- Human Pratices
Integrated Human Practice
In the early stage of brainstorming for the project, our team accidentally saw a video of vlogger Fanren Zhang(the Normal Guy Zhang) sharing his daily life on the website Bilibili (which is the most popular video platform for young people in China). In the video on February 11, 2021. Zhang, who has fasted for a year and a half, records that he finally served his first dinner with his family during the Chinese Lunar New Year, the most important festival in China. Although he could only eat a simple bowl of noodles next to them, he felt happy to be with his relatives. From the traces of his long-term use of the nasal feeding tube, we first noticed the disease of IBD.
This video has been uploaded with the author's permission
After literature investigation, we learned that Inflammatory bowel disease (IBD) is a chronic, non-specific inflammatory reaction mainly manifested in the intestinal mucosa. This disease has a long period of onset, is difficult to cure, easy to recurrence and potential cancer risk. It is mainly divided into Crohn's disease (CD) and Ulcerative colitis (UC). In the video, Zhang, the vlogger, is optimistic about life. However, he sometimes displays frustration and sadness after suffering from Crohn's disease, the "green cancer." After watching most of his videos, our team sincerely felt sorry that such an interesting and charming person would suffer from this disease.
Meanwhile, we also realized that this disease has a particularly significant impact on young people. However, there are limited treatment plans and related science popularization for IBD in China. So we thought, maybe they need some help to live a better life.
In order to know more about this disease, we made a special trip to the hospital for further understanding. In the department of Gastroenterology of Shenzhen Second People's Hospital, we came into contact with a patient with ulcerative colitis. (To protect patients' privacy and make the interview more secure，we drafted the informed consent in advance. Click here to view the details.)
After coming back from the hospital, our team did a lot of literature research. Starting with key concepts such as intestinal flora and colonization, and focusing on the remission period of IBD patients, we came up with an idea -- to develop a "cocktail" of adjuvant maintenance treatment for IBD by using engineered bacteria and taking factors related to the disease progression of IBD as therapeutic targets, combined with the regulation of intestinal flora. We call this the Gutail Floractory. Gutail Floractory = Cocktail + Gut flora + Factory, which represents our customized platform of engineered adjuvants based on synthetic biology and using cocktail therapy to affect intestinal flora. We expect Gutail Floractory to relieve gastrointestinal distress in patients with IBD during convalescence and even improve the quality of life of patients who do not respond to conventional therapies.
In addition, we also focus on non-therapeutic problems caused by diseases and hope to make some meaningful attempts in other parts of Human Practice and Education.
Based on the characteristics of synthetic biology, we hope to modularize our therapeutic components, with particular emphasis on the interchangeability of the promoter and the open reading frame, allowing us to replace the four therapeutic genes and their expression patterns at will.
With a preliminary idea, we started the project experiment design. We found You Conghui, associate professor of biology at the School of Life Sciences, Shenzhen University. She first made an overall evaluation of our project, and we discussed the colonization of bacteria, product safety, expression methods, plasmid loss, plasmid design, bioethics, and other issues. She was very optimistic about our general direction and encouraged us to have a try. Click here to view the details.
Fig.4 We're interviewing Prof. You.
After further literature review, we preliminarily decided to select the commonly used E.coli engineering bacteria such as DH5α or BL21 (DE3), E.coli Nissle 1917, L.lactis and other relatively operable model strains in genetic engineering as the chassis, and determined the four perspectives of "cocktail" therapy: Production of butyric acid, targeting and decomposition of LPS, reversal of peroxide stress state, the abnormal intervention of bile acid metabolism. At the same time, we hope to track each patient who uses our engineered bacteria, through periodic metagenomic stool testing, modeling tools to analyze the dynamic changes in the composition of their intestinal flora, and then use each treatment component in proportion to the specific situation of the patient. For example, precise personalized treatment can be achieved by controlling the proportion of bacteria or promoter strength carrying each treatment element. Finally, we consider safety in terms of resistance and suicide switch.
Based on these ideas, we continue to consult experts and scholars in related fields. With their help, we refined the conception and implementation details of the experimental part of the project.
Dr. Zhu is a senior scientist in molecular biology. She has given us many suggestions on the design and implementation of molecular experiments. In response to questions about the IBD-related targets we had chosen and whether this cocktail of treatments is feasible and practical, she said it was theoretically possible. Because they are all about the symptoms and pathogenesis of IBD, but ultimately it depends on the data.
She also mentioned to us that in the whole process of drug development, the feedback of clinical data is often decisive. Even if a project is successful in Phase I and Phase II trials, it can still fail in phase III.
She also reminded us that strain stability is one of the factors that must be considered in the development of Live Biotherapeutic Products (LBP) drugs. The degradation of strains should be considered in the transfer process of our engineered bacteria from generation to generation, thus affecting the activity of expressed products. Click here to view the details.
Fig.5 We're interviewing Dr. Zhu.
At the same time, we got in touch with Shenzhen Xbiome Biotech Co., Ltd, an industry-leading AI-based microbiome drug development company in China, through our advisor Luo Mingyue. The Company has been selected by MIT Technology Review as one of the world's 50 Smart Companies in 2020, Fast Company magazine as one of the Top 50 Best Innovative Companies in China in 2018, and One of the Top 20 Leading Biotechnology Enterprises in Shenzhen, with international leading comprehensive strength.
At the invitation of Xbiome, our team paid a visit to the Shenzhen headquarters of Xbiome on March 3, 2021. We know that Xbiome is currently trying to relieve or treat intestinal and other systemic diseases through fecal bacteria transplantation, formula bacteria, and other microbial treatments. Rely on an innovative development model and the research of drugs development platform, Xbiome combines AI with gut microbiome technology into its proprietary drug development platform, which ensures powerful data support, significantly speeds up and increases the success rate of drug development and facilitates the transition from laboratory exploration to commercialization. Click here to view the details.
Fig.6 We're visiting the company.
We also described our project design to scientists like Yin Yiming from Xbiome research and development department, and they gave us much feedback. Xbiome, out of support for the iGEM team and social responsibility to guide university students, has reached a two-way cooperation intention with us on the subsequent development of the project! Xbiome is willing to provide transformation and development ideas for our project from the perspective of a biopharmaceutical company. They are also willing to provide us with guidance from product design, construction and validation, as well as support for strains, vectors and animal models if it is possible.
In the metagenomic analysis part, we can use "Xstrain" technology of the company, relying on the integrated public data set of Xbiome and the company's own large amount of microbiota data of healthy individuals and patients with various indications before and after treatment, we can focus on the intestinal microbiota differences of IBD patients and customize their specific treatment regimens.
In the modeling part, we use the efficient AI algorithm independently developed by Xbiome, which can reduce data noise and improve the interpretability of data. At the same time, using a large number of databases to verify the reliability of the model can improve the prediction effect of our model.
Our team may also rely on the freeze-drying platform built by Xbiome to produce a new intestinal flora preparation -- microcapsule. The unique practice can be more stable in transportation and storage while isolating the damage of oxygen and air humidity to intestinal bacteria, effectively masking the unpleasant smell of intestinal bacteria. Moreover, microcapsules are easier to swallow and can be dispersed in various solvents, which can effectively protect intestinal bacteria from crossing the digestive tract and targeting intestinal release during delivery. In its final form, microcapsules may also be stored in a medium such as a yogurt or jelly to improve patient compliance.
In addition, Xbiome is the only microbiological drug manufacturing platform approved by the US FDA in China. We carry out product development and production under their guidance, which will help to ensure the standardization and credibility of our products.
After deciding to cooperate with Xbiome, we also consulted Dr. Hao Huaijie, Dr. Zhang Yulong and Dr. Huang Song from Xbiome, who gave us guidance on cell experiments, mouse experiments and pharmaceutic preparation.
Dr. Hao Huaijie is the senior manager of microbiome R&D in Xbiome. To further test whether the engineered bacteria and its protein products constructed by us can effectively inhibit inflammation, we hope to carry out verification at the cell level. Cell experiments are relatively unfamiliar to us and require a harsh environment. Dr. Hao Huaijie gave us a lot of advice on the design and attention points of cell experiments. Dr. Hao also pointed out the difficulties we might encounter in the experimental process, such as the relative repeatability of experimental results, large differences, etc. Moreover, he suggested that we should first explore conditions, make plans before conducting formal cell interaction, and then verify. Click here to view the details.
Fig.7 We're interviewing Dr. Hao.
Dr. Zhang Yulong is a microbiome R&D scientist in Xbiome, with rich experience in animal experiments. In order to complete the relevant experiments of our drug development according to the IND application standard of the FDA, we plan to complete animal experiments including mice experiments within the competition cycle, to verify the efficacy of our drug further.
Therefore, we asked him about the necessity of conducting mouse experiments, the selection of animal models for intestinal microorganisms, the process of IND application, relevant ethical approval, and the plan of mouse experiments. He gave us a lot of good answers! Besides, Dr. Zhang also reminded us to pay attention to some common indicators to evaluate the severity of IBD diseases, such as body weight, fecal viscosity, blood in the stool and other directly observed indicators. Finally, the above indicators can be integrated and the more authoritative evaluation criteria such as the DAI evaluation system can be used for evaluation. This interview laid a foundation for our subsequent experimental design of mice. This provides us with more and more accurate means to demonstrate the effectiveness of drugs. Click here to view the details.
Fig.8 We're interviewing Dr. Zhang.
Dr. Huang Song is a doctor from the French National Institute for Agricultural Research (INRA). Currently, he serves as the chief pharmaceutical scientist of Xbiome, leading the team to build the pharmaceutical process innovation platform and responsible for developing a variety of new types of probiotics. With his help, we determined the form of the drug formulation. In making this decision, we took into account humanitarian considerations, patient needs, and the effectiveness and stability of the drug. We asked Dr. Huang about the types and details of a range of viable agents. The formulation of the first generation of lyophilized protectants was determined, and several iterations of the protectant formulation were updated under his guidance. In the following experimental implementation process, we also according to the test method mentioned by Dr. Huang, the related performance of the protective agent was evaluated. Click here to view the details.
Fig.9 We're interviewing Dr. Huang.
When it came to June 2021, the experiment part of our project was on track and everything was progressing in an orderly way. Some education activities to popularize synthetic biology knowledge and exchanges with other schools are also actively carried out. At the same time, our thinking about IBD gradually deepened. In our traditional concept of health, "Absence of disease is health". But in the world Health Organization's latest definition of health points out that "Health is not only the absence of physical disease, but also mental health, social adaptation and moral." Therefore, modern people's view of health is holistic health, that is, to meet the "Physiological, Psychological and Social" health factors. Inside and out of our bodies, we should see more!
We want to engage with patients again, understand their broader needs beyond their pathophysiology and do more for them.
We came into contact with a Crohn's disease patient from Anhui, China, and we had a lot of communication with him online. He only received junior high school education, he slowly narrated his story to us in his simple style. Based on these, we learn about the impact of the disease on his life, his story is so typical that what happened to him seems to represent the IBD community. But his strength and optimism also profoundly affected us.
After obtaining his consent, we recorded his story with IBD in a non-fictitious writing way and published it on our WeChat public platform.
If you cannot view the PDF, you can click this link to view or download it
Based on the two patient contact experiences and literature investigation, we concluded that for IBD patients, the pain points that need to be solved are as follows:
(1) Nutritional requirements of IBD patients
(2) Psychological needs of IBD patients
The incidence of IBD in China is still low, so there is insufficient awareness of IBD in the society. This resulting lack of understanding of the disease and will affect the patient's social identity to some extent, which can lead to anxiety and depression in patients.
In addition, IBD is characterized by a younger age group. Patients are often forced to drop out of school or leave work because of severe symptoms. In addition, the recurrent attacks of the disease and long-term drug control may bring tremendous mental pressure to patients and also become the inducement of IBD-related psychological disorders to a certain extent.
Some studies have pointed out that IBD patients are twice as likely to have anxiety as healthy people, and IBD patients have a higher incidence of depression than ordinary people.
(3) There are still large unmet clinical needs for the safety and compliance of IBD drugs
IBD has many problems, such as long onset, painful disease, risk of complications, poor efficacy of conventional treatment, and high price of Infliximab, which is unaffordable for ordinary families. Currently, there is a large unmet clinical need for safety and compliance in the IBD drug market, despite the availability of multiple biological agents.
IFX remains the first-line treatment of choice among many marketed biologics, while Vedolizumab and other anti-TNFα biological agents, as well as Ustekinumab and JAK inhibitors, can also occupy a portion of the patient population due to their different M0A, superior route of administration, or cost-benefit ratio. However, the existing clinical data shows that the proportion of complete clinical remission of moderate and severe IBD is about 50%. Moreover, patients who achieve clinical remission still face a certain proportion of recurrence and drug resistance, and there are still large unmet clinical needs for safety and compliance.
Suppose Gutail Floractory is trying to solve the physical pain of IBD patients at the level of clinical treatment. Also, the dietary and psychological needs of IBD patients should not be ignored by us. These are complementary elements of life and will help IBD patients better return to society from the hospital and live healthy life.
In order to help them better manage their diet, solve their "What to eat and how to eat?" problem. We hope to educate patients to keep a food diary to find out the most suitable diet for them. However, it takes time for patients to develop the habit of a food diary, and the non-standard way of a food diary is not conducive to patients' summary and feedback communication with medical staff. So we wanted to digitize this function, develop e-forms on mobile apps. After entering this page, patients can quickly and accurately record their daily diet following scientific methods under the guidance and prompts of the system.
Fig.10 Diet management.
According to the data recorded by users, we also hope that the system will automatically analyze the nutrition composition and calories, draw a nutrition balance curve, track the nutrition intake of users in real-time, and make automatic adjustments according to the needs of different users, such as dietary preferences, taste and taste, and provide some reference suggestions to develop personalized nutritional recipes. Relevant data can also be printed with one click to give clinicians feedback on the results to meet diagnosis and treatment needs. There is an old saying in China: "Food is the most important thing for people". We hope that starting with a diet can help patients return to normal life.
Given the scattered distribution of IBD patients in China, it is difficult for patients to get to know each other and find comfort in learning about others' experiences or helping each other. In order to help IBD patients for better social adaptation, relieve the mental pressure brought by the disease, we believe that we can help them establish an online IBD patient communication community and provide a communication and dialogue platform for IBD patients.
Fig.11 IBD patient community.
Here, users can freely share IBD treatment stories, IBD daily routine, medication precautions and diet recommendations, etc. Each topic can become a "discussion group". In the group, users can set the permission to ask and answer questions anonymously, which is convenient for users and fulfill our practice to protect patients' privacy. We hope they can help each other solve daily problems. At the same time, in view of the IBD disease may lead to mental health issues, we separately set a psychological consulting sector, introduce third party professional psychological consultants, open and provide a free consultation in a specific period, answer hot problems and alleviate their psychological pressure. At the same time, users can also choose to pay for counseling services, targeted to solve mental health-related problems.
Meanwhile, in order to solve the problem of patients' lack of disease-related knowledge, we hope that the platform can introduce certified medical staff to share doctor resources by cooperating with gastroenterology departments or specialized gastroenterology hospitals. Provide professional advice on the treatment of IBD and other symptoms that may occur in patients with gastroenteropathy. At the same time, a medical Q&A area will be set up, and information about IBD prevention and treatment, the latest diagnosis and treatment plan, the latest research progress and other related information will be updated irregularly. For patients in need of professional consultation, the platform provides paid consultation services, so that patients can better carry out IBD treatment and disease rehabilitation.
Of course, we have also loaded our drug purchase page and process diagram on the APP.
Fig.12 IBD drugs purchase page.
Therefore, we want to systematically integrate IBD patients' health education management and drug adjuvant therapy. In the process of drug research and development, we introduce fecal analysis technology to achieve the purpose of "Diagnosis -- Stool sampling -- Bio information analysis -- Personalized drug administration assisted treatment -- Daily education and health management -- Follow-up visit -- Adjusting drug formulation ratio", which is different from other drugs with its accuracy, adjustability and personalized characteristics.
In terms of health management platform construction, we focus on IBD disease and form differentiated competitive advantages with other food recording platforms. At the same time, the IBD communication community and patient story-sharing area were constructed to reflect the spirit of caring for patients. Finally, these functions will be integrated into an APP to create a health management platform that integrates multiple functions and focuses on serving IBD patients.
Since microcapsule allows us to put drugs in most kinds of food, we suspect that various drug forms will be more popular with patients. So, we started with a lot of ideas like yogurt, jelly, all kinds of snacks... But back to reality, we found that we had been too idealistic. As IBD patients who need to strictly control diet, no matter how to choose the microcapsule carrier, we are faced with the problem of "difficult to adjust to different tastes", and long-term consumption of a specific food will also make patients sick and bored, which is not conducive to drug use. In the end, we still chose the traditional freeze-dried power capsule as the form of medicine.
In cooperation with Xbiome, we have strengthened our determination to carry out the effective transformation of results better to show the potential and value of the project. Therefore, after a multi-party discussion and confirmation of details, we determined the details of the business plan and drew up the first version of it.
IBD patient community function : Provide a platform for patient communication. Find comfort from the experience of others or in helping each other. To help IBD patients better adapt to the society, relieve the mental pressure brought by the disease.
The function of food diary : Provide standardized e-form,to enable patients to better record diet Functions: (1) Help patients find a personalized diet that works for them; ② As feedback for drug customization
Drug customization process :
① After the patient purchases the service, we will mail the stool sampling kit to him.
② Patients collect their own stool and send it back.
③ We perform metagenomic sequencing on stool samples to understand the proportion of intestinal flora in patients. So that we can determine the usage and proportion of different engineering bacteria to accurately， so as to effectively regulate the proportion of patient's intestinal flora and promote intestinal recovery. And Screening effective therapeutic targets for different patients to accurately treat IBD.
④ According to the above analysis results, personalized customized drugs can be produced.
⑤ The patients have been treated with drugs and dietary management, and stool sequencing was performed again after one cycle of treatment. Observe the therapeutic effect and adjust the drug ratio again.
Fig.14 Product introduction.
In the process of writing the business plan, we consulted Will (Wang Jiang), senior manager of talent development in the HR administration group of the operations department of Xbiome. Will gave us complete guidance in writing a business plan. He reminded us to tell a sentimental purpose in the business plan. It is best to compare our project to an investor as a business model that has been recognized by the public. In the process of promotion, we should also pay attention to the patient's family，which is also the target group of advertising. In some sectors, such as business model, competitive advantage, future prospects, it is best to use a sentence or keywords to summarize, so as to attract people's attention. Click here to view the details.
In this competition, we only attempt four IBD treatment factors. In the future, we hope to reinvent ourselves to include all IBD targets in our pipeline. We are committed to taking synthetic biology entrepreneurial projects to the next level, essentially enabling IBD patients to live as healthy people do.
Guided by the Sustainable Development Goals (SDGs) of the United Nations, we hope that in the near future this program will be available worldwide, especially to people affected by gastrointestinal diseases in developing and newly industrialized countries. Our health management platform will continue to grow, carrying more functions and optimizing the functions and forms of dietary guidance, psychological care and other support. In this way, we can also better popularize the knowledge related to intestinal diseases to society, call on people to pay attention to the needs of this group of people, and achieve the purpose of preventing or preventing the deterioration through habit cultivation in daily life. IBD is just the first step in our grand vision.