Difference between revisions of "Team:Oxford/Test/Project"

What?

The threat of antimicrobial resistance is a serious global public health concern. One of the ways bacteria protect themselves against antimicrobial drugs is by growing biofilms. The biological definition for a biofilm: “an assemblage of surface-associated microorganisms that secrete a mucilaginous protective coating in which they are encased.” Van Leeuwenhoek, using his simple microscopes, first observed microorganisms on tooth surfaces and can be credited with the discovery of microbial biofilms. These bacterial slimes are responsible for a whole host of medical, industrial and environmental problems that are very costly and technically challenging to remedy. Biofilms are involved in catheter and implant infections, dental plaque formation as well as infections in cystic fibrosis patients. Biofilm can be found in the urothelium, prostate stones, and implanted foreign bodies. In industry and infrastructure, biofilms are also the main culprit behind the fouling of various plants and pipelines for aquaculture, water treatment, and food production.

Our solution is focused on providing a treatment for urinary tract infections (UTIs). 90% of urinary infections are caused by uropathogenic E. coli (UPEC) and the biofilm that they form in the urinary tract. Resistance to one of the most widely used antibacterial drugs for the oral treatment of urinary infections caused by E. coli – fluoroquinolones – is now widespread and, with UTIs being the most commonly acquired infection at hospital, there is a huge need to find a solution for the treatment of UTIs and resistance to antimicrobial resistance.

See UTIs facts and figures for more information.

Both antimicrobial resistance and the other problems associated with biofilm formation are big issues in their own right but are especially problematic when they’re combined. The bacteria, already constantly evolving to afford themselves more innate resistance against antibiotics, produce biofilms as protective layers that shield them from the drugs even more comprehensively.

Why?

• UTIs are the most common nosocomial infection
• There is growing resistance to the antibiotics currently used to treat urinary infections
• Biofilms are major problem both in health and industry
• Antibiotics have a negative effect on the beneficial gut flora
• There is a current failure to prevent recurrent infections

How?

There is currently no commercial antibiotic that specifically targets bacterial biofilms, but researchers have identified a range of bacterially-derived biomolecules that degrade and destroy biofilms. Our solution aims to investigate how bacterial biofilm disrupting proteins and antimicrobial proteins can be exported from E. coli.

The proteins DispersinB, MicrocinS, DNase and Endolysin will be fused with secretion tags to target them to normal bacterial secretion pathways. By hijacking the natural processes by which E. coli secrete proteins, we can target our anti-biofilm agents out of E. coli and onto a biofilm infected surface. Additionally, our E. coli will lyse upon sensing the presence of a biofilm, releasing a pulse of proteins from the cytoplasm on detection of a high target cell density.

The beauty of the anti-biofilm agents we plan to use is that they have been shown not to induce resistance in the target bacteria, meaning that having them continually produced at a low level will not be nearly bad as with traditional antibiotics. Our system is applicable to a whole host of biofilm environments and with a simple design that can be used in multiple sectors, we hope to get a step further in providing a novel approach to treating microbial infections. In terms of product formulation and design, we hope to ultimately arrive at a functional proof-of-concept e.g. an enzyme-secreting infection-clearing catheter or a modular system that continuously and cheaply cleans out pipelines.

Preclinical stage

Like most iGEM teams with projects in the Health and Medicine track, we have spent the summer developing our project in the preclinical stage. This is the 'laboratory' stage, where the different components of the project are constructed, tested, and optimised, without the use of human volunteers. The first goal is to discover if the team's invention is feasible; past that point, the preclinical goal is to improve the invention to point the point at which its efficacy and safety of use is maximised.

Progression to clinical trials

Extensive preclinical (lab) data is needed to support the use of the treatment on humans in clinical trials. As described above, the researchers must do their best to minimise the level of risk associated with the treatment, whilst maximising its efficacy, through lab models.

Review bodies

Any group wishing to trial their treatment on volunteers in the UK must abide by the Medicines for Human Use (Clinical Trials) Regulations of 2004. To abide by these terms, researchers must be granted a clinical trial authorisation (CTA) by the Medicines and Healthcare Products Regulatory Agency (MHRA). For a CTA application to be granted, the treatment must be reviewed and certified by a number of different review bodies, where each body scrutinises a different aspect of the project. We will use our project as an example here.

Most medically-orientated projects require approval from a Research Ethics Committee (REC). The committee makes sure that the volunteers have been well briefed (by the researchers) with regards to the trial, including; the possible benefits and risks of the treatment, the goals of the treatment, and who they should contact if they have any further questions. There are several RECs, found across the UK, who deal with clinical trial authorisations. There are several borough-based RECs in London - the iGEM team would most likely apply to one of these bodies.

As our treatment involves the use of a novel device (our 'custom catheter'), we need to apply to the MHRA, for a Notice of No Objection, to review the safety of the device. If granted, the notice would allow the device to be used in volunteers.

Potentially, we may attempt to model the effect our bacterial proteins have on human cells. To get hold of human tissue, we would need a license from the Human Tissue Authority (HTA). This includes extraction of tissue from a cadaver and a live participant.

In addition to the above approvals, we would need an organisation, such as a hospital or research institute, to host our trials. There are several funding bodies to which we could apply; however, it would be ideal to have funding from the NHS, as this is where we would most probably intend to host our trials - this is called Management Permission. Ideally, we would like our trials to be hosted by the NHS! At the time of our Management Permission application, we would most likely apply to the NHS for funding as well.

Clinical trials

We would be very pleased if our project managed to get this far! However, there would still be a long way to go before our product could go on the market. The clinical trials are split into 3 phases, with each phase more rigorous than the last.

Phase I

Phase I trials, also known as 'first-in-human' trials, present the first time a treatment is tested on human volunteers; as a result, there is an unavoidable element of risk involved. A typical phase I trial might involve 10 or fewer healthy student volunteers. However, due to the nature of our treatment, the likely candidates for our phase I trials would be people who already require the use of a catheter, but potentially not those who have a urinary tract infection (UTI).

This phase is primarily a risk assessment, so we would be looking for any signs of immune response to the introduction of our bacteria and their secreted proteins; in particular DNase and Dispersin B. In addition, we may be looking to see what range of protein dosages the volunteers might be able to tolerate before they experience significant side effects or discomfort.

Phase II

If the volunteers from phase I show few side effects and the treatment is deemed safe enough, then the trials can proceed to phase II. These involve up to approximately 100 volunteers. This time, all these people selected should be ill, ie have a CAUTI, and the results of their treatment (reduction in the biofilm size) against the best current treatment; in our case this is antibiotic treatment.

Phase III

If the results of the phase II trials suggest that the new treatment could be better than the current treatment, then the trials can proceed to phase III. As this is the last stage, the organisation hosting the trial must be sure, on a statistical level, that the new treatment is significantly better than the currently-administered treatment, for it to pass. Phase III trials therefore involve a very large group of ill volunteers, sometimes greater than 1000 people.

Market licensing

If solUTIon passed phase III, then we could officially license our treatment, and release it onto the market! Wouldn't that be swell?

Phase IV (optional)

This is an additional phase which is sometimes implemented; however it is not always required! Phase IV 'trials' are slightly different to the previous three, as they monitor the treatment success on real patients, ie after a marketing license has been granted. As the treatment has already been licensed by this point, phase IV simply involves analysis of data from patients receiving the treatment to check its safety and efficacy.

Patenting

What is a patent?

A patent is a license, given to an inventor, which prevents any competitor from making, using or selling their invention in a certain territory for a specific time frame. The 'territory' of the patent may be a country, or even an entire continent, such as Europe. The patent 'time frame' is usually 20 years.

What is the point of a patent?

Patenting is essential to the healthy progression of scientific research; why would companies want to invest millions of dollars into an invention, only for it to be stolen by a competitor when completed? Therefore, patenting gives companies a chance to earn back the money they invest in their inventions. However, the patent holder may, during these 20 years, permit certain parties to make use of their product for a license fee.

What can you patent?

In synthetic biology, any organism (aside from a human) which has been genetically modified, and hence gives rise to "a new assembly of chemicals", can be patented. This includes novel bacterial strains, as well as transgenic plants and animals. Evidently, humans cannot be patented for ethical reasons.

However, there are additional factors that must be satisfied; for an invention to be applicable for patenting it must be both of the following:

1. Novel - the invention you present should not already be part of the 'state of the art' (basically anything published in a paper, presented at a conference, or anything freely accessible to the scientific community).
2. Inventive - ie the invention should not be 'obvious' to those skilled in the field. It is often difficult to define if an invention is 'obvious'; however, several 'obvious' inventions can arise from, for example, the correlation of two previously-unlinked scientific papers.

Can Oxford iGEM apply for a patent?

There are a number of aspects to our project which are unpatentable. For example, the BioBricks we have constructed cannot be patented; they have been submitted to The Registry of Standard Biological Parts ('The Registry' for short) as part of our open source agreement. The Registry is iGEM's alternative to patenting; it allows for easy, open distribution of the many hundreds of BioBricks that now exist. In addition, EU law states that methods of therapy, treatment and diagnosis cannot be patented, to avoid conflict with doctors.

However, the device used within the method may be patented. Our method of tackling CAUTIs rests heavily upon the design of our custom-catheter, which is both novel and inventive; we therefore intend to apply for a patent on this device.