Team:Oxford/Applied Design
Product Design
Overview
Product design has been at the front of our project since we came up with our initial ideas. We wanted to spend our summer creating a solution to a real world problem that affects a large proportion of the world’s population. In creating a realistic therapeutic product we have looked into current treatments, safety, manufacture, accessibility and the possibilities for the project after iGEM, throughout each stage we have had the patient at the forefront of our minds. After a range of ideas, we have settled on a final design for a new therapeutic to treat IBD.
Patients
Patient Interviews
We structured the patient interviews in a way that enabled an analysis of how IBD affects specific aspects of the daily lives of patients and how current medications inadequately address these factors. These conversations allowed us to understand the reality of living with IBD and the key points the novel treatment should address to help patients in the most significant way. It was clear that there is “no normal day” in terms of Crohn’s symptoms, with most patients spending variable amounts of time in a sub-optimal state of health (with symptoms largely controlled by medication). This is interspersed with flare ups - times when the disease takes complete control of an individual’s life due to severe pain, excessive inflammation and urgent bowel movements. Flare ups often require a patient to take time off work, stop travel and social interaction, and may often require hospital administration. Tables 1 and 2 summarise how IBD impacts the quality of life of the patients we interviewed during both flare ups and times when the disease is controlled.
| Problem/Consequence of Crohn's Disease | Impact on life |
|---|---|
| Administer drugs each morning | Must remember to take medication every morning, at roughly the same time. Makes spontaneous trips away a difficulty |
| Irregular bowel habits mean regular stops to use the toilet on the way to/during work | Travel to work can be difficult, especially with travel delays. It can be embarrassing to frequently leave the work desk |
| Avoiding specific foods makes meals difficult | Difficult to be spontaneous. Meals at parties and restaurants can be difficult |
| Exercise can be difficult | Fitness is at a lower level than hoped for. Common to feel drained after small amounts of moderate exercise |
| Exhaustion at the end of the day | Inability to take part in social activities after work, making it difficult to maintain friendships |
| Disturbed sleep due to irregular bowel movements or bloating | Continuous low energy level and effect on mood |
Impacts of Crohn’s disease on daily life during flare-ups of the inflammation:
| Problem/Consequence of Crohn's Disease | Impact on life |
|---|---|
| Wake up feeling drowsy and unrested due to a lack of sleep | Unable to do simple daily tasks. Sometimes unable to get out of bed |
| Cannot go to work/social events due to pain/irregular bowel movements | The financial cost of long periods of absence from work and lack of career progression. Difficulty maintaining friendships |
| Need to visit doctors and hospital specialists, may need to stay in hospital or have surgery | Difficulty travelling to appointments, especially with severe flare-ups. Pain and psychological effects of medical treatment have a huge effect on mood and life satisfaction. Low self confidence and anxiety due to scars from surgery |
| Feeling depressed due to the chronic pain, lack of sleep and inability to go to work/socialise | Regularly experience bouts of depression correlated with flare-ups |
| Inability to eat and properly digest food during flare ups | Constant exhaustion and lack of pleasure from food. Often requires hospitalisation or tube feeding. Tube feeding is associated with its own problems, such as social anxiety and difficulties doing so in public |
Most patients shared the opinion that life was manageable with current medication until flare ups occur, when “Crohn’s dominates your life and functioning normally is impossible”. It became apparent that reducing the frequency and severity of flare ups was a required quality of a novel treatment for Crohn’s disease. Moreover, patients complained of the unpredictability of flare ups, making planning events, like holidays, work and social events, difficult since “you’re never sure if a flare up will hit”. In light of this feedback, we focused on designing a treatment that, through residing within the microbiome and responding to increased concentrations of NO (an inflammatory biomarker) should act to suppress the inflammatory response before the inflammation resulting in flare ups can occur.
Although the analysis of the daily impact of Crohn’s disease was useful for understanding how the disease and current medication affects daily life, it was also evident that there are more long term effects that result from IBD. Indeed, many patients discussed how the use of immunosuppressants resulted in an increased susceptibility to infection and resulted in the need to take even more time off work. Others mentioned that the long-term burden of taking daily medication; although normally manageable on a day-to-day basis, there are times when “everything required to just stay alive and healthy becomes overwhelming”. We used Speedboat Analysis in order to understand this longer-term effect of Crohn’s disease and the current treatment options. Speedboat Analysis is a method used to establish the major barriers affecting an individual’s quality of life.
In our analysis, patients were presented with an image of a speedboat representing a journey towards achieving an optimal quality of life, and were asked to draw anchors to represent factors stopping the boat from moving forward. The position of the anchors represented how much the individual factors impaired quality of life; those deeper in the ocean impaired quality of life to a greater extent than those closer to the surface of the water. This type of analysis proved to be a powerful method of determining the most important factors infringing on an individual’s quality of life. This analysis allowed for an appreciation of the uniqueness of patient profiles and demonstrated that the most significant impact of the disease was dependent on the individual. For example, some patients felt that the most significant impact of the disease was not being able to engage in sport due to constant discomfort and bloating, whilst others described the inability to pursue their career goals due to long-term sickness leave as the factor affecting their quality of life to the greatest extent.
Our findings reflect the data from other assessments of the problems faced by individuals with Crohn’s disease; surveys from the Korean Association for the Study of Intestinal Diseases revealed that 70% of patients with Crohn’s disease reported feelings of stress due to missed work due to Crohn’s disease. Moreover, 62% of the patients surveyed believed that Crohn’s disease interfered with the maintenance and formation of friendships, reflecting our findings that the complications of Crohn’s disease can infringe on everyday social activities.1
Additional feedback from patients indicated that many patients hoped to not have to change their type of medication and method of administration frequently, stating that they would rather continue with their current treatments, even if not completely perfect, to avoid having to change daily routines and risk additional side effects. This demonstrated that our product must have a unique and significant benefit in comparison to current treatments in order for patients to take up the solution. This is an important factor to consider in the design of our therapeutic, and we believe that the NO-dependent secretion of an optimised dose of IL-10, instead of a prolonged delivery of a suboptimal dosage of immunosuppressants, is a unique feature compared to current medication methods. The patients interviewed also showed support of this design feature, praising the “controlled and personalised dosage of the anti-inflammatory molecule”.
Safety
Safety of the product was the main concern raised in the survey. The majority of people are not highly knowledgeable about synthetic biology so we believe it is especially important to make safety a priority due to the apprehension towards the topic. We aimed to promote the safety of GE probiotics and make it clear that the patient's genome will be unaffected.
Concern on what we would engineer lead to a greater investigation into species and strains of bacteria we would engineer with a focus on the safety. We also were directed into investigating how our product would alter the natural balance of the microbiome and how we can reduce any possible negative interactions. This is also why we began our initial research into how to test the safety of the product, we realise this is an important issue and aimed to create a plan to ensure the efficacy and safety to the patient and environment. To learn more about how we propose to ensure biosafety in our product you can read about our safety proposal on the safety section here.
Dr Tony Cutler
Dr Tony Cutler is a researcher in novel immune system treatments at the Wellcome Trust Centre for Human Genetics. As well as discussing our design and its impact on the immune system, through his knowledge of probiotic treatments for diabetes he was able to advise us on making a successful probiotic.
He emphasised the requirement of safety in our design. The wariness towards synthetic biology means we have to do everything possible to give the patient confidence in using a new form of treatment. It is also necessary to ensure the treatment would be better than anything else available as patients would rather take a standard effective treatment than a gene therapy. Our meeting with Tony led to contact with immunologists specialising in gut disorders, such as Professor David Greaves and Professor Chris O'Callaghan, to learn more about the impact our product would have on the immune system. You can read more about our work with them on the human practices page here.
Kill Switch
As you can read about on our safety page and parts page, we have designed, synthesised and characterised a kill switch to implement into our device. Tetracycline and it's derivatives can be taken to stimulate artolysin production in the probiotic resulting in killing the bacteria and ending the treatment.
Which Autoimmune Diseases?
We sent out a survey for patients with autoimmune diseases in order get a better idea of what patients would like from a treatment. We received 48 responses from members of the public suffering from autoimmune diseases of ages from 18 up to 70. The responses gave us a greater understanding of the current treatments, the problems with them and what patients would like from a treatment. We were astounded by the positivity towards GE and for our project. There is a great deal of belief from the public in the potential of GE in medicine.
They survey told us the public wanted a treatment that treats “a condition at its source rather than masking symptoms.” that was also “less invasive and less dangerous”. They also showed support of a device that was able to provide personalised doses according to the patient. This led to the initial design of our treatment.
We realised that our initial idea of a general treatment was over ambitious. Many of the responses said that they would feel more comfortable if the treatment was designed with a greater focus on select conditions.
We have specifically designed our treatment with Crohn’s disease and Ulcerative Colitis in mind, however, we also found how closely related other autoimmune diseases are and decided to look into which conditions we have the potential of treating if we were to develop our treatment further. Our treatment has a huge range of applications. For our initial market, we would focus on IBD but the range of diseases affected by the intestinal immune system allows our product to be modified for trials on other relevant autoimmune conditions.
Autoimmune enteropathy, Coeliac disease, Rheumatoid Arthritis, Multiple sclerosis, Psoriasis and Type 1 diabetes have all been shown to be linked to the balance between intestinal Th17 and Treg populations (or IL10 concentration) in the gut. For Coeliac disease, we may also need to combine our system with a mechanism to digest or modify gluten. Other conditions, such as Microscopic colitis, Lupus and Hashimoto’s thyroiditis, also relate to at least one of these populations but more research will be needed to find how they are connected to the gut. As well as this, specific probiotics have been shown to be beneficial in a range of these conditions. Our device may act as an appropriate treatment with some minor modifications for these conditions. An imbalance in the immune cells in the gut has been shown to cause an autoimmune condition in the kidneys due to the migration of Th17 cells showing the importance of bacterial population control in the gut.
Types of epilepsy have also been found to relate autoimmunity in the gut. The gut-brain axis may connect autoimmunity in the gut to nervous system diseases and promote Th17 cells in the CNS, similar to what has been found with multiple sclerosis. 80% of cases of epilepsy are in the developing world, this is thought to be due to the influence of bacteria, such as segmented filamentous bacteria (SFB), from water sources influencing the gut microbiome and immune cells. The recent and sharp increase in cases shows the necessity of a simple and effective treatment. If the condition is confirmed to be linked to autoimmunity in the gut then our product can offer an easily administered treatment that stops the disease at its source.
We summarised this data in a table illustrating which autoimmune diseases have been found to be linked to immune cell balance in the gut. References can be found at the bottom of the page.
| Condition | Linked to the microbiome | Linked to increased intestinal Th17 | Linked to decreased intestinal IL10 | Reference |
|---|---|---|---|---|
| Crohn's Disease | ✔ | ✔ | ✔ | A |
| Ulcerative Colitis | ✔ | ✔ | ✔ | A |
| Autoimmune Enteropathy | ✔ | ✔ | ✔ | B |
| Coeliac Disease | ✔ | ✔ | ✔ | C, D |
| Microscopic Colitis | ✔ | ✔ | E | |
| Rheumatoid Arthritis | ✔ | ✔ | ✔ | F, G |
| Psoriasis | ✔ | ✔ | ✔ | H, I |
| Multiple Sclerosis | ✔ | ✔ | ✔ | J, K |
| Lupus | ✔ | ✔ | L, M | |
| Graves' Disease | ✔ | ✔ | ✔ | N |
| Hashimoto's Thyroiditis | ✔ | ✔ | ✔ | N |
| Type 1 Diabetes | ✔ | ✔ | ✔ | O |
| Myasthenia Gravis | ✔ | ✔ | ✔ | N, P |
Current Treatments
To ensure the necessity of a novel treatment we looked into what is currently available and the efficacy and side effects of current therapies. We had already learnt a lot about treatments out of our survey for autoimmune patients. The survey told us that the majority of patients use a combination of treatments and highlighted the problems with their treatments.
We have created a table to summarise current treatments and their associated side effects:
| Treatment | Delivery | Action | Success | Side Effects |
|---|---|---|---|---|
| Aminosalicylates (5-ASAS) | Oral/suppository/enema | Reduces Inflammation | Works for 7/10 mild cases. Ineffective for severe IBD and maintaining remission | Rarely Serious |
| Immunosuppressants | Tablet | Reduces the activity of the immune system | Effective after 2-3 months | Vulnerable to infection, low red blood cell production |
| Corticosteroids | Oral/suppository/enema/IV | Reduces Inflammation | Short term: acne, weight gain, mood changes, insomnia.
| |
| Ciclosporin | Tablet/7 day infusion | Strong immunosuppressant | Short term: tremor, hair growth, swollen gum, feeling/being sick, diarrhoea.
| |
| Biologics | Infusion/injection | Block receptors for inflammation stimulating proteins | Increased risk of infection, vertigo, dizziness, allergy-like reaction | |
| Surgery | - | Colectomy/ileostomy | Relieve symptoms but they usually come back | Patient spends a week in hospital and a few months recovering |
Current treatments show no effect for 1 out of 5 patients with IBD and those that do often have very serious side effects. From our initial survey, we found a number of patients who are currently not on any treatment as nothing has worked or the side effects have been too severe and more stated their current treatments are not working6. Others were concerned of long term side effects such as increased risk of developing certain cancers. We believe that a new treatment must be developed that is both more effective and more patient friendly.
Professor Simon Travis
We got in contact with Simon Travis, Professor of Clinical Gastroenterology, who has been the President of the European Crohn’s and Colitis Organisation (ECCO) and an elected Member of the International Organisation of Inflammatory Bowel Disease, to gain more of an insight into the current problems with treatments and what a doctor would like out of a new treatment. He believes probiotics have potential in treating Crohn’s but encouraged us to look for evidence showing it’s success. He also thinks patients won’t mind using genetically modified products, they only care that the treatment will improve symptoms.
In terms of safety he believed, especially compared to current treatments such as anti-TNFa, proteins produced by probiotics are far safer as they will be quickly degraded. His concern came from consideration of the environment. He directed our consideration towards the impact the bacteria would have coming out as waste and possible effects in sewage. This is especially important in developing world.
Finally, he encouraged us to think of the strains we would use in terms of its adhesion properties in the intestinal tract rather than just ease of modification. The localisation of IBD is important to consider when choosing a bacteria as we want our treatment to be as close to the source as possible in order to have the greatest effect as possible.
After our meeting with Simon Travis we gained confidence in the use of probiotics and were directed towards further avenues of research in order to ensure our treatment was as efficient as possible.
Combined Treatment
Intestinal epithelial damage is characteristic of IBD due to increased apoptosis of epithelial intestinal cells (EICs). Therefore, a common concern for probiotic treatments is the possibility for bacterial movement across the intestinal epithelium. IL-10, in conjunction with glucocorticoids (a commonly administered treatment for IBD), has been shown to decrease the permeability of damaged intestinal epithelium via an unknown mechanism; IL-10 deficiency has in fact been associated with increased intestinal permeability and development of spontaneous colitis2. Therefore, we believe that our therapeutic will have favourable interactions with current treatments for IBD.
The survival of L.lactis is negatively influenced by gastric acid. Previous studies have countered this by co-treating patients with a proton pump inhibitor with the probiotic. For our product we may recommend taking the product with a proton pump inhibitor as well to promote colonisation in the gut
Gene Therapy Case Studies
There are currently very few treatments that are relevant to our project. Gene therapies are on the rise but the cost of these make them unattainable for patients and mean that they can’t be profitable for pharmaceutical companies preventing further research and expansion of the treatment. There are currently 504 gene therapies in clinical trials with 34 of these in the most advanced stage of testing. The sudden surge in this new type of therapy has enlightened many unseen problems shrouded by the confidence in the efficiency of the treatment.
CAR T
CAR T is the first gene therapy approved by the FDA but has encountered many problems. Patient’s T cells are transformed to recognise and attack cancer cells. Kymriah by Novartis fights against acute lymphoblastic leukaemia, 3,100 new patients a year suffer from this and 30% of these people don’t respond to previous treatments. The treatment has a response rate of over 80% and requires only one injection. Although this seems like a miraculous treatment curing a patient is not a sustainable business model especially with the huge $475,000 price tag for the cure. The high cost is from T cell collection, manufacture involving 151 stages with 54 decision points, transport, testing, low number of patients, one administration cure and trained specialists present in only 32 sites in the USA. The requirement of specialists not only increases costs but restricts the locations that it can be administered.
Although the high cost is thought to be cheaper than the lifelong alternative, the one off payment is unaffordable for most customers. This has required Novartis to seek a new business model. If the patient shows no response within a month there is no charge, this increases the customer's confidence yet doesn’t lower the cost. The cost has already been reduced by the FDA permitting smaller groups for clinical trials, even though side effects such as cytokine release syndrome were found resulting in deaths during the trials it still passed. This shows how necessary a new treatment is and how closely managed the administration must be. Novartis is currently looking into reducing costs by the use of donor T cells rather than the patients and by automating manufacturing systems reducing the need for skilled operators.
Genetically Engineered Probiotics
Probiotics are an effective, patient friendly treatment. Synthetic Biology used for a novel therapy opens up new avenues for treatments. By restricting the genetic engineering to the probiotic rather than the patient dramatically reduces any risks for the patient and allows the treatment to be stopped and the probiotic removed at any point.
GE probiotics are a very new concept, this is demonstrated by how few companies are currently in this market, because of this we have used 4D pharma plc and MaaT pharma as case studies in production and marketing probiotics. 4D pharma plc and MaaT pharma produce natural probiotics, test which strains are effective for which conditions, and research what can be considered a healthy microbiome. Their website contains some basic information about manufacture, clinical trials, finance, patents and more. We used this information with further research to develop our initial model for the manufacture of our product and for our business model.
Whilst at New Scientist Live as well as conducting our outreach work we decided to conduct a survey to get a greater understanding of the public’s support of GE probiotics compared to other gene therapies. Our survey was filled in by school and university students with studying sciences and adults with an interest in science with a range of qualifications. We asked if they agreed with germline cell gene therapy, somatic cell genetic gene therapy and genetically modified probiotics.
The general consensus was that synthetic biology has the potential for good and should be encouraged for the treatment of serious diseases. There was a lot of concern over regulation leading to fear of use for in areas other than therapeutics. The survey illustrated that the public has more support for somatic cell gene therapy and GE probiotics compared to germline cell gene therapy.
Strains
In the lab we have been modifying E.coli, we initially thought we could use this as the probiotic chassis as well as for our lab work. However, as we conducted more research we realised other bacteria may be superior for the treatment of IBD
Dr Chris Barnes
We met with Dr Chris Barnes from the department of Cell and Environmental Biology at UCl to ask for advice for bacterial population control. He directed us to recent studies using L.lactis and agreed they would be safe to ingest and would successfully colonise the gut. He suggested using quorum sensing with a molecule not normally found in the gut to allow accurate control. He also highlighted the variation in the microbiome of different patients would result in large variations in the population of our probiotic. We investigated the range in the bacterial population that our device would be successful at through modelling as you can read about here on our Time Domain Analysis page.
Lactococcus lactis
When we finish testing our device with E.coli we will use Lactococcus lactis as our probiotic. E.coli is safe and easy to engineer but show poor long term colonization of the gut, we have looked into alternatives that would provide a longer term treatment and so require fewer doses. L.lactis is recognised as a safe species and has been engineered greatly including to act as a probiotic producing IL10 for IBD treatment3. L.lactis already has many health benefits so, with our system added, would act as efficient treatment.
L.lactis is able to survive low pH and bile, 98% of the bacteria survive the passage through the stomach and 10-30% survive in the duodenum, which is a relatively high percentage. In the gut the bacteria then adhere to microvilli and form part of the microbiome4.
Delivery
We had been considering how our product would be delivered to the gut from early on the project. Our aim was to develop a 'friendlier' treatment but it is important to consider the possibilities for a probiotic in order to maximise the likelihood of colonisation in the gut.
Psychological Impact
Our initial survey highlighted the importance of delivery method in a psychological way as well as functionally. Patients told us they would like a treatment which is simpler than their current treatments especially compared to having to be on an IV. We were told that the patients found the use of needles for biological treatments can be scary especially for younger patients. We were also informed how these psychological considerations are particularly important for chronic conditions compared to other conditions. For this reason we decided to place a greater focus on the method of treatment and try to ensure we come up with the easiest and safest method for the patient.
We contacted Dr Sam Parsons, Oxford Centre for Emotions and Affective Neuroscience, to gain specialist knowledge on the psychological impacts of autoimmune conditions and treatments. He was able to highlight the impacts autoimmune conditions have that may not as obvious, this includes chronic pain, difficulty with meals leading to isolation and phobias with needles and hospitals. After this we focused on providing the medication in a friendlier form that requires fewer hospital visits as well as providing a consistently high quality of treatment.
Surveys
We initially received support for packaging the product in a yoghurt in our first survey. Furthering this we had comments that drew our attention to the possibility of patients being vegan or lactose intolerant leading to our consideration of the survival and growth of the product in different yoghurts. L. lactis is also susceptible to lysis in the stomach when not taken with food, this is a further encouragement for the product to be taken with yoghurt.
We conducted two surveys with the aim of finding the preferred delivery method of the public. Our first survey was conducted at ‘Meet the Experts’ at Oxford University Museum of Natural History and our second was sent out to members of the Oxford Biochemistry department. The first was at an event for children and families whilst the second was completed by specialists with a higher level of understanding of GMOs.
The most favoured method in the Natural History Museum survey was the yoghurt drink. Injections received many votes but only from children under 12 either because of association of injections with effectiveness or because they found the idea of injections exciting.
From our survey in the department we were able to ask a significantly larger group of people their opinion as well as receiving reasons for their choices. Capsules resulted as the favoured method from this survey. Yoghurts received votes due to their convenience but capsules was preferred for the same reason as well as its establishment in medicine, ease of storage and transport, and its superior half life.
Dr Nick Thomson
We met Dr Nick Thomson from the Quadram Institute, Norwich, to discover how we can encourage the probiotic to successfully inhabit the gut. He suggested the focus should be on adherence to the intestinal wall and stability against gastric acid, bile and enzymes. He also suggested the use of a model colon to test the bacterial populations, which we have included in our plan for pre-clinical testing.
Colonisation
At least 108-9 cells must reach the intestine to successfully colonize. This shows the necessity to have a successful delivery method for our medication. The most common method of administration is orally. Tablets/capsules are easy to administer, storage and are effective and reliable. L.lactis have a greater colony count when administered with milk and other dairy products. Optimized yogurts have been shown as successful delivery methods and chocolate based products and ice cream have given promising results. This also could act as an alternative ‘friendly’ way of administering medicine.
Freeze drying is a simple solution to preserve the viability and stability of the bacteria over long periods of time and shows no negative effect on the survival of bacteria on the way to and in the intestine. Cryoprotection means more variable bacteria are able to survive and decreases the manufacture cost as fewer functional bacteria are lost. Freeze drying bacteria with cryoprotectants allow the bacteria to be stored at 4 degrees C for 5 months with little change in the colony count. Rehydration makes the bacteria less viable to be stored so must remain dried until taken by the patient.
Microencapsulation could be used to coat the cells in a shell to protect them during storage and delivery. Microencapsulation with polysaccharides or proteins offers a more effective alternative than cryoprotection. Strains have been found to survive to different extents in each process allowing us to select select a strain more easily.
Having our product in a capsule makes the medication more reliable but also has the potential to then be delivered in yogurt making the bacteria more viable and promoting a friendly image of the medication.
We are currently unsure of the dose we would prescribe. If the dose is too high then it is possible our probiotic will outcompete other bacteria in the microbiome whilst too lose a dose will mean the treatment is ineffective. To ensure greater control of the product we would prescribe a relatively low dose daily but specific quantification of dosage would require pre-clinical and clinical data.
Regulation
Regulation of a genetically engineered probiotic appeared very vague at first. We have had a lot of help from a range of specialists to get a greater understanding of how regulatory authorities apply to us and how we can get our product from the lab to the patient.
Dr Michael Morrison, HeLEX
We met up with Dr Michael Morrison the principal investigator of biomodifying technologies at HeLEX (Centre for Health, Law and Emerging Technologies).
One of the things he suggested we look into was the regulatory bodies that our product would have to go through. We found, since our product is not a conventional pharmaceutical or medical device, that it is quite unclear which regulatory category our product would come under. We made a clear plan and flowchart of how our device would go from the lab into a commercially available product. This includes how we can prove the safety and effect of the product pre-clinical trials.
Michael suggested we look into the costs that would be associated with our treatment and how this would compare to current treatments. We would need to consider the delivery of our product to patient and regulation to first get an idea of the associated costs. After this, we would confidently be able to say how the price differs from current treatments and if our product is a cost-effective alternative. He also directed our attention towards current gene therapies to use as case studies for regulation and costs for the business and patient.
Cell and Gene Therapy Catapult
Catapult is a centre to help and encourage the growth of cell and gene therapies by aiding with regulation, product testing, logistics, manufacture and business advice.
We met with Daniel Rabbie, the Regulatory Affairs Manager, and Ryan McCoy, the Senior Process Development Scientist to discuss how our product fits in with current government regulations and how we can take it from the lab to the patients. We discussed the differences in regulation in different therapies, the organisations available to speed up the process of getting the treatment from the lab to the patient, current therapies, and considerations involving logistics and manufacture.
ATMP Classification
Our treatment would likely count as an Advanced Therapy Medicinal Product (ATMP) according to the European Medical Agency (EMA). The classification of a therapy is particularly useful for clinical trial design but also helps for its specific regulation, its licensing and what advice is available. The EMA’s Committee for Advanced Therapies (CAT) advise on whether a treatment would be considered an ATMP and what type it would be, such as cell or gene therapy. CAT have a list of previously categorised treatments. In this list we found a therapy involving modified Lactococcus Lactis engineered to produce anti-TNF alpha antibody fragment for the treatment of Ulcerative Colitis. This treatment is very similar to ours allowing us to use this as a basis of what our treatment would be classified as. Even though the patient’s genome is unaffected this treatment still counted as a gene therapy medicinal product as “The introduced recombinant sequence is directly related to the therapeutic effect”. To confirm our treatment has the same characterisation we have submitted an application for ATMP classification with CAT from the EMA which we are waiting to hear back from. Our completed form can be read below. The form can be confusing especially for those lacking knowledge of drug regulation, as we initially did. We are hoping this can be used as a reference for others seeking classification of new types of medicinal therapy in the EU.
Manufacture
Through studying companies including 4D Pharma plc and Genentech we have developed a rough manufacture pathway.
Lyophilisation increases the shelf life of the product to around 18 months5. This decreases the requirement for frequent production and batches, and so reducing manufacture and logistical costs. An added benefit of this is for the patient. A longer shelf life will mean fewer hospital visits and a more reliable medication making treatment significantly more convenient for patients. This also gives the option of adding the medication to a yoghurt to encourage colonisation of the bacteria and allows the treatment to be more patient friendly, but it is not necessary and can be taken just as a pill.
Drawbacks
Although we believe our treatment is a significant improvement on what is currently available we must still confront its problems. We have summarised the problems that we have come up with:
- The kill switch means that the antibiotic tertracycline cannot be taken for infections during treatment as this would result in termination of the therapy.
- Activating the kill switch results in production artilysin, this will kill the probiotic but will also spread and kill neighbouring cells. The impact shouldn't be too severe as although artilysin will be present at a high intracellular concentration in the probiotic, it will be a low concentration in the gut when secreted.
- The SoxS/R system is not specific to Nitric Oxide but responds to any oxidative stress. We have countered this lack of specificity by implementing our feedback system which will prevent IL10 production in response to signals, not from T cells.
- The microbiome is a relatively new area of research because of this there are many areas of our treatment that we are unsure about. Interactions with the microbiome and other areas of the immune system have not been fully characterised. However, we can not learn about these further possible interactions until pre-clinical and clinical trials.
- We are unsure about the doses required and the frequency that the therapy must be taken, this will require clinical data.
Final Design
Our aim was to develop a novel medication for IBD with the focus on needs of the patient. Through patient interviews and consultation with specialists, we have learnt of the severity of IBD and the problems of current treatments. These treatments are often ineffective and work by attacking the whole immune system instead of focusing on the cause of the condition leading to significant side effects on the immune system. We have developed a treatment as a probiotic that works on the cause of the condition and so should have fewer side effects. We have incorporated a biosafety mechanism to allow quick removal of the probiotic and comfort the customer. The treatment can be used alongside glucocorticoids to prevent entry of the product across the intestinal epithelium whilst it is inflamed. Through research and surveys with the public, we have decided on a manufacturing process to allow the treatment to be taken as a pill or in a yoghurt allowing it to be a far more consumer friendly than current treatments. We have investigated current gene therapy treatments and regulation to determine how a GE probiotic would compare and what we can do to ensure its convenience as well as how it would be classed by EU regulatory agencies allowing us to determine the exact regulatory procedures we would go through as well as how we can enable our product to reach patients as quickly as possible.
References
| Index | Reference |
|---|---|
| A | Omenetti S, Pizarro TT. The Treg/Th17 Axis: A Dynamic Balance Regulated by the Gut Microbiome. Frontiers in Immunology. 2015;6:639. |
| B | Paroni M, Magarotto A, Tartari S, et al. Uncontrolled IL-17 Production by Intraepithelial Lymphocytes in a Case of non-IPEX Autoimmune Enteropathy. Clinical and Translational Gastroenterology. 2016;7(7):e182 |
| C | Cicerone C, Nenna R, Pontone S. Th17, intestinal microbiota and the abnormal immune response in the pathogenesis of celiac disease . Gastroenterology and Hepatology From Bed to Bench. 2015;8(2):117-122. |
| D | Granzotto M, dal Bo S, Quaglia S et al. Regulatory T-cell function is impaired in celiac disease. Dig Dis Sci 2009;54:1513. |
| E | Kumawat AK, Strid H, Tysk C, Bohr J, Hörnquist EH. Microscopic colitis patients demonstrate a mixed Th17/Tc17 and Th1/Tc1 mucosal cytokine profile. Molecular Immunology 2013;55(3-4):355-364. |
| F | Gaffen SL. Role of IL-17 in the Pathogenesis of Rheumatoid Arthritis. Current rheumatology reports. 2009;11(5):365-370. |
| G | Cooles, F.A.H., Isaacs, J.D. & Anderson, A.E. Treg Cells in Rheumatoid Arthritis: An Update. Curr Rheumatol Rep. 2013;15:352. |
| H | Opazo MC, Ortega-Rocha EM, Coronado-Arrázola I, et al. Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases. Frontiers in Microbiology. 2018;9:432. |
| I | Asadullah K, Sterry W, Stephanek K, et al. IL-10 is a key cytokine in psoriasis. Proof of principle by IL-10 therapy: a new therapeutic approach. Journal of Clinical Investigation. 1998;101(4):783-794. |
| J | Cosorich I, Dalla-Costa G, Sorini C, et al. High frequency of intestinal TH17 cells correlates with microbiota alterations and disease activity in multiple sclerosis. Science Advances. 2017;3(7):e1700492. |
| K | Nouri M, Bredberg A, Weström B, Lavasani S. Intestinal Barrier Dysfunction Develops at the Onset of Experimental Autoimmune Encephalomyelitis, and Can Be Induced by Adoptive Transfer of Auto-Reactive T Cells. Lees JR, ed. PLoS ONE. 2014;9(9):e106335. |
| L | Slingerland AE, Schwabkey Z, Wiesnoski DH, Jenq RR. Clinical Evidence for the Microbiome in Inflammatory Diseases. Frontiers in Immunology. 2017;8:400. |
| M | Tian, G., Li, JL., Wang, DG. et al. Targeting IL-10 in auto-immune diseases. Cell Biochem Biophys 2014;70:37. |
| N | Köhling H, Plummer S, Marchesi J, Davidge K, Ludgate M, The microbiota and autoimmunity: Their role in thyroid autoimmune diseases. Clinical Immunology. 2017;183:63-74. |
| O | Shao S, He F, Yang Y, Yuan G, Zhang M, Yu X, Th17 cells in type 1 diabetes, Cellular Immunology. 2012;280(1):16-21. |
| P | Danikowski KM, Jayaraman S, Prabhakar BS. Regulatory T cells in multiple sclerosis and myasthenia gravis. Journal of Neuroinflammation. 2017;14:117. |
| 1 | Sun Kim et al. Impact of inflammatory bowel disease on daily life: an online survey by the Korean Association for the Study of Intestinal Diseases. Intestinal Research. 2017;15(3):338-354. |
| 2 | Lorén V, Cabré E, Ojanguren I, Domènech E, Pedrosa E, et al. Interleukin-10 Enhances the Intestinal Epithelial Barrier in the Presence of Corticosteroids through p38 MAPK Activity in Caco-2 Monolayers: A Possible Mechanism for Steroid Responsiveness in Ulcerative Colitis. PLOS ONE 2015;10(6): e0130921 |
| 3 | Braat, Henri et al. A Phase I Trial With Transgenic Bacteria Expressing Interleukin-10 in Crohn’s Disease. Clinical Gastroenterology and Hepatology. 2006;4(6):754 - 759 |
| 4 | Drouault S, Corthier G, Ehrlich SD, Renault P. Survival, Physiology, and Lysis of Lactococcus lactis in the Digestive Tract. Applied and Environmental Microbiology. 1999;65(11):4881-4886. |
| 5 | Montel Mendoza, G. , Pasteris, S. , Otero, M. and Fatima Nader‐Macías, M. , Survival and beneficial properties of lactic acid bacteria from raniculture subjected to freeze‐drying and storage. J Appl Microbiol, 2014;116:157-166. |
| 6 | https://www.nhs.uk/conditions/inflammatory-bowel-disease/ |