The present invention relates to a genetically modified bacteria that produces a material with UV absorbing properties.
Environmental stressors on humans and the pressures caused by them are increasing in an ever-changing climate. Stressors such as ultraviolet radiation, heat, osmotic pressure, and desiccation can have several effects on the human body including causing skin cancers, oxidative damage and photoaging. Skin cancers are particularly of acute concern. Among skin cancers, melanoma is a cancer of melanocytes and is expected to affect almost 100,000 people in the year 2019. An aggressive malignancy that tends to metastasize, melanoma is responsible for a majority of skin cancer related deaths in spite of representing 5% of cutaneous malignancies. Therefore, more efficient and effective strategies to minimize UV related damage to skin is required that affords passive protection.
The sun protection and sunless tanners market is a $1.4 billion industry with 3 out of 4 adults using sunscreen, tanning products or sunless tanners. However, the effectiveness of synthetic sunscreens depends on applying generous amounts, inadequate coverage, more frequent applications as much as reapplying every one to two hours, ensuring proper storage since their potency can be destroyed if stored at higher than normal temperature conditions, and other factors that are difficult to control. In addition, consumers are getting increasingly conscious about the safety of sunscreen ingredients as well as the impact of these ingredients on the environment. Recent research has revealed that some synthetic sunscreen components can accumulate in aquatic environments and potentially cause harm by acting as hormone disruptors.
As per the FDA, only two sunscreens (zinc oxide and titanium dioxide) have sufficient safety data. In fact, the FDA in February 2019 said that there is insufficient data on 12 of the 16 approved sunscreen molecules to include them in the “generally recognized as safe and effective” (GRASE) category. Additionally, the FDA has also recommended against the use of aminobenzoic acid (PABA) and trolamine salicylate and have placed them in the non-GRASE category. Only zinc oxide and titanium dioxide were able to get a GRASE designation with FDA suggesting insufficient data for other molecules to make a GRASE determination. The FDA also cited the high systemic availability (including significant concentrations in urine, blood plasma, amniotic fluid, and breast milk) along with insufficient absorption and carcinogenicity data of oxybenzone as a concern against a positive GRASE designation. The FDA is also concerned about potential hormonal disruption with the present set of sunscreen molecules, particularly associated with long-term use.
Certain sunscreen molecules such as oxybenzone, octinoxate, etc. have been found to be toxic to coral reefs, sea urchins, and other marine organisms. As per the National Ocean Service, even GRASE sunscreens such as nano-titanium and zinc oxides can harm marine life. Popular beach destinations such as Palau and Hawaii have already imposed bans on several reef-toxic sunscreens. Therefore, a need still exists for a new method of protecting the skin from UV that is environmentally friendly.
The present invention addresses this need by providing a probiotic technology involving engineered commensal bacteria which, when applied to the skin surface, act as living biofactories of sunscreen molecules. These engineered bacteria produce mycosporine-like amino acids (MAAs) which are natural photoprotective molecules produced by marine cyanobacteria. The MAAs produced by commensal skin bacteria multiply on the skin surface and provide sun protection in a sustained manner. Therefore, the problem is solved in an eco-friendly manner since MAAs are sourced from marine life itself.
In one embodiment, the present invention involves a genetically modified strain of commensal bacteria Staphylococcus epidermidis which produces a material with UV absorbing properties. In another embodiment, the material with UV absorbing properties is a mycosporine-like amino acid. In one embodiment, the mycosporine-like amino acid is shinorine. In another embodiment, the bacteria includes the nucleotide sequences shown in SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, and SEQ ID NO:9. In one embodiment, bacteria includes the nucleotide sequence shown in SEQ ID NO:5. In another embodiment, the invention is a topical composition where the bacteria is present in the composition at a concentration of at least 0.1% by weight of the total composition. In one embodiment, the present invention involves a composition including the genetically modified strain of commensal bacteria and a sunscreen.
Another embodiment of the present invention involves a genetically modified strain of bacteria Escherichia coli Nissle 1917 which produces a material with UV absorbing properties. In one embodiment, the material with UV absorbing properties is a mycosporine-like amino acid. In another embodiment, the mycosporine-like amino acid is shinorine. In one embodiment, the bacteria includes the nucleotide sequences shown in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:4.
One embodiment of the present invention involves a genetically modified strain of commensal bacteria which produces a material with UV absorbing properties, where the bacteria includes a lysis circuit. In another embodiment, the bacteria undergoes lysis in the presence of increased bacterial density and the absence of UV light.
The foregoing summary, as well as the following detailed description of preferred embodiments of the application, will be better understood when read in conjunction with the appended drawings.
The details of one or more embodiments of the disclosed subject matter are set forth in this document. Modifications to embodiments described in this document, and other embodiments, will be evident to those of ordinary skill in the art after a study of the information provided herein.
The present disclosure may be understood more readily by reference to the following detailed description of the embodiments taken in connection with the accompanying drawing figures, which form a part of this disclosure. It is to be understood that this application is not limited to the specific devices, methods, conditions or parameters described and/or shown herein, and that the terminology used herein is for the purpose of describing particular embodiments by way of example only and is not intended to be limiting. Also, in some embodiments, as used in the specification and including the appended claims, the singular forms “a,” “an,” and “the” include the plural, and reference to a particular numerical value includes at least that particular value, unless the context clearly dictates otherwise. Ranges may be expressed herein as from “about” or “approximately” one particular value and/or to “about” or “approximately” another particular value. When such a range is expressed, another embodiment includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another embodiment.
The term “commensal bacteria” as used herein means a bacteria that lives on or in another organism without causing harm.
While the following terms are believed to be well understood by one of ordinary skill in the art, definitions are set forth to facilitate explanation of the disclosed subject matter. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the disclosed subject matter belongs.
It should be understood that every maximum numerical limitation given throughout this specification includes every lower numerical limitation, as if such lower numerical limitations were expressly written herein. Every minimum numerical limitation given throughout this specification will include every higher numerical limitation, as if such higher numerical limitations were expressly written herein. Every numerical range given throughout this specification will include every narrower numerical range that falls within such broader numerical range, as if such narrower numerical ranges were all expressly written herein.
Application of sunscreens is crucial to mitigate the risk of skin cancers caused as a result of UV radiation-mediated DNA damage. Studies have shown that a majority of the population does not apply sunscreens correctly and in enough quantity to offer the necessary protection. Therefore, most marketed sunscreens end up offering only about 40% of the promised sun protection factor (SPF) due to improper application. These factors leave users more exposed to solar radiation, significantly limiting the sun shielding offered by these products. Additionally, conventional sunscreens presently available in the market are in the form of lotions, creams, or aerosol sprays that need to be frequently reapplied (usually every two to three hours) which further reduces their compliance and increases risks. The present invention introduces a probiotic sunscreen platform which will form an invisible layer of sun protection on the skin surface.
The human skin is the largest organ in the human body and acts as the interface between the insides of the body and the external environment. The exposed part of the skin is composed of entirely dead elements, including epidermis and hair. Incidentally, the only living element on the surface of the skin is the microbiome. The microbiome has an inherent ability to replenish itself, with some bacteria having doubling times as short as 20 minutes. Recent advancements in genetic engineering and synthetic biology have transformed the field and it's now possible to introduce a diverse array of genetically encoded proteins, drugs, enzymes etc into bacteria as plug-and-play systems. The skin microbiome is a vast and underexplored component of the healthy human body and its importance is gradually being appreciated by researchers and dermatologists worldwide.
By genetically engineering bacteria found in healthy human skin, the present invention presents an unprecedented probiotic sunscreen technology that has not been available before. In addition to being novel, the developed technology is the first of its kind to offer sunscreen protection commensurate with the exposure to dermal exposure to sunlight. The developed platform has the potential to be used for numerous parallel dermatological applications.
Mycosporine-like amino acids (MAAs) are natural ultraviolet radiation absorbing metabolites produced by marine microorganisms such as cyanobacteria and other algae. One of the most popular MAAs is Shinorine, which has been used as a constituent of sunscreen formulations in the European Union such as “Helionori” and “Helioguard 365.” MAAs are photoprotective and are commonly referred to as “microbial sunscreen.” They have potent Ultraviolet-A (UV-A) and UV-B absorbing properties along with anti-oxidant characteristics. Additionally, certain MAAs such as mycosporine-glycine and mycosporine-taurine possess significant singlet oxygen scavenging property. They also perform other protective functions in their parent organisms such as protecting against oxidative stress, desiccation, and osmotic stress. UV irradiation promotes the production of MAAs in cyanobacteria. MAAs such as shinorine have also been found to protect against abiotic stress factors such as salinity, dessication, and heat. However, the yield of shinorine, which comes from red algae gathered from the sea, can vary seasonally and geographically, limiting supply.
S. epidermidis
The present invention involves the creation of genetically engineered bacteria, commonly found on the human skin, for production of these molecules. The human skin is home to several species of commensal or non-pathogenic bacteria and among them is Staphylococcus epidermidis. Interestingly, S. epidermidis possesses genes and precursors involved in the biosynthesis of shinorine, and therefore can be a suitable host for production of shinorine through genetic engineering. These genetically engineered strains of S. epidermidis can be applied on the skin surface to provide both short term as well as long term protection as these bacteria would as living factories on the skin surface constantly generating shinorine on-demand.
The present invention hijacks the gene cluster from cyanobacteria and engineers S. epidermidis to synthesize MAAs in a regulated manner (
While S. epidermidis was evaluated as the bacterial template for the “living factory” design, other skin commensal microbiota that might also be effective were screened and identified. For example, commensal bacteria belonging to families, such as Acinetobacter (Moraxellaceae) spp., Bacteroidetes and Proteobacteria spp. are also found abundantly and on specific areas of the skin, thus affording the ability to customize this technology to adapt to heterogeneous body and skin constitutions.
There are several optogenetic response elements (ranging from UV-B to far red) to activate the promoters associated with Shinorine. Bacterial promoters such as recA, lexA, etc. which are part of the robust bacterial SOS response upregulate gene transcription upon detection of DNA damage (e.g., by UV light). Understanding these response elements allows us to respond to UV-B or visible light, given that sunlight is composed of both, to activate and regulate production of Shinorine in a time and intensity sensitive fashion.
To regulate the bacterial population and potentially release Shinorine extracellularly in significant quantities, in some embodiments, the bacteria is programmed with a lysis circuit to undergo quorum sensing based lysis when high concentrations are reached due to increased bacterial density as well as in the absence of UV light (
Other useful MAAs, such as Gadusol and Palythine also extracted from cyanobacteria, can be incorporated in the bacteria to assess if there is an additive or synergistic UV protective effect along with Shinorine.
Engineering S. epidermidis to Synthesize Sunscreen Molecules
The genes responsible for the synthesis of MAA have been identified in cyanobacteria. The present invention introduces a codon-optimized version of these genes in cis in the nonessential attB locus to confer symbiotic S. epidermidis the ability to produce sufficient quantities of MAAs. Successful chromosomal integration of the genes of interest and biosynthesis of MAAs can be confirmed using the pMAD system, HPLC and LC/MS.
In one embodiment, a method for in vitro safety and efficacy studies is disclosed. A 3D skin model using primary keratinocytes obtained from human foreskin is inoculated with the engineered bacteria and exposed to UV light. The treatment samples are: (i) control S. epidermidis, (ii) recombinant S. epidermidis containing Shinorine gene cluster, (iii) MAAs isolated from engineered S. epidermidis, (iv) MAA extract obtained from marine sources (Helioguard 365), (v) marketed sunscreen molecule viz. octocrylene. The skin samples are exposed to UV radiation at various doses viz. 7, 14, 21, or 35 mJ cm′. Different UV lamps emitting different wavelengths in the UV-A and UV-B regions are used. Protection from UV light is evaluated by measuring apoptosis, skin proliferation, and selected gene expression. Toxicity is evaluated by checking for key inflammatory mediators and DNA damage.
Regulated Release of Sunscreen Molecules from Engineered S. epidermidis Using a UV-Sensitive Promoter to Allow Photoresponsive Modulation
Bacterial promoters such as recA, lexA, etc., which are part of the robust bacterial SOS response, upregulate gene transcription upon detection of DNA damage (e.g., by UV light). Introducing a relevant UV-sensitive promoter into S. epidermidis allows release of sunscreen molecules commensurate with the intensity of exposure of UV radiation. In one embodiment of the present invention, another stable plasmid (in trans) is introduced in the engineered bacteria consisting of an optimized UV-sensitive promoter and a darkness-inducible host cell lysis sequence derived from the bacteriophage phi X174 that is activated in the absence of UV light. With this system, bacterial lysis can be observed in the dark, yet viability preserved in the presence of UV light and release of sunscreen compounds commensurate with UV exposure. Using HPLC & LC/MS, the amount of MAAs produced can be correlated with the amount of inoculum required and extent of UV exposure. Once both the plasmids responsible for the (i) synthesis of the sunscreen molecule, recA-MAA, and (ii) for the UV radiation-mediated lysis, recA-ϕXI74E, are inserted into the bacteria, the aforementioned safety and efficacy studies may be performed again to establish the safety and efficacy of the final construct.
Referring the
Table 1 shows a list of optogenetic tools for controlling protein-protein interactions and protein oligomerization.
Table 2 lists a general review of optogenetics tools, from the perspective of mammalian cells. The tools that are microbially sourced are particularly useful for the present invention.
The present invention also encompasses other skin commensal microbiota. Table 3 shows the top 10 abundant bacteria per Byrd et al. Apart from this, other families such as Acinetobacter spp., Bacteroidetes and Proteobacteria can be used.
Propionibacterium acnes
Corynebacterium
Propionibacterium acnes
Corynebacterium
tuberculostearicum
tuberculostearicum
Corynebacterium
Staphylococcus hominis
Staphylococcus epidermidis
Staphylococcus hominis
tuberculostearicum
Streptococcus mitis
Propionibacterium acnes
Corynebacterium
Staphylococcus warneri
tuberculostearicum
Streptococcus oralis
Staphylococcus epidermidis
Staphylococcus capitis
Staphylococcus epidermidis
Streptococcus pseudopneumoniae
Staphylococcus capitis
Corynebacterium simulans
Staphylococcus capitis
Streptococcus sanguinis
Corynebacterium fastidiosum
Streptococcus mitis
Staphylococcus haemolyticus
Micrococcus luteus
Corynebacterium afermentans
Staphylococcus hominis
Micrococcus luteus
Staphylococcus epidermidis
Micrococcus luteus
Corynebacterium aurimucosum
Corynebacterium afermentans
Staphylococcus capitis
Enterobacter aerosaccus
Corynebacterium kroppenstedtii
Corynebacterium simulans
Veillonella parvula
Corynebacterium simulans
Corynebacterium amycolatum
Corynebacterium resistens
To facilitate secretion/excretion of the MAA to the external environment, bacteria's natural secretion system is modified to bind and secrete the MAAs that are generated within. This enables the MAA to provide sufficient protection against UV radiation and other photoaging processes. Table 4 highlights the various gram-positive and gram-negative related secretion systems. The table lists genes and transporters related to amino acid production in Corynebacterium glutamicum and Escherichia coli: uptake and excretion systems.
Corynebacterium glutamicum
Escherichia coli
The present invention is a unique sunscreen technology which not only significantly improves consumer compliance by eliminating the need of frequent reapplications for effective protection, but also circumvents detrimental impact on human health and the environment. Since the strategy of this invention is to deliver the source of the natural sunscreens, the engineered bacteria, as “living skin-protective factories”, it will significantly reduce the cost of the production, unlike current sunscreens that require production, purification and scale-up under good manufacturing practice (GMP) at a pharmaceutical and industrial scale. This platform has the potential to be customizable to different skin and body types—normal, dry, oily—as bacteria other than S. epidermidis, such as those belonging to the Bacteroidetes and Proteobacteria families can be used as templates with unique combinations of promoters and regulatory elements to regulate production, release and activity of synthesized molecules.
In one embodiment, the present invention is a probiotic sunscreen technology that enables continuous and extended release of UV filtering molecules on the skin surface with photo/dark-responsive promoters providing modulated release of these natural sunscreens based on the intensity of UV exposure to mitigate environmental stress.
In another embodiment, the present invention is incorporated in a topical composition (it is applied topically to the skin). In one embodiment, the modified bacteria is present in the topical composition at a concentration of at least 0.1% by weight of the total composition. The topical composition may be in the form of a cream, lotion, emulsion, gel, ointment, liquid or aerosol spray. In another embodiment, the bacteria of the present invention is used in a composition with a traditional sunscreen.
The examples (presented below) show the successful engineering of bacteria containing the genes responsible for MAA production. Transformed colonies submitted for Sanger sequencing gave a positive confirmation for MAA genes. NanoLC-MS/MS data indicated presence of enzymes responsible for production of MAAs. There are four enzymes required to synthesize shinorine and LC-MS/MS chromatogram confirmed their presence (see
Efficacy studies indicated that shinorine was significantly effective in preventing and/or reducing UV-induced DNA damage compared to untreated group three days post exposure. Furthermore, it was also significantly more effective than a 10% zinc oxide which is a gold standard for sun protection (see
Several studies were conducted on MAAs and the underlying genes in cyanobacteria responsible for their production. Codon-optimized double stranded DNA fragments were amplified using polymerase chain reaction (PCR) and purified using gel electrophoresis. The dsDNA fragments were designed in such a way as to allow blunt end ligation in the pCN48 plasmid using the Smal site. A restriction digest using Smal enzyme was performed to linearize the plasmid, followed by dephosphorylation using calf intestinal phosphatase (CIP) to prevent the plasmid to close onto itself.
The gene of interest is ligated into the plasmid using T4 DNA ligase. Post ligation, chemically competent DH5a cells are transformed and selected using ampicillin. The plasmids from several transformed colonies are isolated and sent for Sanger Sequencing to check and corroborate successful addition of the gene of interest into the plasmid. Bacterial colonies containing the correct plasmid are isolated and the above process is performed again until all four genes of interest are successfully incorporated. The complete plasmid is initially incorporated into E. coli Nissle 1917 (EcN) before being transferred to S. epidermidis.
1% of overnight cultures were inoculated into 100 ml of fresh LB broth supplemented with the appropriate antibiotic and similarly grown at 37° C. and 200 rpm until OD600 reaches 0.9-1.0 (approx. 3.00-6.00 hr.). Cultures were spun at 4° C. for 15 min, 3500×g, and cells were resuspended in 5-10 volumes of the Bacterial cell lysis buffer (Gold Bio), supplemented with DTT and EDTA (5 mM), and Lysozyme (40 mg/ml), DNase (800 U/ml) and RNase (24 U/ml). Following vortexing, and 5 min incubation on ice, suspensions were incubated at 37° C. for 60 min and lysates were centrifuged at 20,000×g, 4° C. for 30 min, and the clear lysate was collected and quantified using BCA assay (Thermo Scientific).
Protein samples were dried in a speed vac and resuspended in TEAB buffer according to standard in-solution digestion protocol. Samples were reduced with TCEP (tris-(2-carboxyethyl) phosphine) and alkylated with MMTS (methyl-methane-thiosulfonate). Samples were digested overnight at 37° C. and reactions were stopped by adding 10% formic acid. These samples were dried and resuspended in 0.1% formic acid. 5 (˜1 μg) of each sample was analyzed by NanoLC-MS/MS (Orbitrap Eclipse) and was searched against a combined database consisting of the E. coli Nissle 1917 database accessed from the Biocyc.org website and a database containing the MAA sequences using Proteome discoverer ver 2.4 and the Sequest HT search algorithm using standard LFQ workflow (Thermo scientific).
MAAs extracted from the engineered bacteria of the present invention were evaluated. Human skin was obtained from discarded tissue from elective procedures. The skin tissue was cleaned, trimmed, sterilized and plated in an organ culture medium overnight at 33° C. MAA extract or appropriate controls were applied on skin tissues, after which they were exposed to 135 mJ/cm2 UV-A and UV-B light. The application of live bacteria on human skin tissue was subsequently tested. Different treatments viz. overnight culture of wild type EcN, 10% zinc oxide solution, or overnight culture of EcN expressing shinorine were applied on human skin explants. Treatments were allowed to equilibrate with skin tissue for 1 hour, after which tissues were exposed to UV radiation. The tissues were then incubated for different durations and subsequently fixed. Cleaved caspase-3 immunohistochemical staining was performed to check for DNA damage. Slides were imaged using Leica Slide Scanner and representative images were captured. The captured images were quantified using ImageJ with a modified, previously published protocol (Crowe and Yue, 2019).
All documents cited are incorporated herein by reference; the citation of any document is not to be construed as an admission that it is prior art with respect to the present invention.
It is to be further understood that where descriptions of various embodiments use the term “comprising,” and/or “including” those skilled in the art would understand that in some specific instances, an embodiment can be alternatively described using language “consisting essentially of” or “consisting of”
While particular embodiments of the present invention have been illustrated and described, it would be obvious to one skilled in the art that various other changes and modifications can be made without departing from the spirit and scope of the invention. It is therefore intended to cover in the appended claims all such changes and modifications that are within the scope of this invention.
This application claims priority to U.S. Provisional Application Ser. No. 63/150,137, filed Feb. 17, 2021, which application is hereby incorporated by reference in its entirety.
Number | Date | Country | |
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63150137 | Feb 2021 | US |