micro RNA (miRNA), transfer RNA (tRNA), self-amplifying RNA (saRNA) and ribosomal RNA (rRNA).
- mRNA messenger RNA
- siRNA small interfering RNA
- shRNA short hairpin RNA
- miRNA micro RNA
- tRNA transfer RNA
- saRNA self-amplifying RNA
- rRNA ribosomal RNA
- the RNA cargo molecule may be an mRNA molecule.
- RNA and “messenger RNA” are used interchangeably and refer to a single-stranded RNA molecule involved in protein synthesis.
- Eukaryotic mRNA molecules are transcribed from DNA in the nucleus of a eukaryotic cell, and subsequently exported from the nucleus into the cytoplasm of the eukaryotic cell, where translation of the mRNA molecule into proteins takes place.
- Bacterial mRNA molecules are transcribed from DNA that is non-compartmentalised and translated in the cytosol coupled to transcription. These terms and concepts will be well known to those in the art. RNA molecules are transcribed and translated within the bacterium itself.
- the live attenuated Gram-negative bacterium may encode up to 10 different heterologous mRNA molecules, for example, 1 , 2, 3, 4, 5, 6, 7, 8, 9 or 10 different heterologous mRNA molecules.
- a cargo mRNA molecule itself may encode a peptide and/or protein, whereby the peptide and/or protein may be a therapeutic peptide and/or therapeutic protein.
- the therapeutic peptide and/or therapeutic protein may be a cytokine, a chemokine, an antibody or a functional fragment thereof, a cytotoxic agent, a cancer agent or any combination thereof.
- the invention herein disclosed provides a live attenuated Gram-negative bacterium in which the cargo molecule is expressed within the bacterium itself prior to export.
- the live attenuated Gram-negative bacterium may encode up to 10 different cargo (protein) molecules, for example, 1 , 2, 3, 4, 5, 6, 7, 8, 9 or 10 different cargo (protein) molecules.
- the heterologous polynucleotide encoding the cargo molecule is fused to a hlyAs sequence encoding the translocation peptide, HlyAs.
- the cargo molecule is a protein or peptide
- the HlyAs translocation peptide is positioned on the C-terminus of the cargo molecule.
- the HlyAs protein may be approximately 50 to 220 amino acids in length. In some embodiments, the HlyAs protein is 218 amino acids in length.
- translocation sequence As used herein, the terms “translocation sequence”, “signal sequence”, and “target sequence” may be used interchangeably, and refer to a gene encoding a translocation peptide or protein which is recognised by cellular export machinery and targeted for export or secretion from the cell. Translocation peptides are typically found on the N- or C-terminus of a peptide or protein which is intended to be translocated from one location to another.
- Translocation sequences generally encode peptides with a specific amino acid sequence or motif which can be recognised by cellular export machinery.
- HlyAs translocation peptide is recognised by the HlyB and HlyD structural proteins which engage with TolC to create a trans-periplasm channel, thus enabling the translocation of HlyAs (and any cargo to which it may be fused) through the inner and outer membrane of the live attenuated Gram-negative bacterium.
- the heterologous polynucleotide encoding the cargo molecule is positioned upstream of the HlyAs sequence. In another embodiment, the heterologous polynucleotide encoding the cargo molecule is positioned downstream of the independently controlled promoter. In yet another embodiment, the heterologous polynucleotide encoding the cargo molecule is positioned upstream of the HlyAs sequence and downstream of the independently controlled promoter.
- the hlyCABD operon may further comprise a hlyC gene.
- HlyC is relevant for the activation of HlyA.
- a region on the 3’ end of HlyC can influence secretion yields, and therefore in another embodiment, the hlyCABD operon may further comprise a functional fragment or portion of the hlyC gene.
- the hlyC gene, or functional fragment thereof is positioned upstream of the heterologous polynucleotide which encodes a cargo molecule upstream of a hlyAs translocation sequence.
- the hlyC gene, or functional fragment thereof is positioned downstream of the independently controlled promoter.
- the hlyC gene, or functional fragment thereof is positioned upstream of the heterologous polynucleotide which encodes a cargo molecule upstream of a hlyAs translocation sequence and downstream of the independently controlled promoter.
- the cargo molecule after secretion, retains the HlyAs translocation peptide.
- the HlyAs translocation peptide is removed or cleaved from the cargo molecule after secretion.
- the secretion of any given cargo molecule may be optimised.
- the folding rate of cargo may be modified, as it is suggested in the literature that cargo molecules exhibiting a lower folding rate experience a higher rate of secretion.
- the translation efficiency of the cargo molecule may be modified through the adaptation of ribosome binding sequences.
- the coding sequence may be modified such that one or more codons within the heterologous polynucleotide encoding the cargo molecule may be changed without altering the encoded amino acid (synonymous codon change) due to the redundancy of the genetic code.
- folding rate, translational efficiency, and coding sequence can be optimised for each peptide, protein, or gene involved, and will depend on the nature of the cargo molecule (gene, peptide, or protein cargo molecule) and its envisaged use.
- the second segment (the ‘structural region’) is envisaged to comprise the hly genes involved in secretion.
- the hly genes involved in secretion are hlyB and hlyD.
- the second segment comprises a hlyB gene and a hlyD gene.
- the hlyB and hlyD genes are also referred to as the T 1 SS structural genes.
- the hlyB gene is upstream of the hlyD gene.
- the hlyB gene is downstream of the independently controlled promoter.
- the hlyB gene is upstream of the hlyD gene and downstream of the independently controlled promoter.
- the modified hlyCABD operon of the present invention is therefore split into two segments: a first segment and a second segment, each segment being operably linked to its own independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly genes involved in secretion.
- the heterologous polynucleotide is operably linked to an independently controlled promoter.
- the hly genes involved in secretion is operably linked to an independently controlled promoter.
- independently controlled promoter refers to a promoter which is controlled by regulatory elements which are distinct to that of another promoter in the system.
- the promoter controlling the expression of the first segment may be different, or have distinct regulatory mechanisms, to that of the promoter controlling the expression of the second segment.
- Temporal control of expression can be achieved by using different promoters including invasion-associated SPI-1 , SPI-4, orflagella-related promoters.
- Suitable promoters may include, but are not limited to, invF, hilA, hilD, sicA, siiE, flhDC, and fliC.
- the independently controlled promoters are strong promoters, such that when the strong promoter is used, a high rate of transcription is initiated.
- strong promoter or “active promoter” may be used interchangeably, and refer to a promoter which yields a high rate of transcription of the genes under its regulation. Genes regulated by strong promoters more frequently recruit RNA polymerases and therefore yield more mRNA and therefore more product protein than genes regulated by weak promoters.
- any strong promoter that fulfils the function herein disclosed is suitable, particular examples of suitable strong promoters include, but are not limited to, a ptrc promoter, a ptet promoter, a pcon5 promoter, a pBAD promoter, a placllV5 promoter, invasion-associated promoters (e.g., SPI-1 , SPI-4, or flagella), intracellular promoters (SPI-2), host-cytosolic promoters or a pTac promoter.
- Other suitable examples include, but are not limited to, uphT (Glucose- 6-phosphate), frubKA (fructose).
- SPI-1 are invasion-associated promoters that are active outside of the host cell and when the bacterium is attempting to invade the host cell.
- Additional promoters for use in the present invention may include, but are not limited to, a trc promoter, a tac promoter, a trp promoter, a lac operon promoter, a lac/tac promoter, a tac/trc promoter, a trp/lac promoter, a bad/ara promoter, an ssaG promoter, a pagC promoter, a nirB promoter, a dps promoter or an spv promoter.
- cytosolic promoter refers to intracellular promoters in bacteria.
- Host-cytosolic promoters for use in the present invention may include, but are not limited to, uhpT, mntH, entC, fhuE, iroN, fepB, fepA, fhuA, sitA, stn3250, sufA, yjjZ, soxS, sfbA.
- the SPI-2 gene is an ssa gene.
- Suitable promoters may include, but are not limited to, ssa ssaJ, ssaU, ssaK, ssaL, ssaM, ssaO, ssaP, ssaQ, ssaR, ssaS, ssaT, ssaD, ssaE, ssaG, ssa/, ssaC and ssaH.
- Other vacuolar promoters include PipB2, zinT, mtgC.
- PipB2 and ssaG may be used for intracellular delivery.
- PipB2 is a strong SPI-2-dependent promoter, relative to other SPI-2 promoters.
- SPI-2 promoters can also be used to activate the expression of Type 1 Secretion Systems (T1SS) which facilitate the export of hemolysins from Listeria.
- T1SS Type 1 Secretion Systems
- the strength of the promoters selected for each segment may be manipulated to enhance the efficiency of secretion of the cargo molecule ( Figures 3 and 4).
- Table 1 details the promoters used in screening.
- the bacterium of the present invention is a live attenuated Gram-negative bacterium.
- live attenuated Gram-negative bacteria for use in the present invention include, but are not limited to, Salmonella, Escherichia coli, Shigella, Pseudomonas, Moraxella, Helicobacter, Stenotrophomonas, Bdellovibrio, Legionella, Chlamydia and Yersinia.
- the live attenuated Gram-negative bacterium is Salmonella.
- the Salmonella may be Salmonella Typhi or Salmonella Typhimurium.
- the live attenuated Gramnegative bacterium is a genetically engineered non-natural bacterium.
- the present invention discloses live attenuated Gram-negative bacteria that have been genetically altered to produce bacterial strains that can effectively deliver various cargo molecules.
- genes may be mutated by a number of well-known methods in the art, such as homologous recombination with recombinant plasmids targeted to the gene of interest, in which case an engineered gene with homology to the target gene is incorporated into an appropriate nucleic acid vector (such as a plasmid or a bacteriophage), which is transfected into the target cell.
- the homologous engineered gene is then recombined with the natural gene to either replace or mutate it to achieve the desired inactivating mutation.
- Such modification may be in the coding part of the gene or any regulatory portions, such as the promoter region.
- any appropriate genetic modification technique may be used to mutate the genes of interest, such as the CRISPR/Cas system, e.g., CRISPR/Cas 9, to produce the bacterial strains herein disclosed.
- Table 2 details the sequences used to build expression plasmids.
- Table 2 Sequences used to build expression plasmids, including conserved regions for amplification of DNA blocks and Bsal-dependent cleavage sites for Golden Gate Assembly.
- the live attenuated Gram-negative bacterium is Salmonella.
- the live attenuated Gram-negative bacterium may be selected from the group comprising Ty21a, CVD 908-htrA, CVD 909, Ty800, M01ZH09 (also known as ZH9), x9633, x639, x9640, x8444, DTY88, ZH9PA, MD58, WT05, ZH26, SL7838, SL7207, VNP20009, A1-R, or any combinations thereof.
- the live attenuated Gram-negative bacterium is M01ZH09 (also known as ZH9).
- EP 2 801 364 A1 discloses Ty21a, CVD 908-htrA, CVD 909, Ty800, M01ZH09, x9633, X9640, and x8444.
- EP 3 917 565 A1 discloses in detail ZH9 strains and derivatives thereof, including ZH9PA. Further references to these strains can be found in the literature, in particular in Petrovska 2004, Hindle 2002, Lehouritis 2017, and Kimura 2010. Also intended to be included are any derivatives or variants of the strains, including genetically engineered or genetically modified strains.
- the genetically engineered non-natural bacterium may further comprise one or more gene cassettes.
- Such gene cassettes may be used to deliver additional prokaryotic molecules to support the function of the genetically engineered nonnatural bacterium to condition the immune system, or to support the activity of the cargo molecule.
- the present invention provides a way in which cargo molecules can be delivered to the extracellular space, including the interstitial space, between eukaryotic cells. Accordingly, the present invention provides a bacterial delivery system with broad usability across numerous disease areas. As the skilled person will appreciate, such a system has a significant and wide-reaching therapeutic benefit.
- the heterologous polypeptide may encode a cargo molecule which may be a therapeutic peptide, therapeutic protein and/or a heterologous antigen (dependent on the indication to be treated).
- the therapeutic peptide or protein is a cytokine, a chemokine, an antibody, or a functional fragment thereof, a cytotoxic agent, a cancer agent, or any combination thereof.
- the resulting therapeutic protein may be IL-15, IL-21 , CXCL9, CXCL10, IL-18, IL-27, IFNy, IFNct, IFN
- the live attenuated Gram-negative bacteria comprising a modified hlyCABD operon encoding a therapeutic cargo molecule which is intended to be secreted into the extracellular environment between eukaryotic cells.
- the terms “extracellular environment”, “extracellular space”, “extracellular compartment”, or “extracellular surroundings” are used interchangeably and refer to the region within a multicellular organism which is outside the cells, i.e. , beyond the plasma membrane, and is occupied by extracellular matrix.
- the extracellular environment comprises three compartments: the interstitial, intravascular and transcellular compartments.
- the cargo molecule is intended to be secreted into the interstitial space.
- interstitial compartment As used herein, the terms “interstitial compartment”, “interstitial environment”, “interstitial space”, “tissue space” or “interstitial surroundings” are used interchangeably and refer to the space surrounding tissue cells (i.e., the space outside blood and lymph vessels and parenchymal cells), also known as the tissue microenvironment.
- the interstitial space consists of two major phases: interstitial fluid which provides the immediate microenvironment between eukaryotic cells, and the structural molecules comprising the extracellular matrix.
- the eukaryotic cells may be mammalian cells. In a preferred embodiment, the eukaryotic cells are human cells. Where the eukaryotic cell is a human cell, the target cell may be a cancerous human cell or a non-cancerous human cell.
- tissue microenvironment is relevant to solid and haematological cancers.
- TME tumor microenvironment
- the TME is created by the tumour and is dominated by tumour-induced interactions but may also comprise immune effector cells which have been recruited to the tumour, fibroblasts, signalling molecules, and blood vessels. Therefore, it is envisaged that the live attenuated Gramnegative bacteria can be modified to deliver therapeutically relevant proteins in the interstitial space of the TME in a subject suffering from a tumour.
- the live attenuated Gram-negative bacteria is administered intratumourally, peritoumorally, intravenously, intraperitoneally, subcutaneously, intradermally, or orally administered.
- the live attenuated Gram-negative bacteria is administered intratumourally.
- other methods of administration may be used in some cases.
- the live attenuated Gram-negative bacterium of the present invention may be administered by injection, infusion, continuous infusion, intradermally, intraarterially, intralesionally, intravaginally, intrarectally, intramuscularly, subcutaneously, subconjunctival, mucosally, intrapericardially, intraumbilically, intraocularally, intracranially, intraarticularly, intraprostaticaly, intrapleurally, intratracheally, intranasally, via a catheter, via a lavage, or by other method or any combination of the forgoing as would be known to one of ordinary skill in the art (see, for example, Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990).
- the amount of the live attenuated Gram-negative bacterium administered to the subject is sufficient to deliver the cargo molecule to the interstitial space in high enough concentrations for it to have the desired effect.
- the skilled person will readily understand that the precise amount to be administered will be dependent on a number of factors, for example, the disease to be treated and the medical history of the subject to be treated.
- the live attenuated Gram-negative bacterium may be administered at a dose of between 10 5 and 10 12 CFU, where CFU is a colony-forming unit.
- suitable doses may be between 10 5 and 10 6 CFU, 10 5 and 10 7 CFU, 10 5 and 10 8 CFU, 10 5 and 10 9 CFU, 10 5 and 10 1 ° CFU, 10 5 and 10 11 CFU, 10 6 and 10 7 CFU, 10 6 and 10 8 CFU, 10 6 and 10 9 CFU, 10 6 , and 10 1 ° CFU, 10 6 and 10 11 CFU, 10 6 and 10 12 CFU, 10 7 and 10 8 CFU, 10 7 and 10 9 CFU, 10 7 and 10 1 ° CFU, 10 7 and 10 11 CFU, 10 7 and 10 12 CFU, 10 8 and 10 9 CFU, 10 8 and 10 1 ° CFU, 10 8 and 10 11 CFU, 10 8 and 10 12 CFU, 10 9 and 10 1 ° CFU, 10 9 and 10 11 CFU, 10 9 and 10 12 CFU, 10
- the live attenuated Gram-negative bacterium of the present invention is envisaged to allow for the delivery of a therapeutically relevant cargo molecule to the interstitial space in between eukaryotic cells of the TME in a subject suffering from a tumour.
- the live attenuated Gram-negative bacterium herein disclosed may be for therapeutic use.
- the live attenuated Gram-negative bacteria may be used in the treatment, reduction, inhibition, prevention, prevention of recurrence, or control of a disease.
- the disease is a human disease.
- the disease may be a neoplastic disease, an infectious disease, a cardiovascular disease, a neurodegenerative disease, a gastrointestinal disease, a respiratory disease, a renal disease, a liver disease, an autoimmune disease, an inflammatory disease or a genetic disorder.
- the live attenuated Gram-negative bacterium is for use in the treatment, reduction, inhibition, prevention, prevention of recurrence, or control of a neoplastic disease or an infectious disease.
- the neoplastic disease may be associated with a solid tumour or haematological tumour.
- the neoplastic disease is associated with a cancer selected from prostate cancer, oesophageal cancer, liver cancer, renal cancer, lung cancer, breast cancer, colorectal cancer, bladder cancer, breast cancer, pancreatic cancer, brain cancer, mesothelioma, hepatocellular cancer, lymphoma, leukaemia, gastric cancer, endometrial cancer, vulvar cancer, vaginal cancer, cervical cancer, ovarian cancer, thyroid cancer, melanoma, carcinoma, head and neck cancer, skin cancer or sarcoma.
- Neoplasia, tumours, and cancers include benign, malignant, metastatic and non- metastatic types, and include any stage (I, II, III, IV or V) or grade (G1 , G2, G3, etc.) of neoplasia, tumour, or cancer, or a neoplasia, tumour, cancer or metastasis that is progressing, worsening, stabilized or in remission.
- Cancers that may be treated according to the invention include but are not limited to cells or neoplasms of the bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, gastrointestines, gum, head, kidney, liver, lung, nasopharynx, neck, ovary, prostate, skin, stomach, testis, tongue, or uterus.
- the cancer may specifically be of the following histological type, though it is not limited to the following: neoplasm, malignant; carcinoma; undifferentiated; giant and spindle cell carcinoma; small cell carcinoma; papillary carcinoma; squamous cell carcinoma; lymphoepithelial carcinoma; basal cell carcinoma; pilomatrix carcinoma; transitional cell carcinoma; papillary transitional cell carcinoma; adenocarcinoma; gastrinoma, malignant; cholangiocarcinoma; hepatocellular carcinoma; combined hepatocellular carcinoma and cholangiocarcinoma; trabecular adenocarcinoma; adenoid cystic carcinoma; adenocarcinoma in adenomatous polyp; adenocarcinoma, familial polyposis coli; solid carcinoma; carcinoid tumour, malignant; bronchiolo-alveolar adenocarcinoma; papillary adenocarcinoma; chromophobe carcinoma; acid
- the neoplastic disease may be tumours associated with a cancer selected from prostate cancer, liver cancer, renal cancer, lung cancer, breast cancer, colorectal cancer, pancreatic cancer, brain cancer, hepatocellular cancer, lymphoma, leukaemia, gastric cancer, endometrial cancer, vulvar cancer, vaginal cancer, cervical cancer, ovarian cancer, thyroid cancer, melanoma, head and neck cancer, skin cancer and soft tissue sarcoma and/or other forms of carcinoma.
- the tumour may be metastatic or a malignant tumour.
- the neoplastic disease is associated with a cancer selected from bladder cancer, prostate cancer, lung cancer, mesothelioma, hepatocellular cancer, melanoma, oesophageal cancer, gastric cancer, endometrial cancer, vulvar cancer, vaginal cancer, cervical cancer, ovarian cancer, colorectal cancer, head and neck cancer or breast cancer.
- a cancer selected from bladder cancer, prostate cancer, lung cancer, mesothelioma, hepatocellular cancer, melanoma, oesophageal cancer, gastric cancer, endometrial cancer, vulvar cancer, vaginal cancer, cervical cancer, ovarian cancer, colorectal cancer, head and neck cancer or breast cancer.
- the present invention provides a vaccine composition
- a vaccine composition comprising a live attenuated Gram-negative bacterium comprising a modified hlyCABD operon, wherein the modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly genes involved in secretion.
- the vaccine composition of the present invention may be for therapeutic use.
- the live attenuated Gram-negative bacterium may be for use in the treatment, reduction, inhibition, prevention, prevention of recurrence, or control of a disease.
- the vaccine composition herein disclosed may be used in the treatment, reduction, inhibition, prevention of recurrence or control of an infectious disease, for example, a disease caused by a bacteria, a virus, a parasite or a fungi.
- the heterologous polynucleotide of the present invention may encode for an antigen of the causative agent of the specific infectious disease in order to produce an immune response in the host.
- the vaccine composition herein disclosed may be used as a cancer vaccine.
- the vaccine composition comprises Gram-negative bacteria comprising a heterologous polynucleotide encoding a cancer antigen that is capable of producing an immune response in the host.
- the heterologous polynucleotide may encode an siRNA or shRNA molecule, which is designed to enhance immune anti-infectious function or tissue anti-infectious defences.
- the vaccine composition of the present invention may further comprise an adjuvant, a pharmaceutically acceptable carrier or excipient.
- pharmaceutically acceptable camer/adjuvant/diluent/excipient includes any and all solvents, dispersion media, coatings, surfactants, antioxidants, preservatives (e.g., antibacterial agents, antifungal agents), isotonic agents, absorption delaying agents, salts, preservatives, drugs, drug stabilizers, gels, binders, excipients, disintegration agents, lubricants, sweetening agents, flavouring agents, dyes, such like materials and combinations thereof, as would be known to one of ordinary skill in the art (see, for example, Remington's Pharmaceutical Sciences, 18th Ed.
- Examples include, but are not limited to disodium hydrogen phosphate, soya peptone, potassium dihydrogen phosphate, ammonium chloride, sodium chloride, magnesium sulphate, calcium chloride, sucrose, borate buffer, sterile saline solution (0.9 % NaCI) and sterile water.
- Suitable aqueous and non-aqueous carriers that may be employed in the vaccine compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate.
- polyols such as glycerol, propylene glycol, polyethylene glycol, and the like
- vegetable oils such as olive oil
- injectable organic esters such as ethyl oleate.
- Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.
- the vaccine compositions herein disclosed may further contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of presence of unwanted microorganisms may be ensured both by sterilization procedures, supra, and by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents that delay absorption such as aluminium monostearate and gelatin.
- the vaccine composition may also optionally include additional therapeutic agents, known to be efficacious in, for example, infectious disease or neoplastic disease. Accordingly, the vaccine composition herein disclosed may also comprise antiretroviral drugs, antibiotics, antifungals, antiparasitics and anticancer agents.
- the vaccine composition may also comprise additional components intended for enhancing an immune response in a subject following administration.
- additional components include but are not limited to; aluminium salts such as aluminium hydroxide, aluminium oxide and aluminium phosphate, oil-based adjuvants such as Freund's Complete Adjuvant and Freund's Incomplete Adjuvant, mycolate-based adjuvants (e.g., trehalose dimycolate), bacterial lipopolysaccharide (LPS), peptidoglycans (e.g., mureins, mucopeptides, or glycoproteins such as N-Opaca, muramyl dipeptide [MDP], or MDP analogs), proteoglycans (e.g., extracted from Klebsiella pneumoniae), streptococcal preparations (e.g., OK432), muramyldipeptides, Immune Stimulating Complexes (the "Iscoms” as disclosed in EP 109942, EP 180564 and EP 231
- the live attenuated Gram-negative bacterium of the vaccine composition herein disclosed may include any one of, or any combination of the features of the live attenuated Gram-negative bacterium herein disclosed.
- the present invention provides a method of treating, preventing, inhibiting, preventing recurrence or controlling a disease in a subject, wherein the method comprises administering to a subject a live attenuated Gram-negative bacterium, said live attenuated Gram-negative bacterium comprising a modified hlyCABD operon, wherein the modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly
- the method of treating, preventing, inhibiting, preventing recurrence or controlling a disease in a subject of the third aspect may comprise one or more of the aforementioned embodiments in respect to any preceding aspect.
- the present invention provides a method of delivering a therapeutic molecule to the interstitial space in between eukaryotic cells of the tumour microenvironment in a subject suffering from a tumour, said method comprising the steps of: i) modifying a live attenuated Gram-negative bacterium, said live attenuated Gram-negative bacteria comprising a modified hlyCABD operon, wherein the modified hlyCABD operon is split into a first segment and a second segment, each segment being operably linked to an independently controlled promoter, wherein the first segment comprises a heterologous polynucleotide encoding a cargo molecule upstream of a hlyAs translocation sequence, wherein the heterologous polynucleotide encoding a cargo molecule replaces a hlyA gene, and wherein the second segment comprises hly genes involved in secretion and ii) administering said modified Gram-negative bacterium to the subject in need thereof.
- the therapeutic molecule may be a protein or peptide.
- the therapeutic molecule may be a RNA molecule that is subsequently translated into a protein or peptide.
- the term “therapeutic molecule” refers to any molecule that may result in the reduction, amelioration, palliation, lessening, delaying, and/or alleviation of one or more of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system.
- a therapeutic molecule may be one which results in the size of a tumour shrinking.
- the method of delivering a therapeutic molecule to the interstitial space in between eukaryotic cells of the tumour microenvironment in a subject suffering from a tumour of the fourth aspect may comprise one or more of the aforementioned embodiments in respect to any preceding aspect.
- the live attenuated Gram-negative bacteria comprising the modified hylCABD operon of the present invention may also have applications in allowing for the safe, efficient, and reliable delivery of RNA molecules into target eukaryotic cells. Accordingly, in one embodiment, a method for delivering an RNA molecule into a eukaryotic cell using the modified live attenuated Gram-negative bacterium herein disclosed is provided.
- the term “bactofection” refers to the process of transduction of genetic material from a bacterium (e.g., Salmonella) into a mammalian cell.
- bactofection in the context of the present invention refers to the use of live attenuated Gram-negative bacteria to deliver RNA molecules to the cytosol of a eukaryotic cell following delivery of the live attenuated Gram-negative bacteria to the target eukaryotic cell.
- SPI-2 promoters can be used to activate the expression of Type 1 Secretion Systems (T1SS) which facilitate the export of hemolysins from Listeria and enable, for example, the release of bacterial cells from a vacuole into the cytoplasm of a eukaryotic cell, thus granting bacteria access to the cytoplasm of a eukaryotic cell.
- T1SS Type 1 Secretion Systems
- Fragments were as dsDNA blocks through integrated DNA technologies (IDT). The dsDNA blocks were cloned into pJET plasmid and validated by sequencing and further used as reference material. Fragments for Golden Gate Assembly (GGA) were generated from validated plasmids via PCR.
- IDT integrated DNA technologies
- GGA Golden Gate Assembly
- the plasmid library was assembled via Bsal-dependent GGA and using the ECHO 525 Liquid Handling Platform to perform the reaction mixtures, on a 96-well PCR plate (reaction volume, 5 pL) with mixture DNA volume brought to 3 pL and topped up with 2 pL of NEB Bridge + Bsal (1 .667 pL NEB Bridge and 0.333 pL of Bsal) per reaction.
- reaction volume 5 pL
- Bsal (1 .667 pL NEB Bridge and 0.333 pL of Bsal) per reaction.
- Plasmid assembly was initially confirmed visually (no red background colonies) and then 2x each were grown overnight.
- Plasmids from the library were transformed into DH5a cells via Heat Shock (standard protocol), plated in vLBA and grown at 37°C overnight. A total of 3x single colonies per construct were picked and inoculated in 1 mL of vLBA on a 96- deep well plate supplemented with chloramphenicol 12.5 pg mL' 1 and grown overnight at 200rpm and 37°C. Samples were then diluted down 1 :100 in 500 uL of vLBA supplemented with Chloramphenicol. A volume of 100 uL was transferred to a 96-well plate and used to monitor growth over time on a ClarioStar by shaking at 700rpm and at 37°C. The remaining volume was grown on the deep-well plate under the same conditions.
- Hi Bit assay was performed on supernatant from bacterial cultures grown at 37°C in the deep-well plate. Samples were allowed to reach OD 6 oo ⁇ 0.5 and then an aliquot was taken and processed as: (1) an aliquot was extracted from the deepwell plate (100 pL) and used to measure the cell density (OD 6 oo), (2) cells were spun down from all plates at 4000xg for 10 min at room temperature, (3) the supernatant was carefully transferred to a fresh plate, (4) 10 pL of the supernatant were mixed with HiBit MasterMix (10 pL) previously prepared and used to determine the amount of HiBit tag in the supernatant by measuring luminescence.
- HiBit MasterMix 10 pL
- the plasmid library with LLO also known as ListeroLysin O
- LLO also known as ListeroLysin O
- mScarlet was obtained by performing Bbsl-dependent Golden Gate Assembly on a 96-well PCR plate (reaction volume, 2uL) of the previously generated library and a block encoding hly from Listeria monocytogenes surrounded by appropriate Bbsl sites.
- the conditions used the were standard ones (0.67 pL of NEB Bridge, 0.264 pL of 10 pM hly insert, 0.5 pL of 2.5 pM vector, 0.132 pL of Bbsl, 0.434 pL of water).
- Validated plasmids from the library were transformed into DH5alpha cells via Heat Shock (standard protocol), plated in vLBA, and grown at 37°C overnight. A total of 3x single colonies per construct were picked and inoculated in 1 mL of vLBA on a 96-deep well plate supplemented with chloramphenicol 12.5 ug mL' 1 and grown overnight at 200 rpm and 37°C. Samples were then diluted down 1 :100 in 500 uL of vLBA supplemented with Chloramphenicol. A volume of 100 uL was transferred to a 96-well plate and used to monitor growth over time on a ClarioStar by shaking at 700rpm and 37°C. The remaining volume was grown on the deep well plate under the same conditions.
- a dual-plasmid expression system was designed and built.
- a cargocontaining plasmid is integrated into a p15A ori plasmid (circa 10 copies I cell) that allows for in-frame cloning (Bbsl-dependent) of any relevant cargo with the hlyAs sequence. Additional control over the expression levels can be achieved by Bsal- dependent cloning of a promoter of interest.
- Export of such cargo is then achieved by introduction of a second plasmid with a compatible origin of replication (e.g., pSC101 , ⁇ 5 copies I cell) expressing the hlyBD operon under the control of a relevant promoter, which has been introduced via Bsal-dependent Golden Gate, as previously done with cargo-hlyAs fusion.
- a compatible origin of replication e.g., pSC101 , ⁇ 5 copies I cell
- a relevant promoter which has been introduced via Bsal-dependent Golden Gate, as previously done with cargo-hlyAs fusion.
- Both plasmids were built using the same eBlocks previously employed for the one-plasmid system.
- pro1 hlyAs-1
- proC hlyAs-4
- J23199 hlyAs- 6
- Ruano-Gallego D., et al., Screening and purification of nanobodies from E. coli culture supernatants using the hemolysin secretion system. Microbial Cell Factories, 2019. 18(1): p. 47.
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