EXPRESSION OF THE HUMAN LEKTI GENE FROM THE CHROMOSOME OF STAPHYLOCOCCUS EPIDERMIDIS
20240092869 ยท 2024-03-21
Inventors
Cpc classification
C07K2319/036
CHEMISTRY; METALLURGY
C07K14/8135
CHEMISTRY; METALLURGY
C12N15/74
CHEMISTRY; METALLURGY
A61K48/0075
HUMAN NECESSITIES
C12P21/02
CHEMISTRY; METALLURGY
International classification
Abstract
The present disclosure provides, inter alia, engineered microbes expressing one or more therapeutic proteins from a nucleotide sequence chromosomally integrated, which is effective to treat or ameliorate a disease or disorder, e.g., a skin disease. In certain embodiments, composition, methods, and kits are provided comprising microbes expressing one or more therapeutic proteins from a chromosomally integrated nucleotide sequence.
Claims
1. A recombinant microorganism capable of secreting one or more therapeutic polypeptide, wherein the recombinant organism comprises (i) a first coding sequence comprising a nucleic acid sequence encoding one or more therapeutic polypeptide; (ii) a second coding sequence comprising a nucleic acid sequence encoding one or more secretion sequences that are not associated with the one or more therapeutic polypeptide in nature; and (iii) a third coding sequence comprising a pro-peptide, wherein the first coding sequence, second coding sequence, and third coding sequence are in-frame, wherein the one or more therapeutic polypeptides are encoded by one or more SPINK genes, or one or more protein domains thereof.
2. The recombinant microorganism of claim 1, wherein the first coding sequence, the second coding sequence, and the third coding sequence are chromosomally integrated into the hld gene.
3. (canceled)
4. The recombinant microorganism of claim 1, wherein the recombinant microorganism is attenuated by auxotrophy.
5. The recombinant microorganism of claim 4, wherein the recombinant microorganism is a D-alanine auxotroph.
6. The recombinant microorganism of claim 1, wherein the expression of the first coding sequence, second coding sequence, and third coding sequence is operable linked to a promoter, wherein the promoter is P3 and/or P.sub.yxiE, wherein P.sub.yxiE comprises SEQ ID NO: 120.
7. (canceled)
8. (canceled)
9. (canceled)
10. The recombinant microorganism of claim 1, wherein the secretion peptide is Bacillus subtilis yfhK gene; and/or wherein the secretion peptide comprises SEQ ID NO: 122; and/or wherein the pro-peptide comprises SEQ ID NO: 123.
11. (canceled)
12. (canceled)
13. (canceled)
14. The recombinant microorganism of claim 1, wherein the microorganism is selected from the group consisting of Moraxella, Corynebacteria, Pasteurella, Haemophilus, Streptococcus, or Staphylococcus.
15. (canceled)
16. The recombinant microorganism of claim 1, wherein the one or more SPINK genes are selected form the group consisting of SPINK1, SPINK2, SPINK4, SPINK5, SPINK6, SPINK7, SPINK8, SPINK9, SPINK13, and SPINK14, wherein the one or more SPINK gene encodes a LEKTI protein, or one or more protein domains thereof.
17. (canceled)
18. (canceled)
19. The recombinant microorganism of claim 1, wherein the recombinant microorganism secretes the one or more therapeutic polypeptide.
20. The recombinant microorganism of claim 16, wherein the LEKTI protein domain is selected from the group consisting of D1, D2, D3, D4, D5, D6, D7, D8, D9, D10, D11, D12, D13, D14, and D15.
21. (canceled)
22. A method of producing a live biotherapeutic composition, the method comprising: (a) transfecting a cell with a nucleic acid sequence comprising (i) one or more LEKTI protein domains, (ii) a secretion peptide that is not associated with the one or more therapeutic polypeptide in nature, (iii) a pro-peptide, and (iv) a promoter; and (b) integrating the nucleic acid sequence into the hld gene in the chromosome of the cell; and (c) obtaining the live biotherapeutic.
23. The method of claim 22, wherein the secretion peptide is selected from Bacillus subtilis yfhK gene; and/or wherein the secretion peptide comprises SEQ ID NO: 122 and/or wherein the pro-peptide comprises SEQ ID NO: 123.
24. (canceled)
25. (canceled)
26. (canceled)
27. The method of claim 22, wherein the promoter is P.sub.yxiE, wherein P.sub.yxiE comprises SEQ ID NO: 120.
28. (canceled)
29. The method of claim 22, wherein the nucleic acid sequence is under the control of an endogenous promoter, wherein the endogenous promoter is P3.
30. (canceled)
31. The method of claim 22, wherein the arrangement of the LEKTI protein domain, secretion peptide, and pro-peptide are in-frame.
32. (canceled)
33. The method of claim 22, wherein the recombinant microorganism is selected from the group consisting of Moraxella, Corynebacteria, Pasteurella, Haemophilus, Streptococcus, or Staphylococcus.
34. (canceled)
35. The method of claim 22, wherein the recombinant microorganism secretes the one or more LEKTI protein domain, or variants thereof.
36. A composition obtained by the method of claim 22, wherein the composition comprises a pharmaceutically acceptable carrier, wherein the pharmaceutically acceptable carrier is selected from the group consisting of an aqueous solution, an emulsion, a cream, a lotion, a gel, and an ointment.
37. (canceled)
38. A live biotherapeutic composition comprising a recombinant microorganism, wherein the recombinant microorganism comprises: a nucleic acid sequence comprising (i) one or more LEKTI protein domains, (ii) one or more secretion peptides, (iii) a pro-peptide, and (iv) a promoter, wherein the recombinant microorganism is capable of secreting the one or more LEKTI protein domains, or a variant thereof.
39. The composition of claim 38, wherein the nucleic acid sequence is integrated into the hld gene in the chromosome of the cell.
40. (canceled)
41. The composition of claim 38, wherein the secretion peptide is from Bacillus subtilis yfhK gene; and/or wherein the secretion peptide comprises SEQ ID NO: 122; and/or wherein the pro-peptide comprises SEQ ID NO: 123.
42. (canceled)
43. (canceled)
44. The composition of claim 38, wherein the promoter is P.sub.yxiE, wherein P.sub.yxiE comprises SEQ ID NO: 120.
45. (canceled)
46. The composition of claim 44, wherein the one or more LEKTI protein domains, one or more secretion peptides, and pro-peptide are under the control of an endogenous promoter; and/or wherein the endogenous promoter is P3; and/or wherein the arrangement of the one or more LEKTI protein domains, one or more secretion peptides, and pro-peptide are in-frame.
47. (canceled)
48. (canceled)
49. (canceled)
50. The composition of claim 38, wherein the recombinant microorganism is selected from the group consisting of Moraxella, Corynebacteria, Pasteurella, Haemophilus, Streptococcus, or Staphylococcus.
51. (canceled)
52. The composition of claim 38, comprising a pharmaceutically acceptable carrier, wherein the pharmaceutically acceptable carrier is selected from the group consisting of an aqueous solution, an emulsion, a cream, a lotion, a gel, and an ointment.
53. A kit comprising the composition of claim 38 and instructions for use.
54. A method of treating a disease or disorder comprising administering to a subject in need thereof the composition of claim 38, wherein the disease or disorder is selected from a skin disease, a disease or disorder associated with pain, cancer, and a viral infection, wherein the skin disease is selected from the group consisting of pruritus, rosacea, psoriasis, atopic dermatitis, Ichthyosis vulgaris, and Netherton Syndrome; wherein the disease or disorder associated with pain is selected from the group consisting of acute pain, chronic pain, nociceptive pain, neuropathic pain, traumatic pain, inflammatory pain, post-operative incision pain, pain associated with cancer, fracture pain, osteoporotic pain, bone cancer pain, and gout joint pain; wherein the cancer is selected from the group consisting of malignant melanoma, colon cancer, breast cancer, lung cancer, ovarian cancer, gastric cancer, oral tongue squamous cell carcinoma, squamous cell cancer, prostate cancer, pancreatic cancer, liver cancer, kidney cancer, bladder cancer, cervical cancer, endometrial cancer, gallbladder cancer, brain cancer and oral cancer; and wherein the viral infection is selected from a group consisting of a respiratory infection, dermal infection, and a viral infection that causes cancer in a subject.
55.-59. (canceled)
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION OF THE INVENTION
[0063] One aspect of the present disclosure provides skin-colonizing bacteria, e.g., Staphylococcus epidermidis, that are genetically altered to express chromosomally integrated recombinant proteins to treat or ameliorate skin disease. The genetically altered protein-producing bacteria are able to treat skin disease by expressing and, optionally, secreting a therapeutic protein that treats the underlying cause of the skin disease or its symptoms. According to some embodiments, the therapeutic protein comprises one or more LEKTI domains that are effective to inhibit serine proteases within or on the skin of a mammal. According to some embodiments, the recombinant LEKTI domains compensate for the defective endogenous LEKTI protein naturally produced by the skin in the mammal. According to some embodiments, the genetically altered bacteria are able to self-replicate while retaining the ability to produce the recombinant protein, thereby providing a continuous supply of therapeutic agent.
[0064] According to some embodiments, the disclosure provides a composition for the treatment of a skin disease comprising a microbe genetically modified to express and provide one or more LEKTI protein domains onto the skin of a mammal, wherein the LEKTI protein domains are effective to penetrate one or more layers of the mammal's skin and effective to inhibit serine protease activity of at least one serine protease in or on the mammal's skin.
[0065] According to some embodiments, the disclosure provides a recombinant Staphylococcus epidermidis strain containing a DNA cassette in its chromosome which expresses a secreted form of the domain 6 of LEKTI protein (hLEKTI-d6) of the human SPINK5 gene. The host strain harboring this expression cassette in its chromosome is S. epidermidis strain SE.sub.???, a strain containing deletions of three genes involved in the biosynthesis of the essential amino acid, D-alanine [two alanine racemase genes (alr1 and alr2) and the D-alanine aminotransferase gene (dat)], making the strain auxotrophic to this amino acid.
[0066] According to some embodiments, the chromosomal hLEKTI-d6 construct strain possesses several differentiating properties as compared to another strain, S. epidermidis 27a, which is S. epidermidis SE.sub.??? expressing secreted hLEKTI-d6 protein from a plasmid construct that also contains an alrA gene complementing D-alanine auxotrophy. These properties include: 1) retention of the D-alanine auxotrophy of SE.sub.???, providing a measure of growth control using D-alanine supplementation; 2) an unexpected enhanced production of secreted hLEKTI-d6 protein, presumably influenced by the genetic environment at the chromosomal site of integration, enhanced levels of secreted hLEKTI-d6 protein may be due to a synergy of promoter combinations driving hLEKTI-d6 gene expression (1; 2), activation of transcription triggered by quorum sensing in dense cultures (3; 4), and/or unique DNA or RNA structure associated with regulation of the delta-toxin gene, hld (4); and 3) potential enhanced stability of the expression cassette, and reduced potential for lateral transmission to commensal flora, due to the chromosomally integrated nature of the expression cassette vs. being carried on an extrachromosomal genetic element (plasmid).
[0067] As used herein the term skin disease and grammatical variations thereof means a skin state or condition that is generally undesirable or deleterious compared to the normal or baseline condition of human skin. Examples of abnormal skin conditions include, without limitation, Netherton Syndrome, psoriasis, acne, atopic dermatitis, allergic contact dermatitis, epidermolytic hyperkeratosis, seborrheic dermatitis, eczema, dry skin, allergy, rashes, UV-irritated skin, detergent irritated skin (including irritation caused by enzymes and molecules used in washing detergents and sodium lauryl sulfate), thinning skin (e.g. skin from the elderly and children), bullous pemphigoid, pemphigus vulgaris, impetigo, vitiligio, baldness, and hirsutism.
[0068] As used herein, the term genetically modified and grammatical variations thereof are used to describe a microbial organism (e.g., bacteria) that has been genetically modified or engineered by the introduction of DNA prepared outside the microbe. For example, the introduction of plasmid DNA containing new genes into bacteria will allow the bacteria to express those genes. Alternatively, the DNA containing new genes can be introduced to the bacteria and then integrated into the bacteria's genome, where the bacteria will express those genes.
[0069] As used herein, the term microorganism or recombinant microorganism refers to a microorganism, e.g., bacteria cell, that has been genetically modifies form its native state. Thus, a recombinant bacterial cell or recombinant bacteria refers to a bacterial cell or a bacteria that have been genetically modified form their native state. For instance, a recombinant bacterial cell may have nucleotide insertions, nucleotide deletions, nucleotide rearrangements, and nucleotide modifications introduced into their DNA. These genetic modifications may be present in the chromosome of the bacteria or bacterial cell. Recombinant bacterial cells may comprise exogenous nucleotide sequences stably incorporated into their chromosome.
[0070] As used herein, the terms treat, treating, treatment and grammatical variations thereof mean providing to a subject a protocol, regimen, process or remedy, in which it is desired to obtain a physiologic response or outcome in that subject, e.g., a patient. In particular, the methods and compositions of the present invention may be used to slow the development of disease symptoms or delay the onset of the disease or condition, or halt the progression of disease development. However, because every treated subject may not respond to a particular treatment protocol, regimen, process or remedy, treating does not require that the desired physiologic response or outcome be achieved in each and every subject or subject population, e.g., patient population. Accordingly, a given subject or subject population, e.g., patient population may fail to respond or respond inadequately to treatment.
[0071] In the present invention, the subject may be a mammal. As used herein, a mammal and grammatical variations thereof means any category of mammal. In the present invention, mammals include, for example, humans, farm animals, domestic animals, laboratory animals, etc. Some examples of farm animals include cows, pigs, horses, goats, etc. Some examples of domestic animals include dogs, cats, etc. Some examples of laboratory animals include primates, rats, mice, rabbits, guinea pigs, etc. Preferably, the mammal is a human.
[0072] As used herein, the term effective amount or a therapeutically effective amount of a compound or composition disclosed herein is an amount of such compound or composition that is sufficient to effect beneficial or desired results as described herein when administered to a subject. Effective dosage forms, modes of administration, and dosage amounts may be determined empirically, and making such determinations is within the skill of the art. It is understood by those skilled in the art that the dosage amount will vary with the route of administration, the rate of excretion, the duration of the treatment, the identity of any other drugs being administered, the age, size, and species of mammal, e.g., human patient, and like factors well known in the arts of medicine and veterinary medicine. In general, a suitable dose of a composition according to the invention will be that amount of the composition, which is the lowest dose effective to produce the desired effect. The effective dose of a composition of the present invention may be administered as two, three, four, five, six or more sub-doses, administered separately at appropriate intervals throughout the day.
[0073] Microbial compositions: According to some embodiments, the disclosure provides microbial compositions comprising one or more of a wide range of bacteria suitable for use on a mammal's skin. Examples include, but are not limited to, non-pathogenic and commensal bacteria. Bacteria suitable for use in the present invention include, but are not limited to, Bifidobacterium, Brevibacterium, Propionibacterium, Lactococcus, Streptococcus, Staphylococcus (e.g., S. epidermidis and/or S. hominis), Lactobacillus (e.g., L. acidophilus), Pediococcus, Leuconostoc, or Oenococcus. According to some embodiments, microbial compositions comprise one or more of Staphylococcus warneri, Streptococcus pyogenes, Streptococcus mitis, Propionibacterium acnes, Corynebacterium spp., Acinetobacter johnsonii, Pseudomonas aeruginosa. According to some embodiments, other related or similar species found on the skin are used.
[0074] Certain embodiments involve the use of bacterium Staphylococcus epidermidis. According to some embodiments, the strain of S. epidermidis to be used is incapable of producing biofilms. An example of this is S. epidermidis strain ATCC 12228 or NRRL B-4268.
[0075] According to some embodiments, the recombinant microbe is adapted to live indefinitely or for a controlled duration on the surface of the mammal's skin to provide a continuous supply of LEKTI protein domains. In some embodiments, the recombinant microbe lives alongside commensal microorganisms naturally occurring on the mammal's skin. In some embodiments, the recombinant microbe lives to the exclusion of commensal microorganisms that naturally occur on the mammal's skin. According to some embodiments, the recombinant microbe is adapted to multiply on the skin of the mammal. In other embodiments, the recombinant microbe is no longer alive, but contains effective amounts of a therapeutic polypeptide, e.g., LEKTI or therapeutically effective domain(s) thereof. Such cells may be intact or not depending upon the particulars of delivering the therapeutic peptide (or domain(s) thereof) to the target site.
[0076] As used herein, the term recombinant and grammatical variations thereof means relating to or denoting an organism, protein, or genetic material formed by or using recombined DNA comprising DNA pieces from different sources or from different parts of the same source. For example, the term recombinant DNA means a DNA molecule formed through recombination methods to splice fragments of DNA from a different source or from different parts of the same source. In some embodiments, two or more different sources of DNA are cleaved using restriction enzymes and joined together using ligases. As another example, the term recombinant protein or recombinant domains and grammatical variations thereof means a protein molecule formed through recombination methods originating from spliced fragments of DNA from a different source or from different parts of the same source. As another example, the term recombinant microbe or recombinant bacteria and grammatical variations thereof mean a microbe/bacteria that comprises one or more recombinant DNA/protein molecules.
[0077] LEKTI gene: According to some embodiments, the recombinant microbe is engineered to express a mammalian gene encoding LEKTI protein. The LEKTI gene can be obtained from any mammal, such as mouse, rat, rabbit, goat, sheep, horse, cow, dog, primate, or human gene sequences. According to some embodiments, the LEKTI gene sequence is a human gene sequence. According to some embodiments, the recombinant microbe is engineered to comprise a fragment of the LEKTI gene.
[0078] According to some embodiments, the recombinant protein expressed by the engineered microbe comprises one or more protease inhibitory domains of the LEKTI protein. Some non-limiting examples include one or more of domains D1, D2, D3, D4, D5, D6, D7, D8, D9, D10, D11, D12, D13, D14, and D15. According to some embodiments, the recombinant protein expressed by the engineered microbe comprises LEKTI inhibitory domain 6 or domains D8 to D11.
[0079] According to some embodiments, the recombinant protein expressed by the engineered microbe comprises LEKTI D8-11. According to some embodiments, the recombinant protein expressed by the engineered microbe comprises LEKTI-D6. According to some embodiments, one or more fragments of LEKTI are expressed by the engineered microbe. In one embodiment, the fragment comprises one or more LEKTI domains. In a specific embodiment, the LEKTI domain is Domain 6.
[0080] The present disclosure also relates to allelic variants of LEKTI, or portions thereof (one or more of domains D1, D2, D3, D4, D5, D6, D7, D8, D9, D10, D11, D12, D13, D14, and D15), as well as synthetic or mutated genes of SPINK (e.g., SPINK5) that have been modified to change, for example, the expression or activity of the recombinant protein. It is also noted that degeneracy of the nucleic acid code can be considered variations in the nucleotide sequences that encode the same amino acid residues. Accordingly, the disclosure includes nucleic acid residues that are able to hybridize under moderately stringent conditions. One skilled in the art can determine effective combinations of salt and temperature to constitute a moderately stringent hybridization condition. It is also envisioned that orthologs of LEKTI are present in other species, for example, dog, sheep, rat, hamster, chicken and pig. Therefore in another embodiment of the present invention relates to SPINK (e.g., SPINK5) nucleic acids that encode polypeptides having at least about 70% to 80% identity, preferably 90% to 95% identity, more preferably 98% to 99% identity to LEKTI set forth in SEQ ID NO: 103 or portions thereof (one or more of domains D1, D2, D3, D4, D5, D6, D7, D8, D9, D10, D11, D12, D13, D14, and D15).
[0081] According to some embodiments, the LEKTI domains are selected from the non-limiting examples below, Tables 1 and 2.
TABLE-US-00001 TABLE1 LEKTIAminoAcidsequences LEKTI SEQID Sequence AminoAcidsequence NO: LEKTIamino MKIATVSVLLPLALCLIQDAASKNEDQEMCHEFQAFMKNGK 103 acidsequence LFCPQDKKFFQSLDGIMFINKCATCKMILEKEAKSQKRARHL Residues1-1064 ARAPKATAPTELNCDDFKKGERDGDFICPDYYEAVCGTDGK TYDNRCALCAENAKTGSQIGVKSEGECKSSNPEQDVCSAFRP FVRDGRLGCTRENDPVLGPDGKTHGNKCAMCAELFLKEAE NAKREGETRIRRNAEKDFCKEYEKQVRNGRLFCTRESDPVR GPDGRMHGNKCALCAEIFKQRFSEENSKTDQNLGKAEEKTK VKREIVKLCSQYQNQAKNGILFCTRENDPIRGPDGKMHGNL CSMCQAYFQAENEEKKKAEARARNKRESGKATSYAELCSEY RKLVRNGKLACTRENDPIQGPDGKVHGNTCSMCEVFFQAEE EEKKKKEGKSRNKRQSKSTASFEELCSEYRKSRKNGRLFCTR ENDPIQGPDGKMHGNTCSMCEAFFQQEERARAKAKREAAK EICSEFRDQVRNGTLICTREHNPVRGPDGKMHGNKCAMCAS VFKLEEEEKKNDKEEKGKVEAEKVKREAVQELCSEYRHYVR NGRLPCTRENDPIEGLDGKIHGNTCSMCEAFFQQEAKEKERA EPRAKVKREAEKETCDEFRRLLQNGKLFCTRENDPVRGPDG KTHGNKCAMCKAVFQKENEERKRKEEEDQRNAAGHGSSGG GGGNTQDECAEYREQMKNGRLSCTRESDPVRDADGKSYNN QCTMCKAKLEREAERKNEYSRSRSNGTGSESGKDTCDEFRS QMKNGKLICTRESDPVRGPDGKTHGNKCTMCKEKLEREAAE KKKKEDEDRSNTGERSNTGERSNDKEDLCREFRSMQRNGKL ICTRENNPVRGPYGKMHINKCAMCQSIFDREANERKKKDEE KSSSKPSNNAKDECSEFRNYIRNNELICPRENDPVHGADGKF YTNKCYMCRAVFLTEALERAKLQEKPSHVRASQEEDSPDSFS SLDSEMCKDYRVLPRIGYLCPKDLKPVCGDDGQTYNNPCML CHENLIRQTNTHIRSTGKCEESSTPGTTAASMPPSDE LEKTIDomain KNEDQEMCHEFQAFMKNGKLFCPQDKKFFQSLDGIMFINKC 104 1(residues23- ATCKMILEKEAKSQ 77) LEKTIDomain APTELNCDDFKKGERDGDFICPDYYEAVCGTDGKTYDNRCA 105 2(residues91- LCAENAKTGSQIGVKSEGECKS 153) LEKTIDomain NPEQDVCSAFRPFVRDGRLGCTRENDPVLGPDGKTHGNKCA 106 3(residues155- MCAELFLKEAENAKREGETRI 216 LEKTIDomain NAEKDFCKEYEKQVRNGRLFCTRESDPVRGPDGRMHGNKC 107 4(residues219- ALCAEIFKQRFSEENSKTDQNLGKAEE 285) LEKTI_Domain REIVKLCSQYQNQAKNGILFCTRENDPIRGPDGKMHGNLCS 108 5(residues291- MCQAYFQAENEEKKKAEARAR 352) LEKTI_Domain ESGKATSYAELCSEYRKLVRNGKLACTRENDPIQGPDGKVH 109 6(residues356- GNTCSMCEVFFQAEEEEKKKKEGKSRN 423) LEKTIDomain ASFEELCSEYRKSRKNGRLFCTRENDPIQGPDGKMHGNTCS 110 7(residues431- MCEAFFQQEERARAKAKR 489) LEKTIDomain EAAKEICSEFRDQVRNGTLICTREHNPVRGPDGKMHGNKCA 111 8(residues490- MCASVFKLEEEEKKNDKEEKG 550) LEKTIDomain EAVQELCSEYRHYVRNGRLPCTRENDPIEGLDGKIHGNTCSM 112 9(residues561- CEAFFQQEAKEKERAEPRAK 622) LEKTIDomain EAEKETCDEFRRLLQNGKLFCTRENDPVRGPDGKTHGNKCA 113 10(residues MCKAVFQKENEERKRKEEEDQR 626-688) LEKTIDomain GNTQDECAEYREQMKNGRLSCTRESDPVRDADGKSYNNQC 114 11(residues TMCKAKLEREAERKNEY 701-757) LEKTIDomain ESGKDTCDEFRSQMKNGKLICTRESDPVRGPDGKTHGNKCT 115 12(residues MCKEKLEREAAEKKKKEDEDRS 768-830) LEKTIDomain NDKEDLCREFRSMQRNGKLICTRENNPVRGPYGKMHINKCA 116 13(residues MCQSIFDREANERKKKDEEKSS 843-905) LEKTIDomain NNAKDECSEFRNYIRNNELICPRENDPVHGADGKFYTNKCY 117 14(residues MCRAVFLTEALERAKLQEKPS 910-970) LEKTIDomain SLDSEMCKDYRVLPRIGYLCPKDLKPVCGDDGQTYNNPCML 118 15(residues CHENLIRQTNTHIRSTGKCEE 987-1048)
TABLE-US-00002 TABLE2 LEKTIFullLengthNucleotideSequence LEKTIFulllengthNucleicacid sequence(SEQIDNO:119) ATGAAGATAGCCACAGTGTCAGTGCTTCTGCCCTTGGCTCTTTGCC TCATACAAGATGCTGCCAGTAAGAATGAAGATCAGGAAATGTGCC ATGAATTTCAGGCATTTATGAAAAATGGAAAACTGTTCTGTCCCC AGGATAAGAAATTTTTTCAAAGTCTTGATGGAATAATGTTCATCA ATAAATGTGCCACGTGCAAAATGATACTGGAAAAAGAAGCAAAAT CACAGAAGAGGGCCAGGCATTTAGCAAGAGCTCCCAAGGCTACTG CCCCAACAGAGCTGAATTGTGATGATTTTAAAAAAGGAGAAAGAG ATGGGGATTTTATCTGTCCTGATTATTATGAAGCTGTTTGTGGCA CAGATGGGAAAACATATGACAACAGATGTGCACTGTGTGCTGAGA ATGCGAAAACCGGGTCCCAAATTGGTGTAAAAAGTGAAGGGGAAT GTAAGAGCAGTAATCCAGAGCAGGATGTATGCAGTGCTTTTCGGC CCTTTGTTAGAGATGGAAGACTTGGATGCACAAGGGAAAATGATC CTGTTCTTGGTCCTGATGGGAAGACGCATGGCAATAAGTGTGCAA TGTGTGCTGAGCTGTTTTTAAAAGAAGCTGAAAATGCCAAGCGAG AGGGTGAAACTAGAATTCGACGAAATGCTGAAAAGGATTTTTGCA AGGAATATGAAAAACAAGTGAGAAATGGAAGGCTTTTTTGTACAC GGGAGAGTGATCCAGTCCGTGGCCCTGACGGCAGGATGCATGGCA ACAAATGTGCCCTGTGTGCTGAAATTTTCAAGCAGCGTTTTTCAG AGGAAAACAGTAAAACAGATCAAAATTTGGGAAAAGCTGAAGAAA AAACTAAAGTTAAAAGAGAAATTGTGAAACTCTGCAGTCAATATC AAAATCAGGCAAAGAATGGAATACTTTTCTGTACCAGAGAAAATG ACCCTATTCGTGGTCCAGATGGGAAAATGCATGGCAACTTGTGTT CCATGTGTCAAGCCTACTTCCAAGCAGAAAATGAAGAAAAGAAAA AGGCTGAAGCACGAGCTAGAAACAAAAGAGAATCTGGAAAAGCAA CCTCATATGCAGAGCTTTGCAGTGAATATCGAAAGCTTGTGAGGA ACGGAAAACTTGCTTGCACCAGAGAGAACGATCCTATCCAGGGCC CAGATGGGAAAGTGCATGGCAACACCTGCTCCATGTGTGAGGTCT TCTTCCAAGCAGAAGAAGAAGAAAAGAAAAAGAAGGAAGGTAAAT CAAGAAACAAAAGACAATCTAAGAGTACAGCTTCCTTTGAGGAGT TGTGTAGTGAATACCGCAAATCCAGGAAAAACGGACGGCTTTTTT GCACCAGAGAGAATGACCCCATCCAGGGCCCAGATGGAAAAATGC ATGGCAACACCTGCTCCATGTGTGAGGCCTTCTTTCAACAAGAAG AAAGAGCAAGAGCAAAGGCTAAAAGAGAAGCTGCAAAGGAAATCT GCAGTGAATTTCGGGACCAAGTGAGGAATGGAACACTTATATGCA CCAGGGAGCATAATCCTGTCCGTGGCCCAGATGGCAAAATGCATG GAAACAAGTGTGCCATGTGTGCCAGTGTGTTCAAACTTGAAGAAG AAGAGAAGAAAAATGATAAAGAAGAAAAAGGGAAAGTCGAGGCTG AAAAAGTTAAGAGAGAAGCAGTTCAGGAGCTGTGCAGTGAATATC GTCATTATGTGAGGAATGGACGACTCCCCTGTACCAGAGAGAATG ATCCTATTGAGGGTCTAGATGGGAAAATCCACGGCAACACCTGCT CCATGTGTGAAGCCTTCTTCCAGCAAGAAGCAAAAGAAAAAGAAA GAGCTGAACCCAGAGCAAAAGTCAAAAGAGAAGCTGAAAAGGAGA CATGCGATGAATTTCGGAGACTTTTGCAAAATGGAAAACTTTTCT GCACAAGAGAAAATGATCCTGTGCGTGGCCCAGATGGCAAGACCC ATGGCAACAAGTGTGCCATGTGTAAGGCAGTCTTCCAGAAAGAAA ATGAGGAAAGAAAGAGGAAAGAAGAGGAAGATCAGAGAAATGCTG CAGGACATGGTTCCAGTGGTGGTGGAGGAGGAAACACTCAGGACG AATGTGCTGAGTATCGGGAACAAATGAAAAATGGAAGACTCAGCT GTACTCGGGAGAGTGATCCTGTACGTGATGCTGATGGCAAATCGT ACAACAATCAGTGTACCATGTGTAAAGCAAAATTGGAAAGAGAAG CAGAGAGAAAAAATGAGTATTCTCGCTCCAGATCAAATGGGACTG GATCAGAATCAGGGAAGGATACATGTGATGAGTTTAGAAGCCAAA TGAAAAATGGAAAACTCATCTGCACTCGAGAAAGTGACCCTGTCC GGGGTCCAGATGGCAAGACACATGGCAATAAGTGTACTATGTGTA AGGAAAAACTGGAAAGGGAAGCAGCTGAAAAAAAAAAGAAAGAGG ATGAAGACAGGAGCAATACAGGAGAAAGGAGCAATACAGGAGAAA GGAGCAATGACAAAGAGGATCTGTGTCGTGAATTTCGAAGCATGC AGAGAAATGGAAAGCTTATCTGCACCAGAGAAAATAACCCTGTTC GAGGCCCATATGGCAAGATGCACATCAATAAATGTGCTATGTGTC AGAGCATCTTTGATCGAGAAGCTAATGAAAGAAAAAAGAAAGATG AAGAGAAATCAAGTAGCAAGCCCTCAAATAATGCAAAGGATGAGT GCAGTGAATTTCGAAACTATATAAGGAACAATGAACTCATCTGCC CTAGAGAGAATGACCCAGTGCACGGTGCTGATGGAAAGTTCTATA CAAACAAGTGCTACATGTGCAGAGCTGTCTTTCTAACAGAAGCTT TGGAAAGGGCAAAGCTTCAAGAAAAGCCATCCCATGTTAGAGCTT CTCAAGAGGAAGACAGCCCAGACTCTTTCAGTTCTCTGGATTCTG AGATGTGCAAAGACTACCGAGTATTGCCCAGGATAGGTTATCTTT GTCCAAAGGATTTAAAGCCTGTCTGTGGTGACGATGGCCAAACCT ACAACAATCCTTGCATGCTCTGTCATGAAAACCTGATACGCCAAA CAAATACACACATCCGCAGTACAGGGAAGTGTGAGGAGAGCAGCA CCCCAGGAACCACCGCAGCCAGCATGCCCCCGTCTGACGAA
[0082] According to some embodiments, the recombinant microbe comprises a sequence as disclosed herein that has at least about 75% identity, or 80% identity, or 85% identity, or 90% identity, or 95% identity to any one or more of the SEQ ID NOS listed herein. As used herein, the term identity and grammatical versions thereof means the extent to which two nucleotide or amino acid sequences have the same residues at the same positions in an alignment. Percent (%) identity is calculated by multiplying the number of matches in a sequence alignment by 100 and dividing by the length of the aligned region, including internal gaps.
[0083] According to some embodiments, the recombinant protein expressed by the engineered microbe comprises one or more protease inhibitory domains of the LEKTI protein. Some non-limiting examples include one or more of domains D1, D2, D3, D4, D5, D6, D7, D8, D9, D10, D11, D12, D13, D14, and D15. According to some embodiments, the recombinant protein expressed by the engineered microbe comprises LEKTI inhibitory domain 6 or domains D8 to D11.
[0084] According to some embodiments, the LEKTI protein domains are effective to ameliorate the symptoms of Netherton Syndrome. As used herein, the terms ameliorate, ameliorating and grammatical variations thereof mean to decrease the severity of the symptoms of a disease in a subject. In some embodiments, the LEKTI protein domains act as a competitive or non-competitive inhibitor of one or more proteases present on or in the skin of a mammal. In some embodiments, the LEKTI protein domain acts as a serine protease inhibitor. As used herein, the terms protease and proteinase are used interchangeably, with both terms referring to an enzyme that performs proteolysis.
[0085] According to some embodiments, the microbe is genetically modified by transfection/transformation with a recombinant DNA plasmid encoding the LEKTI protein domains. Other conventional or to-be-discovered methods for introducing DNA into a microbe may also be used in the present invention. According to some embodiments, the recombinant DNA plasmid comprises sequences encoding the LEKTI protein domain and one or more secretory peptides and/or cell penetration peptides. According to some embodiments, the LEKTI domains are operably linked to one or more recombinant protein domains that are effective to enhance secretion from the microbe and/or penetration of the mammal's skin.
[0086] The term operably linked refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is regulated by the other or is not hindered by the other. For example, a promoter is operably linked with a coding sequence when it is capable of regulating the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in a sense or antisense orientation. In another example, two proteins can be operably linked, such that the function of either protein is not compromised. Generally, operably linked means that the nucleic acid sequences being linked are contiguous and, where necessary to join two protein coding regions, contiguous and in the same reading frame.
[0087] As used herein the term secretory peptides or secretory sequences or secretion tags or signal peptides or export signals and grammatical variations thereof means any peptide sequence that is capable of targeting the synthesized protein to the secretory pathway of a cell. In some embodiments, the secretory peptide may be positioned on the N-terminal end of a recombinant protein, and may co-translationally or post-translationally target the tagged protein for secretion. According to some embodiments, at least one LEKTI domain is operably linked to a SecA domain (SEQ ID NO: 3).
[0088] Secretion peptides: According to some embodiments, the therapeutic LEKTI domain is operably linked to one or more secretion signals or export signals that tag the protein for transport through the secretory pathway. Any secretion signal that facilitates exit of the LEKTI protein out of the bacterial cell may be used as a secretion peptide. Non-limiting examples of secretion peptides signals are set forth in Table 3, below:
TABLE-US-00003 TABLE3 SEQID AminoAcidSequence NO: MKKLAFAITAASGAAAVLSHHDAEA 9 WLDNRAFSKKFVPVVMATSVALFFLNLAFA 10 MAKKFNYKLPSMVALTLFGTAFTAHQANA 11 MKKRFLSICTMTIAALATTTMVNTSYA 12 NLKKQSKLILIFICIFTFFIMIIQSQFLMG 13 MKIFKLTSLTLAALTLAFPFSHVAQA 14 MKKTVIASTLAVSLGIAGYGLSGHEAH 15 MKKNKFLVYLLSTALITPTFATQTAFA 16 MKTRQNKYSIRKFSVGASSILIAALLFM 17 GGGSAQA MKNNNETRRFSIRKYTVGVVSIITGITI 18 FVSGQHAQA MKKKLSYMITIMLAFTLSLALGLFFNSAHA 19 MKKRFLSICTMTIAALATTTMVNTSYA 77 MKKKQVMLALTAAAGLGLTALHSAPAAKA 78 (yfhK)
[0089] According to some embodiments, the therapeutic LEKTI domain is operably linked to one or more signal sequences derived from endogenous proteins of Staphylococcus epidermidis. Non-limiting examples of secretion signal peptides derived from endogenous proteins of Staphylococcus epidermidis are set forth in Table 4 below:
TABLE-US-00004 TABLE4 Staphylococcusepidermidis Amino SEQ Acid ID ProteinName Length SignalSequence NO Serine-aspartate 45 MKKRRQGPINKRVDFLSNK 20 repeat-containing VNKYSIRKFTVGTASILVGA proteinF TLMFGA Glutamyl 27 MKKRFLSICTMTIAALATTT 21 endopeptidase MVNTSYA Bifunctionalautolysin 29 MAKKFNYKLPSMVALTLFG 22 TAFTAHQANA Serine-aspartate 50 MIKKNNLLTKKKPIANKSNK 23 repeat-containing YAIRKFTVGTASIVIGAALLF proteinG GLGHNEAKA BiofilmPIAsynthesis 30 MKPFKLIFISALMILIMTNAT 24 deacetylaseicaB PISHLNAQA Lipase 35 MKTRQNKYSIRKFSVGASSI 25 LIAALLFMGGGSAQA Epiderminleader 23 MNKFKFFIVFLILSLVFLQNE 26 peptide-processing YA serineproteaseepiP Fibrinogen-binding 51 MINKKNNLLTKKKPIANKSN 27 protein KYAIRKFTVGTASIVIGATLL FGLGHNEAK A Staphylococcal 26 MKKIATATIATAGIATFAFA 28 secretoryantigen HHDAQA ssaA Extracellularelastase 28 MKNFSKFALTSIAALTVASP 29 LVNTEVDA n/a 37 MKNNNETRRFSIRKYTVGV 30 VSIITGITIFVSGQHAQA Uncharacterized 19 MRYLKRITIYISLLILVSG 31 lipoproteinSE_0145 FoldaseproteinprsA 20 MKLMNKIIVPVTASALLLGA 32 Probablecellwall 40 MKKIDSWLTKHGLKNRLTL 33 amidaselytH VVIVIFIIFLILLFMFVNLSD Membraneprotein 19 MKKKALLPLFLGIMIFLAG 34 oxaA2 Probable 28 MKKTVIASTLAVSLGIAGYG 35 transglycosylaseisaA LSGHEAHA Probablequinol 19 MSKFKSLLLLFGTLILLSG 36 oxidasesubunit2 Probable 27 MKKTLVASSLAIGLGVVAG 37 transglycosylasesceD NAGHDAHA Bifunctionalautolysin 29 MAKKFNYKLPSMVALTLFG 38 TAFTAHQANA Extracellularcysteine 30 MKKKLSYMITIMLAFTLSLA 39 protease LGLFFNSAHA Membraneprotein 18 MHKRLFITLLGFIILLAG 40 oxaA1 Uncharacterized 19 MRYLKRITIYISLLILVSG 41 lipoproteinSE_0144 N-acetylmuramoyl-L- 25 MQKKYITAIIGTTALSALAST 42 alanineamidasesle1 HAQA Uncharacterized 22 MKHSSKIIVFVSFLILTIFIGG 43 lipoproteinSE_0142 Phosphate-binding 20 MKKWQLVGTTVLGASVLLG 44 proteinpstS A Accumulation- 52 MGKRRQGPINKKVDFLPNK 45 associatedprotein LNKYSIRKFTVGTASILLGST LIFGSSSHEAKA Staphylococcal 26 MKKIATATIATAGIATFAFA 46 secretoryantigen HHDAQA ssaA Serine-aspartate 45 MKKRRQGPINKRVDFLSNK 47 repeat-containing VNKYSIRKFTVGTASILVGA proteinF TLMFGA Glutamyl 27 MKKRFLSICTMTIAALATTT 48 endopeptidase MVNTSYA Lipase 35 MKTRQNKYSIRKESVGASSI 49 LIAALLFMGGGSAQA Extracellularelastase 28 MKNFSKFALTSIAALTVASP 50 LVNTEVDA Uncharacterized 17 MKKVLASATILSLMLVG 51 lipoproteinSE_1947 Uncharacterized 22 MKYYGKCISYISILILTFFIGG 52 lipoprotein SE_0186/SE_0187 Uncharacterized 22 MKHSSKIIVFVSFLILTIFIGG 53 lipoprotein SERP2423 BiofilmPIAsynthesis 30 MKPFKLIFISALMILIMTNAT 54 deacetylaseicaB PISHLNAQA Probablequinol 19 MSKFKSLLLLFGTLILLSG 55 oxidasesubunit2 Probable 27 MKKTLVASSLAIGLGVVAG 56 transglycosylasesceD NAGHDAHA Uncharacterized 19 MHYLKKVTIYISLLILVSG 57 lipoprotein SERP2447 N-acetylmuramoyl-L- 25 MQKKYITAIIGTTALSALAST 58 alanineamidasesle1 HAQA Uncharacterized 22 MKHSKKLLLCISFLLITFFIGG 59 lipoprotein SERP2445 Staphylococcal 26 MKKIATATIATAGIATFAFA 60 secretoryantigen HHDAQA ssaA Uncharacterized 19 MRYLKKVTIYISLLILVSG 61 lipoprotein SERP2443 Glutamyl 27 MKKRFLSICTMTIAALATTT 62 endopeptidase MVNTSYA Phosphate-binding 20 MKKWQLVGTTVLGASVLLG 63 proteinpstS A Bifunctionalautolysin 29 MAKKFNYKLPSMVALTLFG 64 TAFTAHQANA Extracellularcysteine 30 MKKKLSYMITIMLAFTLSLA 65 protease LGLFFNSAHA Membraneprotein 18 MHKRLFITLLGFIILLAG 66 oxaA1 Uncharacterized 22 MRYLKKVTIYISLLILTIFIGG 67 lipoprotein SERP2422 Uncharacterized 17 MKKVLASATILSLMLVG 68 lipoprotein SERP1959 Uncharacterized 22 MKHSKKLLLCISFLLITVFISG 69 lipoprotein SERP2453 Uncharacterized 22 MKHSKKLLLCISFLLITFFISG 70 lipoprotein SERP2465 Probable 28 MKKTVIASTLAVSLGIAGYG 71 transglycosylaseisaA LSGHEAHA Uncharacterized 22 MKHSKKLLLCISFLLITIFISG 72 lipoprotein SERP2451 Probablecellwall 40 MKKIDSWLTKHGLKNRLTL 73 amidaselytH VVIVIFIIFLILLFMFVNLSD Membraneprotein 19 MKKKALLPLFLGIMIFLAG 74 oxaA2 FoldaseproteinprsA 20 MKLMNKIIVPVTASALLLGA 75 Lipase 35 MKTRQNKYSIRKFSVGASSI 76 LIAALLFMGGGSAQA
[0090] According to some embodiments, the therapeutic LEKTI domain is operably linked to one or more secretion signal sequences derived from endogenous proteins of other bacteria. Non-limiting examples of secretion signal peptides derived from endogenous proteins of various bacteria are set forth in Appendix A.
[0091] According to some embodiments, the recombinant LEKTI domain is operably linked to a cell penetration peptide sequence that enhances the ability of the LEKTI domain to pass through a cell membrane. The term enhance as used to describe the cell penetration peptide/LEKTI, means that the cell penetration sequence improves the passage of recombinant LEKTI domain through a cell membrane relative to a recombinant LEKTI domain lacking the cell penetration sequence.
[0092] Cell penetration peptides: According to some embodiments, one or more cell penetrating peptides are used to mediate delivery of therapeutic proteins in vivo without using cell surface receptors and without causing significant membrane damage. According to some embodiments, one or more cell penetrating peptides are operably linked to therapeutic proteins to facilitate entry into skin cells (e.g. keratinocytes). Non-limiting examples are set forth in Table 5, below:
TABLE-US-00005 TABLE5 SEQ ID Cellpenetratingsequence NO GRKKRRQRRRPPQ 125 GWTLNSAGYLLGKINLKALAALAKKIL 126 KLALKLALKALKAALKLA 79 WEAKLAKALAKALAKHLAKALAKALKACEA 80 KETWWETWWTEWSQPKKKRKV 81 RRRRRRRRR 82 LGTYTQDFNKFHTFPQTAIGVGAP 83 RQIKWFQNRRMKWKK 84 YGRKKRRQRRR 85 RGGRLSYSRRRFSTSTGR 86 RRLSYSRRRF 87 PIRRRKKLRRLK 88 RRQRRTSKLMKR 89 RRRRNRTRRNRRRVR 90 KMTRAQRRAAARRNRWTAR 91 TRRQRTRRARRNR 92 GRKKRRQRRRPPQ 93 GRRRRRRRRRPPQ 94 GWTLNSAGYLLGKINLKALAALAKKIL 95 KLALKLALKLALALKLA 96 MGLGLHLLVLAAALQGAWSQPKKKRKV 97 GALFLGWLGAAGSTMGAWSQPKKKRKV 98 GALFLGFLGAAGSTMGAWSQPKKKRKV 99 GALFLGFLGAAGSTMGAWSQPKSKRKV 100 KETWWETWWTEWSQPKKKRKV 101 KETWFETWFTEWSQPKKKRKV 102
[0093] According to some embodiments, cell penetrating peptides comprise periodic amino acid sequences. Non-limiting examples of periodic cell penetrating sequences include: Polyarginines, R?n (wherein 4<n<17); Polylysines, K?n (wherein 4<n<17); arginine repeats interspaced with 6-aminocaprotic acid residues (RAca), wherein there are 2 to 6 arginine repeats; arginine repeats interspaced with 4-aminobutyric acid (RAbu), wherein there are 2 to 6 arginine repeats; arginine repeats interspaced with methionine, wherein there are 2 to 6 arginine repeats; arginine repeats interspaced with threonine, wherein there are 2 to 6 arginine repeats; arginine repeats interspaced with serine, wherein there are 2 to 6 arginine repeats; and arginine repeats interspaced with alanine, wherein there are 2 to 6 arginine repeats.
[0094] According to some embodiments, expression of the LEKTI domain is controlled by an operon and the amount of LEKTI provided to the mammal's skin is proportional to the availability of an extrinsic factor. For example, in some embodiments the recombinant LEKTI gene may be under the control of a xylose inducible promoter (e.g. xylose repressor (xylR), xylose operator (xylO), xylose isomerase gene (xylA) including the cis-acting catabolite-responsive element (CRE)), and the amount of recombinant LEKTI protein made available to the skin of the mammal controlled by the amount of exogenous xylose available to the recombinant microbe. According to some embodiments, the expression of the LEKTI domain is controlled by a promoter that is constitutively active. According to some embodiments, the expression of the LEKTI domain is controlled by a CmR promoter according to SEQ ID NO: 8.
[0095] According to some embodiments, the microbe is genetically modified by chromosomal integration of a DNA plasmid encoding the LEKTI protein domains. According to some embodiments, the DNA plasmid integrated into the bacterial chromosome comprises one or more sequences of the pJB38 vector. In some embodiments, the recombinant LEKTI protein is operably linked to an inducible promoter, ribosome binding site, export signal, and/or cell penetrating peptide in the pJB38 vector. In some embodiments, the recombinant LEKTI protein is fused in frame to a secretion peptide, and a synthetic propeptide. In some embodiments, the secretion peptide is yfhK secretion peptide from Bacillus subtilis. In some embodiments, the secretion peptide has at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 78. In some embodiments, the secretion peptide comprises, or consists of SEQ ID NO: 78.
[0096] According to some embodiments, the DNA plasmid encoding the recombinant LEKTI protein fused in frame to a secretion peptide and propeptide is integrated into the bacteria's chromosome. In some embodiments, the DNA plasmid encoding the recombinant LEKTI protein fused in frame to a secretion peptide and propeptide in integrated into the hld gene (delta-toxin gene). In some embodiments, the integrated nucleotide sequence encoding LEKTI protein fused in frame to a secretion peptide and propeptide is operably linked to one or more promoters. In some embodiments, the one or more promoters are endogenous, e.g., originate from the bacteria's chromosome. In some embodiments, the one or more promoters are P.sub.yxiE and P3. The P.sub.yxiE promoter is located immediately upstream of the hld gene and the P3 promoter is part of the neighboring accessory gene regulator (agr) operon. According to some such embodiments, the microbe is selected from the group consisting of Bifidobacterium, Brevibacterium, Propionibacterium, Lactococcus, Streptococcus, Staphylococcus (e.g., S. epidermidis and/or S. hominis), Lactobacillus (e.g., L. acidophilus), Enterococcus, Pediococcus, Leuconostoc, or Oenococcus, and mixtures thereof.
[0097] According to one aspect, the present disclosure provides a method of treating or ameliorating the effects of a skin disease of a mammal in need thereof comprising, providing onto a surface of the skin of the mammal a microbe genetically modified to express one or more LEKTI protein domains, wherein the LEKTI protein domains are effective to penetrate one or more layers of the mammal's skin and effective to inhibit activity of at least one serine protease in or on the mammal's skin. According to some embodiments, the microbe is adapted to live for a controlled duration on the surface of the mammal's skin and to provide a continuous supply of LEKTI protein domains.
[0098] According to another aspect, the present disclosure provides a kit for the treatment or amelioration of the effects of a skin disease of a mammal in need thereof comprising: (1) a composition comprising a microbe that is genetically modified to express one or more LEKTI protein domains, wherein the LEKTI protein domains are effective to penetrate one or more layers of the mammal's skin and effective to inhibit serine protease activity of at least one serine protease in or on the mammal's skin; and (2) reagents for applying the composition to the skin of the mammal. According to some embodiments, the microbes are adapted to live for a controlled duration on the surface of the mammal's skin and to provide a continuous supply of LEKTI protein domains.
[0099] In addition to the above components, the subject kits will further include instructions for use of the components and/or practicing the subject methods. These instructions may be present in the subject kits in a variety of forms, one or more of which may be present in the kit. One form in which these instructions may be present is as printed information on a suitable medium or substrate, such as a piece or pieces of paper on which the information is printed, in the packaging of the kit, or in a package insert. Yet another means would be a computer readable medium, such as diskette, or CD, on which the information has been recorded. Further, another means by which the instructions may be present is a website address used via the internet to access the information at a removed site. Any convenient means may be present in the kits.
[0100] The components of the kits may be packaged either in aqueous media or in lyophilized form. The kits will generally be packaged to include at least one vial, test tube, flask, bottle, syringe or other container means, into which the described reagents may be placed, and preferably, suitably aliquoted. Where additional components are provided, the kit will also generally contain a second, third or other additional container into which such component may be placed.
[0101] The kits of the present disclosure will also typically include a means for containing the reagent containers in close confinement for commercial sale. Such containers may include injection or blow-molded plastic containers into which the desired vials are retained.
Formulations
[0102] According to some embodiments the formulation for use according to the present invention can comprise any pharmaceutically effective amount of the recombinant bacteria to produce a therapeutically effective amount of the desired polypeptide or therapeutically effective domain(s) thereof, for example, at least about 0.01%, about 0.05%, about 0.1%, about 0.2%, about 0.3%, about 0.4%, about 0.5%, about 0.6%, about 0.7%, about 0.8%, about 0.9%, about 1.0%, about. 1.5%, about 2.0%, about 3.0%, about 4.0%, about 5.0%, about 6.0%, about 7.0%, about 8.0%, about 9.0%, about 10.0%, about 11.0%, about 12.0%, about 13.0%, about 14.0%, about 15.0%, about 16.0%, about 17.0%, about 18.0%, about 19.0%, about 20.0%, about 25.0%, about 30.0%, about 35.0%, about 40.0%, about 45.0%, about 50.0% or more by weight of recombinant bacteria, the upper limit of which is about 90.0% by weight of recombinant, bacteria.
[0103] According to some embodiments, the formulation for use according to the present invention can comprise, for example, at least about 0.01% to about 30%, about 0.01% to about 20%, about 0.01% to about 5%, about 0.1% to about 30%, about 0.1% to about 20%, about 0.1% to about 15%, about 0.1% to about 10%, about 0.1% to about 5%, about 0.2% to about 5%, about 0.3% to about 5%, about 0.4% to about 5%, about 0.5% to about 5%, about 1% to about 5%, or more by weight of recombinant bacteria.
[0104] According to some embodiments, the topical formulation can be in any form suitable for application to the body surface, such as a cream, lotion, sprays, solution, gel, ointment, paste, plaster, paint, bioadhesive, suspensions, emulsions, or the like, and/or can be prepared so as to contain liposomes, micelles, and/or microspheres. Such a formulation can be used in combination with an occlusive overlayer so that moisture evaporating from the body surface is maintained within the formulation upon application to the body surface and thereafter. According to some embodiments, the formulation can include a living cell culture composition and can comprise at least one engineered bacterial strain that produces a therapeutically effective recombinant polypeptide or therapeutically effective domain(s) thereof. This engineered living cell culture composition can deliver the polypeptide directly to the skin for treating or preventing abnormal skin conditions.
[0105] Topical formulations include those in which any other active ingredient(s) is (are) dissolved or dispersed in a dermatological vehicle known in the art (e.g. aqueous or nonaqueous gels, ointments, water-in-oil or oil-in-water emulsions). Constituents of such vehicles can comprise water, aqueous buffer solutions, non-aqueous solvents (such as ethanol, isopropanol, benzyl alcohol, 2-(2-ethoxyethoxy)ethanol, propylene glycol, propylene glycol monolaurate, glycofurol or glycerol), oils (e.g. a mineral oil such as a liquid paraffin, natural or synthetic triglycerides such as Miglyol?, or silicone oils such as dimethicone). Depending, inter alia, upon the nature of the formulation as well as its intended use and site of application, the dermatological vehicle employed can contain one or more components (for example, when the formulation is an aqueous gel, components in addition to water) selected from the following list: a solubilizing agent or solvent (e.g. a ?-cyclodextrin, such as bydroxypropyl ?-cyclodextrin, or an alcohol or polyol such as ethanol, propylene glycol or glycerol); a thickening agent (e.g. hydroxyethylceliulose, hydroxypropylcellulose, carboxymethylcellulose or carbomer); a gelling agent (e.g. a polyoxyethylene-polyoxypropylene copolymer); a preservative (e.g. benzyl alcohol, benzalkonium chloride, chlorhexidine, chlorbutol, a benzoate, potassium sorbate or EDTA or salt thereof); and pH buffering agent(s) (such as a mixture of dihydrogen phosphate and hydrogen phosphate salts, or a mixture of citric acid and a hydrogen phosphate salt).
[0106] A pharmaceutically acceptable carrier can also be incorporated in the formulation of the present invention and can be any carrier conventionally used in the art. Examples thereof include water, lower alcohols, higher alcohols, polyhydric alcohols, monosaccharides, disaccharides, polysaccharides, hydrocarbon oils, fats and oils, waxes, fatty acids, silicone oils, nonionic surfactants, ionic surfactants, silicone surfactants, and water-based mixtures and emulsion-based mixtures of such carriers. The term pharmaceutically acceptable or pharmaceutically acceptable carrier is used herein to refer to a compound or composition that can be incorporated into a pharmaceutical formulation without causing undesirable biological effects or unwanted, interaction with other components of the formulation, Carriers or vehicles as used herein refer to carrier materials suitable for incorporation in a topically applied composition. Carriers and vehicles useful herein include any such materials known in the art, which are non-toxic and do not interact with other components of the formulation in which it is contained in a deleterious manner. The term aqueous refers to a formulation that contains water or that becomes water-containing following application to the skin or mucosal tissue.
[0107] A film former, when it dries, forms a protective film over the site of application. The film inhibits removal of the active ingredient and keeps it in contact with the site being treated. An example of a film former that is suitable for use in this invention is Flexible Collodion, US P. As described in Remington: The Science and Practice of Pharmacy, 19th Ed. (Easton, PA: Mack Publishing Co., 1995), at page 1530, collodions are ethyl ether/ethanol solutions containing pyroxylin (a nitrocellulose) that evaporate to leave a film of pyroxylin. A film former can act additionally as a carrier. Solutions that dry to form a film are sometimes referred to as paints. Creams, as is well known in the arts of pharmaceutical formulation, are viscous liquids or semisolid emulsions, either oil-in-water or water-in-oil.
[0108] Cream bases are water-washable, and contain an oil phase, an emuisifier, and an aqueous phase. The oil phase, also called the internal phase, is generally comprised of petrolatum and a fatty alcohol such as cetyl or stearyl alcohol. The aqueous phase usually, although not necessarily, exceeds the oil phase in volume, and generally contains a humectant. The emulsifier in a cream formulation is generally a nonionic, anionic, cationic or amphoteric surfactant.
[0109] Lotions are preparations to be applied to the skin surface without friction, and are typically liquid or semiliquid preparations in which particles, including the active agent, are present in a water or alcohol base. Lotions are usually suspensions of solids, and preferably, comprise a liquid oily emulsion of the oil-in-water type. Lotions are preferred formulations herein for treating large body areas, because of the ease of applying a more fluid composition. It is generally necessary that the insoluble matter in a lotion be finely-divided.
[0110] Lotions will typically contain suspending agents to produce better dispersions as well as compounds useful for localizing and holding the active agent in contact with the skin, e.g., methylcellulose, sodium carboxymethyl-cellulose, or the like.
[0111] Solutions are homogeneous mixtures prepared by dissolving one or more chemical substances (solutes) in a liquid such that the molecules of the dissolved substance are dispersed among those of the solvent. The solution can contain other pharmaceutically or cosmetically acceptable chemicals to buffer, stabilize or preserve the solute. Common examples of solvents used in preparing solutions are ethanol, water, propylene glycol or any other acceptable vehicles. As is of course well known, gels are semisolid, suspension-type systems. Single-phase gels contain organic macromolecules distributed substantially uniformly throughout the carrier liquid, which is typically aqueous, but also, preferably, contain an alcohol, and, optionally, an oil. Preferred organic macromolecules, i.e., gelling agents, are cross-linked acrylic acid polymers such as the carbomer family of polymers, e.g., carboxypolyalkylenes that can be obtained commercially under the Carbopol trademark. Also preferred are hydrophilic polymers such as polyethylene oxides, polyoxyethylene-polyoxypropylene copolymers and polyvinylalcohol; cellulosic polymers such as hydroxy-propyl cellulose, hydroxyethyl cellulose, hydroxypropyl methylcellulose, hydroxy-propyl methylcellulose phthaiate, and methylcellulose; gums such as tragacanth and xanthan gum; sodium alginate; and gelatin, In order to prepare a uniform gel, dispersing agents such as alcohol or glycerin can be added, or the gelling agent can be dispersed by trituration, mechanical mixing or stirring, or combinations thereof. Ointments, as also well known in the art, are semisolid preparations that are typically based on petrolatum or other petroleum derivatives. The specific ointment base to be used, as will be appreciated by those skilled in the art, is one that will provide for a number of desirable characteristics, e.g., emolliency or the like. As with other carriers or vehicles, an ointment base should be inert, stable, nonirritating, and nonsensitizing. As explained in Remington: The Science and Practice of Pharmacy, 19th Ed. (Easton, PA: Mack Publishing Co., 1995), at pages 1399-1404, ointment bases can be grouped in four classes: oleaginous bases; emulsifiable bases; emulsion bases; and water-soluble bases. Oleaginous ointment bases include, for example, vegetable oils, fats obtained from animals, and semisolid hydrocarbons obtained from petroleum.
[0112] Emulsifiable ointment bases, also known as absorbent ointment bases, contain little or no water and include, for example, hydroxystearin sulfate, anhydrous lanolin, and hydrophilic petrolatum.
[0113] Emulsion ointment bases are either water-in-oil (W/O) emulsions or oil-in-water (O/W) emulsions, and include, for example, acetyl alcohol, glyceryl monostearate, lanolin, and stearic acid. Preferred water-soluble ointment bases are prepared from polyethylene glycols of varying molecular weight; see Remington: The Science and Practice of Pharmacy for further information.
[0114] Pastes are semisolid dosage forms in which the active agent is suspended in a suitable base. Depending on the nature of the base, pastes are divided between fatty pastes or those made from single-phase aqueous gels. The base in a fatty paste is generally petrolatum or hydrophilic petrolatum or the like. The pastes made from single-phase aqueous gels generally incorporate carboxy-methylcellulose or the like as a base.
[0115] Enhancers are those lipophilic co-enhancers typically referred to as plasticizing enhancers, i.e., enhancers that have a molecular weight in the range of about 150 to 1000, an aqueous solubility of less than about 1 wt. %, preferably less than about 0.5 wt. %, and most preferably less than about 0.2 wt. %. The Hildebrand solubility parameter 6 of plasticizing enhancers is in the range of about 2.5 to about 10, preferably in the range of about 5 to about 10. Preferred lipophilic enhancers are fatty esters, fatty alcohols, and fatty ethers. Examples of specific and most preferred fatty acid esters include methyl laurate, ethyl oleate, propylene glycol nionolaurace, propylene glycerol dilaurate, glycerol monolaurate, glycerol monooleate, isopropyl n-decanoate, and octyldodecyl myristate. Fatty alcohols include, for example, stearyl alcohol and oleyl alcohol, while fatty ethers include compounds wherein a diol or triol, preferably a C.sub.2-C.sub.4 alkane diol or triol, are substituted with one or two fatty ether substituents.
[0116] Additional permeation enhancers will be known to those of ordinary skill in the art of topical drug delivery, and/or are described in the pertinent texts and literature. See, e.g., Percutaneous Penetration Enhancers, eds. Smith et al. (CRC Press, 1995)(incorporated herein by reference).
[0117] Various other additives can be included in the compositions of the present invention in addition to those identified above. These include, but are not limited to, antioxidants, astringents, perfumes, preservatives, emollients, pigments, dyes, humectants, propeliants, and sunscreen agents, as well as other classes of materials whose presence can be pharmaceutically or otherwise desirable. Typical examples of optional additives for inclusion in the formulations of the invention are as follows: preservatives such as sorbate; solvents such as isopropanol and propylene glycol; astringents such as menthol and ethanol; emollients such as polyalkylene methyl glucosides; humectants such as glycerine; emulsifiers such as glycerol stearate, PEG-100 stearate, polyglyceryl-3 hydroxylauryl ether, and polysorbate 60; sorbitol and other polyhydroxyalcohols such as polyethylene glycol; sunscreen agents such as octyl methoxyl cinnamate (available commercially as Parsol MCX) and butyl methoxy benzoylmethane (available under the tradename Parsol 1789); antioxidants such as ascorbic acid (vitamin C), a-tocopherol (Vitamin E), ?-tocopherol, ?-tocopherol, ?-tocopherol, ?-tocopherol, ?.Math.-tocopherol, Z.sup.?-tocopherol, ?-tocopherol, and retinol (vitamin A); essential oils, ceramides, essential fatty acids, mineral oils, vegetable oils (e.g., soya bean oil, palm oil, liquid fraction of shea butter, sunflower oil), animal oils (e.g., perhydrosqualene), synthetic oils, silicone oils or waxes (e.g., cyclomethicone and dimethicone), fluorinated oils (generally perfluoropolyethers), fatty alcohols (e.g., cetyl alcohol), and waxes (e.g., beeswax, carnauba wax, and paraffin wax); skin-feel modifiers; and thickeners and structurants such as swelling clays and cross-linked carboxypolyalkylenes that can be obtained commercially under the Carbopol trademark. Other additives include beneficial agents such as those materials that condition the skin (particularly, the upper layers of the skin in the stratum corneum) and keep it soft by retarding the decrease of its water content and/or protect the skin. Such conditioners and moisturizing agents include, by way of example, pyrrolidine carboxylic acid and amino acids; organic antimicrobial agents such as 2,4,4-trichloro-2-hydroxy diphenyl ether (triclosan) and benzoic acid; anti-inflammatory agents such as acetylsalicylic acid and glycyrrhetinic acid; anti-seborrhoeic agents such as retinoic acid; vasodilators such as nicotinic acid; inhibitors of melanogenesis such as kojic acid; and mixtures thereof. Further additional active agents including, for example, alpha hydroxyacids, alpha ketoacids, polymeric hydroxyacids, moisturizers, collagen, marine extract, and antioxidants such as ascorbic acid (Vitamin C), a-tocopherol (Vitamin E), ?-tocopherol, ?-tocopherol, 6-tocopherol, ?-tocopherol, ?.Math.-tocopherol, ?.sub.2-tocopherol, ?-tocopherol, and retinol (Vitamin A), and/or pharmaceutically acceptable salts, esters, amides, or other derivatives thereof. A preferred tocopherol compound is a-tocopherol. Additional agents include those that are capable of improving oxygen supply in skin tissue, as described, for example, in Gross, et al, WO 94/00098 and Gross, et al, WO 94/00109, both assigned to Lancaster Group AG (incorporated herein by reference). Sunscreens and UV absorbing compounds can also be included. Non-limiting examples of such sunscreens and UV absorbing compounds include aminobenzoic acid (PABA), avobenzone, cinoxate, dioxybenzone, homosalate, menthyl anthranilate, oxtocrylene, octyl methoxycmnamate, octyl salicylate, oxybenzone, padirnate O, phenylbenzirmdazole sulfonic acid, sulisobenzone, titanium dioxide, trolamine salicylate, zinc oxide, ensulizole, meradiraate, octinoxate, octisalate, and octocrylene. See Title 21. Chapter 1. Subchapter D. Part 352. Sunscreen drug products for over-the-counter human use incorporated herein in its entirety.
[0118] Other embodiments can include a variety of non-carcinogenic, non-irritating healing materials that facilitate treatment with the formulations of the invention. Such healing materials can include nutrients, minerals, vitamins, electrolytes, enzymes, herbs, plant extracts, glandular or animal extracts, or safe therapeutic agents that can be added to the formulation to facilitate the healing of dermal disorders.
[0119] The amounts of these various additives are those conventionally used in the cosmetics field, and range, for example, from about 0.01% to about 20% of the total weight of the topical formulation.
[0120] The formulations of the invention can also include conventional additives such as opacifiers, fragrance, colorant, stabilizers, surfactants, and the like. In certain embodiments, other agents can also be added, such as antimicrobial agents, to prevent spoilage upon storage, i.e., to inhibit growth of microbes such as yeasts and molds.
[0121] Suitable antimicrobial agents are typically selected from the group consisting of the methyl and propyl esters of p-hydroxybenzoic acid (i.e., methyl and propyl paraben), sodium benzoate, sorbic acid, imidurea, and combinations thereof. In other embodiments, other agents can also be added, such as repressors and inducers, i.e., to inhibit (i.e. glycose) or induce (i.e. xylose) the production of the polypeptide of interest. Such additives can be employed provided they are compatible with and do not interfere with the function of the formulations.
[0122] The formulations can also contain irritation-mitigating additives to minimize or eliminate the possibility of skin irritation or skin damage resulting from the chemical entity to be administered, or other components of the composition.
[0123] Suitable irritation-mitigating additives include, for example: a-tocopherol; monoamine oxidase inhibitors, particularly phenyl alcohols such as 2-phenyl-1-ethanol; glycerin; salicylates; ascorbates; ionophores such as monensin; amphophilic amines; ammonium chloride; N-acetylcysteine; capsaicin; and chloroquine. The irritation-mitigating additive, if present, can be incorporated into the compositions at a concentration effective to mitigate irritation or skin damage, typically representing not more than about 20 wt. %, more typically not more than about 5 wt. %, of the formulation.
[0124] Further suitable pharmacologically active agents that can be incorporated into the present formulations in certain embodiments and thus topically applied along with the active agent include, but are not limited to, the following: agents that improve or eradicate pigmented or non-pigmented age spots, keratoses, and wrinkles; antimicrobial agents; antibacterial agents; antipruritic and antixerotic agents; anti-inflammatory agents; local anesthetics and analgesics; corticosteroids; retinoids; vitamins; hormones; and antimetabolites.
[0125] Some examples of topical pharmacologically active agents include acyclovir, amphotericins, chlorhexidine, clotrimazole, ketoconazole, econazole, miconazole, metronidazole, minocycline, nystatin, neomycin, kanamycin, phenytoin, para-amino benzoic acid esters, octyl methoxycmnamate, octyl salicylate, oxybenzone, dioxybenzone, tocopherol, tocopheryl acetate, selenium sulfide, zinc pyrithione, diphenhydramine, pramoxine, lidocaine, procaine, erythromycin, tetracycline, clindamycin, crotamiton, hydroquinone and its monomethyl and benzyl ethers, naproxen, ibuprofen, cromolyn, retinol, retinyl palmitate, retinyl acetate, coal tar, griseofulvin, estradiol, hydrocortisone, hydrocortisone 21-acetate, hydrocortisone 17-valerate, hydrocortisone 17-butyrate, progesterone, betamethasone valerate, betamethasone dipropionate, triamcinolone acetonide, fluocinonide, clobetasol propionate, minoxidil, dipyridamole, diphenylhydantoin, benzoyl peroxide, and 5-fluorouracil.
[0126] A cream, lotion, gel, ointment, paste or the like can be spread on the affected surface and gently rubbed in. A solution can be applied in the same way, but more typically will be applied with a dropper, swab, or the like, and carefully applied to the affected areas.
[0127] The application regimen will depend on a number of factors that can readily be determined, such as the severity of the condition and its responsiveness to initial treatment, but will normally involve one or more applications per day on an ongoing basis. One of ordinary skill can readily determine the optimum amount of the formulation to be administered, administration methodologies and repetition rates. In general, it is contemplated that the formulations of the invention will be applied in the range of once or twice weekly up to once or twice daily.
[0128] The pharmaceutical compositions of the invention comprise one or more active ingredients, e.g. therapeutic agents, in admixture with one or more pharmaceutically-acceptable diluents or carriers and, optionally, one or more other compounds, drugs, ingredients and/or materials. Regardless of the route of administration selected, the agents/compounds of the present invention are formulated into pharmaceutically-acceptable dosage forms by conventional methods known to those of skill in the art. See, e.g., Remington, The Science and Practice of Pharmacy (21st Edition, Lippincott Williams and Wilkins, Philadelphia, Pa.).
[0129] Pharmaceutically acceptable diluents or carriers are well known in the art (see, e.g., Remington, The Science and Practice of Pharmacy (21st Edition, Lippincott Williams and Wilkins, Philadelphia, Pa.) and The National Formulary (American Pharmaceutical Association, Washington, D.C.)) and include sugars (e.g., lactose, sucrose, mannitol, and sorbitol), starches, cellulose preparations, calcium phosphates (e.g., dicalcium phosphate, tricalcium phosphate and calcium hydrogen phosphate), sodium citrate, water, aqueous solutions (e.g., saline, sodium chloride injection, Ringer's injection, dextrose injection, dextrose and sodium chloride injection, lactated Ringer's injection), alcohols (e.g., ethyl alcohol, propyl alcohol, and benzyl alcohol), polyols (e.g., glycerol, propylene glycol, and polyethylene glycol), organic esters (e.g., ethyl oleate and tryglycerides), biodegradable polymers (e.g., polylactide-polyglycolide, poly(orthoesters), and poly(anhydrides)), elastomeric matrices, liposomes, microspheres, oils (e.g., corn, germ, olive, castor, sesame, cottonseed, and groundnut), cocoa butter, waxes (e.g., suppository waxes), paraffins, silicones, talc, silicylate, etc. Each pharmaceutically acceptable diluent or carrier used in a pharmaceutical composition of the invention must be acceptable in the sense of being compatible with the other ingredients of the formulation and not injurious to the subject. Diluents or carriers suitable for a selected dosage form and intended route of administration are well known in the art, and acceptable diluents or carriers for a chosen dosage form and method of administration can be determined using ordinary skill in the art.
[0130] The pharmaceutical compositions of the invention may, optionally, contain additional ingredients and/or materials commonly used in pharmaceutical compositions. These ingredients and materials are well known in the art and include (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and silicic acid; (2) binders, such as carboxy-methylcellulose, alginates, gelatin, polyvinyl pyrrolidone, hydroxypropylmethyl cellulose, sucrose and acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, sodium starch glycolate, cross-linked sodium carboxymethyl-cellulose and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as cetyl alcohol and glycerol monostearate; (8) absorbents, such as kaolin and bentonite clay; (9) lubricants, such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, and sodium lauryl sulfate; (10) suspending agents, such as ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth; (11) buffering agents; (12) excipients, such as lactose, milk sugars, polyethylene glycols, animal and vegetable fats, oils, waxes, paraffins, cocoa butter, starches, tragacanth, cellulose derivatives, polyethylene glycol, silicones, bentonites, silicic acid, talc, salicylate, zinc oxide, aluminum hydroxide, calcium silicates, and polyamide powder; (13) inert diluents, such as water or other solvents; (14) preservatives; (15) surface-active agents; (16) dispersing agents; (17) control-release or absorption-delaying agents, such as hydroxypropylmethyl cellulose, other polymer matrices, biodegradable polymers, liposomes, microspheres, aluminum monostearate, gelatin, and waxes; (18) opacifying agents; (19) adjuvants; (20) wetting agents; (21) emulsifying and suspending agents; (22), solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan; (23) propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane; (24) antioxidants; (25) agents which render the formulation isotonic with the blood of the intended recipient, such as sugars and sodium chloride; (26) thickening agents; (27) coating materials, such as lecithin; and (28) sweetening, flavoring, coloring, perfuming and preservative agents. Each such ingredient or material must be acceptable in the sense of being compatible with the other ingredients of the formulation and not injurious to the subject. Ingredients and materials suitable for a selected dosage form and intended route of administration are well known in the art, and acceptable ingredients and materials for a chosen dosage form and method of administration may be determined using ordinary skill in the art.
[0131] Dosage forms for the topical or transdermal administration include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches, drops and inhalants. The active agent(s)/compound(s) may be mixed under sterile conditions with a suitable pharmaceutically-acceptable diluent or carrier. The ointments, pastes, creams and gels may contain excipients. Powders and sprays may contain excipients and propellants.
[0132] The pharmaceutical compositions of the present invention suitable for parenteral administrations may comprise one or more agent(s)/compound(s) in combination with one or more pharmaceutically-acceptable sterile isotonic aqueous or non-aqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain suitable antioxidants, buffers, solutes which render the formulation isotonic with the blood of the intended recipient, or suspending or thickening agents. Proper fluidity can be maintained, for example, by the use of coating materials, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants. These pharmaceutical compositions may also contain suitable adjuvants, such as wetting agents, emulsifying agents and dispersing agents. It may also be desirable to include isotonic agents. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption.
[0133] The following examples are provided to further illustrate the methods of the present invention. These examples are illustrative only and are not intended to limit the scope of the invention in any way.
EXAMPLES
Example 1
[0134] Method of Integration of the hLEKTI-d6 Cassette into the Chromosome of S. epidermidis SE???.
[0135] The chromosomal hLEKTI-d6 expressing strain was constructed by the procedure that follows. The expression cassette from plasmid pLEKTI-27a-d6 (
[0136] For chromosomal integration, the exchange plasmid, pJB38-SE1634-KO-P.sub.yxiE-d6-KI, was designed using Benchling (an online sequence design tool, www.benchling.com). A set of eight overlapping oligonucleotide primers were designed to amplify four DNA fragments by PCR using a high-fidelity DNA polymerase (Table 6). Four PCR reactions using Q5? High-Fidelity 2? Master Mix (New England Biolabs (NEB)) were performed on the following DNA templates: 1) pJB38 plasmid ((8); one reaction producing ?7 kb), 2) S. epidermidis NRRL B-4268 strain genomic DNA (two reactions, each producing a ?1 kb fragment, one flanking the 5 and one flanking the 3 region of SE1634 gene), and 3) pLEKTI-27a-d6 (one reaction producing a fragment of 690 bp encoding the LEKTI-d6 expression cassette). All reactions were confirmed by agarose gel electrophoresis for the presence and correct sizes of amplified DNA fragments.
TABLE-US-00006 TABLE6 Primerstoconstructandanalyzechromosomal integrationofexchangeplasmid pJB38-SE1634-KO-PyxiE-d6-KI Number Name bp Sequence 97 GA-pJB-32-F 31 CGGATCCTACCCGGATCGATCCTCTAG A(SEQIDNO:127) 166 5ofSEagr-pJB- 58 TTCGAGCTCGCCCGCTAAGCGCTACCC GA-F GCGAGCTGATAAAAATCTTAAAGACAG CTCT(SEQIDNO:128) 241 5ofSE1634-GA-R 35 TAATTTTTGAATGAGTCTATTGTAACT TTTGTAAC(SEQIDNO:129) 242 5ofSE1634-GA- 50 CAATAGACTCATTCAAAAATTCATTAA d6-F TTTCGACTTTTGCCCTC(SEQIDNO:130) 243 PyxiE-GA- 46 CGAAAGGAGTGAAGTTATAATGAC 3SE1634R GATTACAGAATCAACTATCTGC(SEQID NO:131) 244 3ofSE1634-F 30 CATTATAACTTCACTCCTTTCGAATTA AGG(SEQIDNO:132) 245 3ofSE1634-GA-R 58 CGATCCGGGTAGGATCCGCTAAGGGTT ATATTTACTCGTATAGTTTAGTCAG (SEQIDNO:133) 146 5outSEagr-F 25 CAGAAATGTGGAATAACGGTTATGC(SEQ IDNO:134) 147 3outSEagr 22 GCTTCGACTGAATCTGGTCAAG(SEQID NO:135)
[0137] One microliter of each PCR reaction was combined and assembled using NEBuilder? HiFi DNA Assembly Master Mix (NEB). A portion of the assembly reaction was transformed into competent Escherichia coli NEB 5-? cells. The plasmids from transformants were analyzed by agarose gel electrophoresis and by DNA sequencing using the PCR primers. Sequence-verified plasmids were transformed in an E. coli dcm? strain to obtain unmethylated plasmid DNA. Plasmid DNA from the dcm? strain was also sequence-verified and transformed by electroporation into S. epidermidis SE.sub.??? cells. Plasmid was also isolated and the sequence-verified from strain SE.sub.???.
[0138] Plasmid pJB38-SE1634-KO-PyxiE-d6-KI was integrated into the chromosome of SE.sub.??? by growing cells at the non-permissive temperature for plasmid replication, 44? C. Four colonies of SE.sub.??? containing pJB38-SE1634-KO-P.sub.yxiE-d6-KI were streaked on tryptic soy agar (TSA) containing 100 ?g/mL D-alanine (to supplement auxotrophy) and 10 ?g/mL chloramphenicol (to select for the plasmid) and incubated at 44? C. for 24-36 hours. Resulting colonies were analyzed by PCR with primers anchored in 5 and 3 flanking regions outside of integration and plasmid-specific primers. To obtain a second recombination event, confirmed integrant colonies were incubated in tryptic soy broth (TSB) with 100 ?g/mL D-alanine, and no chloramphenicol, at the permissive temperature for plasmid replication, 30? C. After one or two passages in TSB+D-ala/no chloramphenicol, cells were plated on TSA+D-ala for single colonies. Colonies were assayed for plasmid loss by patching on TSA+/?chloramphenicol. Choramphenicol-sensitive (Cam-S) colonies were analyzed by PCR with primer pairs located outside and inside of allelic exchange region. Eight colonies were identified that were both Cam-S and PCR-positive.
[0139] The chromosomal cassette in all eight strains was PCR-amplified and sequence-verified. All eight strains were also confirmed for D-ala auxotrophy by their inability to grow without D-ala supplementation in growth media. The chromosomal constructs were stored and designated as: SE350, SE351, SE352, SE353, SE354, SE355, SE356, and SE357.
[0140] Each strain was confirmed to contain a single copy of the [-P.sub.yxiE-RBSsod-SPyfhK-pro9-LEKTI-d6-] cassette inserted into the delta-toxin gene encoded by S. epidermidis gene SE1634, located downstream of the P3 promoter immediately outside of the agrACDB operon, encoding quorum sensing regulatory proteins (
[0141] In both chromosomal and plasmid constructs, hLEKTI-d6 is constitutively expressed and protein is secreted to the culture medium. However, several key features distinguish the chromosomal construct strain from the plasmid construct strain: 1) The chromosomal construct is single copy, whereas the plasmid construct is expected to be multicopy. This may impact the overall level of expression of the hLEKTI-d6 gene; 2) The chromosomal construct strain has a deletion of the delta-toxin gene due to insertion of the hLEKTI-d6 expression cassette; 3) The chromosomal construct strain retains the auxotrophy of SE.sub.??? (dependence on D-alanine supplementation) since, unlike in strain 27a, the auxotrophy is not complemented by the plasmidic alrA gene; and 4) The chromosomal construct may have an enhanced intrinsic stability of the expression cassette due to its integration into the chromosome versus being carried on an extrachromosomal genetic element (plasmid).
Example 2
[0142] The Chromosomal Construct Strains Require D-Alanine Supplementation and Constitutively Express Secreted hLEKTI-d6 at Higher Levels than Plasmid Construct Strain 27a.
[0143] The growth of the independently isolated 8 sequence-verified strains with the chromosomal hLEKTI-d6 expression cassette (SE350-SE357) was examined in TSB with and without D-alanine supplementation (100 ?g/mL). Cultures were grown for 22 hours at 30? C. with aeration. In the absence of D-alanine, no growth was observed for the chromosomal construct strains, however, saturated growth was observed in the presence of D-alanine (Table 7). As expected, the plasmid-containing strain, 27a, was able to grow in the absence of D-alanine due to complementation of auxotrophy by the alanine racemase gene present on plasmid pLEKTI-27a-d6.
TABLE-US-00007 TABLE 7 Growth of chromosomal construct strains with and without D-alanine supplementation. OD600 of overnight culture Strain +D-ala ?D-ala 27a ND 12.9 SE350 8.2 0 SE351 8.5 0 SE352 8.7 0 SE353 8.0 0 SE354 9.8 0 SE355 8.8 0 SE356 9.6 0 SE357 8.8 0 Growth in TSB; ND: not done; D-ala: 100 ?g/mL
[0144] Duplicate cultures of the chromosomal construct strains SE350-SE357, and the plasmid construct strain 27a, were grown in TSB+D-alanine (100 ?g/mL) for 22 hours at 30? C. with aeration, and culture supernatants were analyzed by western blot. Culture supernatants were sampled and run on a 12% SDS-PAGE gel. The electrophoresed proteins were transferred to a PVDF membrane by western blot, and hLEKTI-d6 was detected by the primary chicken IgY antibody (anti-LEKTI-d6 antibody #337) and a secondary goat anti-chicken IgY horseradish peroxidase (HRP) conjugate. The HRP reaction was detected by chemiluminescence. Results showed that the western blot bands for the chromosomal construct strains were generally heavier than the those for the plasmid construct strain 27a (
[0145] The levels of active hLEKTI-d6 related species in the S. epidermidis culture supernatants analyzed by western blot in
[0146] All samples contained measurable levels of active hLEKTI-d6 species, which ranged from 39-333 zmol/CFU. There was a high variation in the zmol/CFU hLEKTI-d6 levels between the biological replicates of the same strain. The strains expressing chromosomal hLEKTI-d6 displayed 2- to 5-fold higher levels of active hLEKTI-d6 species compared to the strain expressing LEKTI-d6 in an episomal plasmid. This result was consistent with the observation by western blot that the chromosomal construct strains expressed more hLEKTI-d6 protein, as detected with anti-LEKTI-d6 antibody #337.
[0147] The timing of hLEKTI-d6 expression was examined in growth curve experiments with plasmid construct strain 27a, and two chromosomal hLEKTI-d6 strains, SE352 and SE355. Cultures were grown in TSB at 30? C. with aeration and culture supernatants were sampled at the onset of stationary phase and at several time points during stationary phase. Results showed that while the optical density at 600 nm did not change between the 19 and 23.5 hr time points, hLEKTI-d6 production in plasmid and chromosomal construct strains was enhanced at the later time point, as visualized by western blot and quantified by KLK14 assay. Enhancement of hLEKTI-d6 production during stationary phase may in part be due to stimulation by nutrient depletion (phosphate depletion) of the P.sub.yxiE promoter driving expression of the hLEKTI-d6 gene in both plasmid and chromosomal construct strains (
TABLE-US-00008 TABLE8 ExemplarySequences Description Sequence PyxiE ACGATTACAGAATCAACTAT (SEQIDNO: CTGCGTGATCATTTAATTGA 120) AGCGCGCGAAGCCATTGCGG ACGGCGTTGAATTAATCGGA TACACATCATGGGGGCCAAT TGACCTTGTCAGCGCATCTA CTGCGGAAATGAAAAAGCGC TACGGCTTCATTTATGTAGA CCGGGACAATGAAGGAAATG GAACATTTAACCGCATCAAG AAAAAAAGCTTCAACTGGTA TCAGCAGGTTATCGCCACAA ACGGAGAGAGTCTCTGACAA TTTTTTGAAAACTCATGCGC TTCAATTGACAATAACGAAA TGCAGGCGGACAATAAAAGA GAAAGg RBSsod GGTACCTTAGGAGGATGATT (SEQIDNO: ATTT 121) yfhK ATGAAAAAGAAACAAGTAAT (SEQIDNO: GCTCGCTTTAACAGCTGCCG 122) CAGGACTGGGTTTGACAGCA CTTCATTCCGCTCCCGCAGC AAAAGCT Pro9 TTAGAAATTTCATCAACATG (SEQIDNO: TGATGCA 123) P.sub.yxiE-RBSsod- acgattacagaatcaactat SPyfhK-pro9- ctgcgtgatcatttaattga LEKTI-d6 agcgcgcgaagccattgcgg (SEQIDNO: acggcgttgaattaatcgga 124) tacacatcatgggggccaat tgaccttgtcagcgcatcta ctgcggaaatgaaaaagcgc tacggcttcatttatgtaga ccgggacaatgaaggaaatg gaacatttaaccgcatcaag aaaaaaagcttcaactggta tcagcaggttatcgccacaa acggagagagtctctgacaa ttttttgaaaactcatgcgc ttcaattgacaataacgaaa tgcaggcggacaataaaaga gaaaggtcgactaccttagg aggatgattatttatgaaaa agaaacaagtaatgctcgct ttaacagctgccgcaggact gggtttgacagcacttcatt ccgctcccgcagcaaaagct gccgaattcttagaaatttc atcaacatgtgatgcagaat ctggtaaagcaacgagttac gctgaattgtgctcagaata ccgtaagttagtcagaaacg gaaagttggcgtgtactcgt gagaacgaccctatccaggg accggacggcaaggtacatg gaaatacttgcagtatgtgc gaggtgtttttccaggcgga ggaagaagaaaagaagaaaa aggagggcaaaagtcgaaat taatgaataa
REFERENCES
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INCORPORATION BY REFERENCE
[0158] The entire disclosure of each of the patent documents, including patent application documents, scientific articles, governmental reports, websites, and other references referred to herein is incorporated by reference herein in its entirety for all purposes. In case of a conflict in terminology, the present specification controls. All sequence listings, or Seq. ID. Numbers, disclosed herein are incorporated herein in their entirety.
[0159] The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.
[0160] Although illustrative embodiments of the present invention have been described herein, it should be understood that the invention is not limited to those described, and that various other changes or modifications may be made by one skilled in the art without departing from the scope or spirit of the invention.