Our aim with the DAISY project was to engage in positive and responsible action for the world.
We had to get out of our lab and meet other people to evaluate how positive and how responsible this project is, as well as to make it evolve. Indeed, we worked on a diagnosis project with consequences on public health. This requires a high level of both accuracy and acceptability, none being attainable without a strong commitment to meeting the general public and state-of-the-art experts. To meet these objectives, we opted for an ethical approach to identify all the stakeholders in allergy detection, as well as the needed specialists at each step. We gave major importance to integrating our project into society by calling on the key players. It was even more mandatory since allergies are an important health matter and concern. This work is described in our Integrated Human Practices section below.
Following our first meeting with the general public, we concluded that both synthetic biology and allergies are little-known to people. Since one-third of the French population is affected by allergies and therefore a major stakeholder, it seemed obvious to us that our education effort has to ally scientific communication and education on these themes, in a way to ensure mutual learning afterward. The biggest challenge here was to reach and include everyone in this discussion, no matter the scientific background, group age, or location. To have a variety of educational tools appeared essential to us, as well as to adopt a language adapted to a wide public. In this scope, our most important effort is our series of ten short online videos, “Cracking Allergies”, that answer the main questions we got about allergies during our meetings with the general public at Exposciences Occitanie 2022. It required designing and creating models of bacteria and immune cells as tools to explain biology and allergies. The second axis of our work was directed towards education about synthetic biology and was mainly supported by media communication and interventions in high school. These interventions were the occasion to give an insight into synthetic biology to more than 150 high-schoolers thanks to laboratory practice, quizzes, and presentations.
All the processes of design and production of these tools are documented in our Education and Communication section.
Integrated Human Practices
Overview
We choose to integrate our whole project with an ethical approach because of the importance of ethics for a health theme. This approach was based on three main axes: the source of the project, its use, and its future. These led to in-depth considerations nourished by impacting exchanges with stakeholders of allergy detection, specialists, and the general public. These meetings helped us to plainly understand the allergy context. Since allergies are a little-explored subject in iGEM and since we are not experts in every discipline that was required in this project, we consulted specialists at each step of our journey. This reasoning was summed up in our Integrated Human Practices in a creative and illustrated form with the aim to make our approach available to future iGEM teams. For the same purpose, a summary of every interview can be found in the IHP section to share this accumulated knowledge with the iGEM community.
An ethical approach
Allergies are an important health matter and concern, for example, a third of the French population. Because ethics were a central theme in our work and choices, we chose to apply an ethical approach to our project to structure our Integrated Human Practices work. With that goal, we met with Emmanuelle Rial-Sebbag, a research
director in bioethics and health law at INSERM to discuss our project. We followed the
ethical approach presented by Béatrice Jalenques-Vigouroux who is a lecturer in ethics
and sciences of information and communication. This approach allows bringing together
ethics and engineering, questioning our ideas, and justifying them.
It is structured following three questions, that lead to three thoughts to answer it:
One thing to keep in mind is that “By definition, an ethical question is a question that does
not have a solution” (Etienne Klein, 2018). Therefore, the output of our efforts for answering these
ethical questions is more of a suggestion that an absolute solution. The aim is to question
our ideas to build our project on solid foundations.
To answer these questions, we had to collect information from people, companies, and
organizations. This information shaped our project, from the first choices, its design, and the
final production, to its application in the real world.
Each interview is presented for a rapid glance by clicking on the specialists and stakeholders' pictures. They are of interest to any
future iGEM team that wants to engage in a project bringing together synthetic biology and
immunology.
What is the source?
Through this question, we are looking for the source of our project.
Why did we choose to work on allergies? Why did we think that a new diagnostic tool was
needed? What is the situation of allergies in our society? A critical reflection on society is
required to provide answers.
First, the reason why we chose to work on allergies comes from one of our team members,
Samy.
Samy is 22 years old and suffers from multiple allergies which are the cause of daily
discomfort and pain. He is allergic to a lot of fruits and vegetables, but also some
drugs. His first proposal in our brainstorming to find a project was to create an
alternative desensitization way to injection. The idea was to produce recombinant
allergens with yeasts and probiotics to administer them to the patient in a sublingual
way. The obvious problem was that consuming living GMOs in Europe for medical
purposes is legally very limited. Several of our team members are also affected by
allergies, such as Charline, Juliette, and Morgane.
From an ethical point of view, we started referring to reciprocity ethics, which is the idea
that we have to do for others what we would like them to do for us. This is a kind of
individualist thinking. For example, Samy would love to be desensitized to allergens causing
his allergies, so he proposed to create a new method of desensitization for others. What we
aimed for was referring to utilitarian ethics. This is the idea that we should do what is best
for the greatest number of people. For example, in France, it would concern a third of the
French population is affected by allergies.
We met the general public through events such as the Exposciences Occitanie 2022, interventions in high school, and online interactions. The exchanges witnessed the veracity of the statistics because many people told us that they were allergic or knew someone who was allergic. A lot of them had no test to confirm their “self-diagnostic”, which means that allergies are not known and recognized enough to be well-treated. All details of our exchanges can be found in our Education and Communication section.
By doing more research on allergies, we realized that the step even before desensitization,
which is to diagnose allergies thanks to tests, had limitations. These limitations are detailed
on our Description page. We imagined a new diagnostic tool to outpass the limitations of
already existing tests and keep our idea of desensitization using recombinant allergens as a
perspective of our project. This was in our opinion the best thing to do for the greatest
number of people affected by allergies.
However, we needed the opinion of allergy specialists to be sure that we could add
something to what is already existing.
That is why we met Luc Colas, an allergist but also a researcher at the university
hospital of Nantes and a lecturer in allergology and immunology.
He confirmed our impression that a high throughput method of specific IgE detection
was missing today in the scope of already existing methods. He also gave us advice
regarding our desensitization phase. Using a probiotic strain to produce the allergens
and administer it to the patient would induce a better tolerance to the treatment. His
opinion was important for us because he represents one of the project stakeholders
by working in a university hospital. University hospitals are involved in allergy
detection and the use of tests.
We also met Jean-Luc Menardo, a former allergist who used to work in a doctor’s
office. Allergists are obviously important stakeholders in allergy detection. Jean-Luc
Menardo has also worked as a researcher on desensitization, and as clinic director of
the Montpellier university hospital. According to him, a high throughput method of
specific IgE detection would greatly complement the traditional Prick test method.
Using first a high throughput method is very appropriate for precision medicine, which
needs more tools to be plainly exploited (Ansotegui et al., 2020).
Because usual allergy detection tests can be performed in medical laboratories, we met
Annabelle Gordon-Le Goff, a biologist and doctor in a medical analysis laboratory in Toulouse. Medical laboratories are also a
stakeholder in allergy detection. Annabelle Gordon-Le Goff provided us with a lot of useful information about current tests, the operating model of medical laboratories, and the prices. This helped us to build our own operating business model and to identify the need of the allergy detection stakeholders. Together we also were able to highlight the strengths of our method among the ones existing on the market. This meeting was an opportunity to discuss our project with an important stakeholder in allergy detection.
With the confirmation from the main stakeholders in allergy detection that there was a
missing gap in allergy detection, we started to imagine a new method of detection of
allergies, focused on the IgE recognition in the patient’s serum with a high throughput
method. We came up with the following idea.
An agglutination between three parts:
- a cell displaying an allergen (cell A)
- a specific IgE binding to the allergen by its variable part
- a cell displaying a DARPin, a protein binding specifically to the constant part of IgE
(cell D)
This agglutination can be the signal that the patient serum contains IgE specific to the
allergen displayed by cell A. This idea was the basis of our project but required to be developed according to the potential
use and needs of the stakeholders.
Click on the picture of each expert for more detail about their interview!
What is the use?
Through this question, we were looking for the use of our project from a local aspect. How
our method could be used? What are the user’s needs? How to design our project to fit
these needs? A reflection on the meaning of the project was required.
To understand what use could be done of our method, we needed more information about its
main components.
Because antibodies are central in our method design and because we are not
specialists, we discussed this matter with Jasper Kamphuis. He is a postdoctoral
researcher at Infinity INSERM, in a team working on food allergies and antibodies.
He gave us useful advice about the use of antibodies and labeled antibodies.
To improve our thinking, we met Chloé Beuraud, a researcher in immuno-oncology
at Evotec, and a former researcher at Stallergenes Greer. One of her remarks
supported the one of Luc Colas: she thought that using probiotic strain for
desensitization could increase the treatment tolerance. Chloé Beuraud also
suggested using detection methods of the agglomerate through FACS and FRET
approaches. This greatly influenced the scope of our project.
Thanks to our meeting with Luc Colas, we knew that FACS is not a routine in a
medical analysis laboratory, but can easily be found in a research laboratory. We
learned that university hospitals often outsource allergy tests to research
laboratories. It means that our local operating business model could be based on the one of a
research laboratory, that is performing tests for medical laboratories and university
hospitals, to send the results back to the allergologist. This was inspiring for our
Entrepreneurship effort. This also reinforced the idea that FACS was worth
considering.
To detect an aggregation with FACS, the easiest would be to clone genes coding for different
fluorescent proteins in our strains A and D. We would then obtain a double-signal in case of
aggregation sorting.
To check this hypothesis we met Yvan Canitrot, a researcher at LBCMCP and a
FACS specialist. He approved this idea and gave us recommendations about what
cell dilutions to use for sorting with the FACS.
We pursued our idea with Delphine Lestrade and Chloé Habouzit, both working at
TWB (Toulouse White Biotechnology). Delphine Lestrade is a manager of the flux
cytometry platform at TWB and used to work at Infinity INSERM on immunology and
antibodies. Chloé is a research engineer at the flux cytometry platform of TWB, who
worked on microbiota and probiotics. In addition to several meetings to develop
together the test protocol of our method with FACS, Delphine Lestrade and Chloé
Habouzit helped with the experiments on TWB’s FACS and the analysis of our
results.
During a presentation of our project to our partner TBI (Toulouse Biotechnology Institute), we
met Emmanuelle Trevisiol who worked on biochips for specific IgE detection. We learned
that the price of the test as well as the required IgE volume is two parameters that can
impact the utilization and promotion of an allergy detection test by allergists. The price of our
method is hard to evaluate since it is extremely innovative. It can evaluate a lot by working
on its optimization. One thing we can work on is the used volume of IgE.
After meeting her at the same presentation as Emmanuelle Trevisiol, Gabrielle Potocki-Veronese told
us about a patent that her team was developing that could be used to detect aggregations.
This patent used a microfluidics technique by forming droplets. As Luc Colas told us that
microfluidics machines could be found in research laboratories, this was an interesting
potential development for our method. Sophie Lajus provided us with all information about
their microfluidics machine and helped us to execute this idea at TBI by testing the detection
of aggregates.
One necessary aspect of our project was to model the aggregation between cells and
antibodies.
To do so, we received the help of Alain Liné, a process engineering teacher, who
specialized in mixing for aggregation control, and Jérôme Morchain, lecturer at
INSA Toulouse and researcher at TBI, in the TIM team. The modeling effort is more
detailed in the Modeling section.
Thanks to these meetings as well as our own research, we were able to come to a design
that could be socially integrated from a local aspect.
Click on the picture of each expert for more detail about their interview!
What is the future?
Through this question, we were looking at the future of our project from a global aspect. How
does it impact society? How would it be implanted in time and space? What is our goal? A
reflection on the aims and impacts of the project is required.
One of our project perspectives was to produce desensitization medicine, using probiotic
strain as chassis.
We met Pascal Lebourgeois, professor at UPS and researcher at TBI, a specialist
of Lactococcus lactis. Lactococcus lactis is a well-known probiotic strain of bacteria.
Following this discussion, we agreed that engineering Lactococcus lactis in the same
way we planned to do with E. coli would be too complex to be added to the project.
However, the idea is of interest for later development.
Thanks to our meeting with Julien Durand, co-founder, and CEO of Sweetech, we
learned that it is common for a start-up to rent space in laboratories at the beginning,
before having private investors. This impacted our vision for the future of our project.
Our meeting with Marianne Lefèvre, Intellectual Property specialist from the
consulting firm Adamante, brought us much information on patents and intellectual
property. This helped to structure our entrepreneurship direction.
Through our project, we regularly met with Colette Schenker, our main counselor
from Le Catalyseur. Le Catalyseur is a pre-incubator in Toulouse that offers to guide
project promoters through the process of creating a start-up. We defined together the
aims and missions of our company. Le Catalyseur also provided us with a SWOT
and business model canvas and explains how to use it. We did a project diagnostic
with the Catalyseur to evaluate the project progress and what remains to be done. We also defined together the entrepreneurial profile of our team members to find
what skills we had and which ones we needed.
More details on the future of our project can be found on the Entrepreneurship pages.
Click on the picture of each expert for more detail about their interview!
Conclusion
During this project, we met with numerous stakeholders and specialists who contributed to
its evolution. Each meeting was enriching and helped to change a simple idea into a
developed and complete project with industrial perspectives.
Who? Luc Colas: lecturer in allergology and immunology, researcher at the university hospital of Nantes.
Why? He took part in the quinquennial plan for the fight against allergies initiated by ALK, a danish laboratory that is specialized in immunotherapy for allergies. His advice for our project was important for its relevance and credibility.
Rationale:
Subjects and raised issues:
Generalities about allergies: we discussed the definition of allergy, which is according to Luc Colas “to react to an allergen with symptoms of allergy (redness, itching, swelling…) and to have IgE-specific memory of the allergen”. Luc Colas brought us precisions about the four different types of allergies. The one that we are interested in is mediated by IgE.
Different available methods to detect allergies: he gave us a more detailed view of the current detection methods of allergies (prick test, ELISA test, biochips, ImmunoCap), especially about their precision, false positives, and false negatives. He confirmed that a high throughput method of specific IgE detection is missing today in the scope of already existing methods.
What are the machines available in laboratories: he provided us with an overview of which machines and techniques are possible to use in hospitals. Research laboratories can possess microfluidic machines, but it is rarer in hospitals and medical laboratories. However, hospitals often subcontract this kind of test to research laboratories.
Desensitization: we also talked about the desensitization phase. He advised us to add an adjuvant to force the immunizing reaction of the patient. He also recommended putting the allergen and adjuvant inside of a gastro-resistant capsule instead of a sublingual treatment. We mentioned the idea of taking out bacterial DNA to have a ghost bacterium that displays allergens on its surface. If we choose a probiotic species, we could avoid purification of the allergens and obtain desensitization by the exact allergen that is detected by IgE.
Conclusion: Following this meeting, we choose to change our sublingual desensitization for desensitization with a gastro-resistant capsule. We kept in mind the available machines in laboratories and the process used by hospitals to perform an allergy test, intending to adapt our project to reality.
Portraits of the experts we met
Methodology:
Context:
Who? Jean-Luc Menardo: former allergist, pulmonologist, and pediatrician. He researched desensitization to wasp venom. He is a founder of the European Society of Paediatric Allergy and a member of the American Academy of Allergy & Clinical Immunology. He was clinic director of the Montpellier university hospital.
Why? We needed more information about desensitization as well as the opinion of a practitioner about our test and desensitization method.
Rationale:
Subjects and raised issues:
Current tests: Jean-Luc Menardo listed the current tests used by allergists for their patients. He gave us his opinion on each of them.
Prick test: the most common is the prick test because a certain number of them are reimbursed by the french Social security. Prick tests can test respiratory, food, and professional allergens. He thinks that Prick tests are a good first test because it is easy to do, results are quick to come, and make the patient understand better what are allergic reactions and their risks. It is interesting to first perform the Prick test and then test the specific IgE. The DAISY method would be first a complement to prick tests.
Biochips: according to Jean-Luc Menardo biochips are usually less reliable because of the high number of tested allergens. There are especially fake positives.
Tests of IgE total rate: he recommends testing the total rate of IgE for young children. This allows the detection of allergy risks but is useless to know what the patient is allergic to because it does not test the specific IgE.
Allergens for the tests: Jean-Luc Menardo said that tests made with recombinant allergens may be more precise than tests made with allergen extract. Indeed, the recombinant allergen allows knowing exactly which molecule is tested.
Desensitization methods: according to Dr. Menardo, there are three main administration ways for desensitization, with different characteristics:
- by injection: a big amount of allergen is injected into the system, it can trigger important reactions because a higher quantity of allergen can reach the lymphoid organs where the antibodies are produced. Injections must often be performed by a doctor and this method is not very convenient for the patient.
- by ingestion: the patient ingested small amounts of allergen. Only a little part of the ingested allergen can be used by the body for desensitization because most of it is altered by digestion.
- in a sublingual way: the penetration of allergens is very quick and efficient. There are very few incidents with this method. This is the most common and convenient method today.
Desensitization efficiency: Dr. Menardo told us that the efficiency of the patient is known after three months of treatment. Their tolerance to the allergen must increase. Otherwise, it is useless to keep trying the desensitization, because it will not work if it did not in less than three months. Allergenic immunotherapy does not work for everyone, as well as it does not work for every allergen. According to Jean-Luc Menardo, persons with multiple allergies tend to be less receptive to desensitization. It is easier for people with only one allergy.
General information about allergies: we learned that allergy symptoms are supposed to decrease with age, but today more and more adults can declare new allergies later in life. Dr. Menardo also explained that having IgE specific for an allergen does not always mean that you will have an allergic reaction when you’re exposed to it. It depends on a lot of factors such as frequency of exposure, age, the immune system… It is possible to start an allergy very late, but also to lose the allergy without any treatment.
Opinion about desensitization: Jean-Luc Menardo told us that in France, only too few people follow allergenic immunotherapy, especially for food allergies such as peanut allergy.
Opinion about DAISY: according to Dr. Menardo, our DAISY project is interesting. The allergy test should be in complement to the prick test, to identify the exact allergen the patient is allergic to, or to know their predisposition. Our desensitization method also really caught his attention. He liked the idea of using a probiotic ghost bacterium displaying allergens on its surface and thought it was innovative.
Conclusion: We learned a lot about the treatment of allergies in daily life and what can be done by a practitioner in allergology. It gave us a better idea about how could be applied our method of test and desensitization by doctors and allergists. It also allowed us to find out what allergists expect from an allergy test. The main criteria that can make our project stand out would be the efficiency, the number of tested allergens, the convenience of the test, its price, and the method of desensitization. These are the criteria that we worked on for the implementation part.
Portraits of the experts we met
Methodology:
Context:
Who? Annabelle Gordon-Le Goff: she is a doctor and biologist in a medical analysis laboratory.
Why? We wanted information on current tests performed by a medical laboratory (time, precision, price), their business model, the price of the medical act for blood collection, as well as the machines used in medical laboratories for detection.
Rationale:
Subjects and raised issues:
Current tests: ImmunoCAP™ Phadiatop™ and Trophatop™ are the most performed tests by medical laboratories. They respectively test 250 respiratory allergens using both purified or recombinant allergens, and 3 mixes of 4 to 5 food allergens. Results can be obtained in 5 to 7 days because the tests are performed at the national technology platform for allergy tests in Paris. According to the results of the ImmunoCAP™ test and Prick test, the allergist can demand to test other allergens or to test only one allergen to verify the results. Each ImmunoCAP™ costs 19.40 Euros. Cla30 is a test for respiratory and food allergens but is not very used because it is less precised.
Blood collection: it costs 6 to 7 Euros for one blood collection.
Operating business model of a medical laboratory: local medical laboratories are present everywhere on the territory and collect biological samples. They are sent to global technology platforms that will test the samples and send back the results. These results are analyzed by the biologist of the local medical laboratory and sent to the allergist.
Cytometer and FACS: technology platforms have cytometers, and some have FACS.
Conclusion: Annabelle Gordon-Le Goff provided us with a lot of useful information about current tests, the operating model of medical laboratories, and the prices.
Portraits of the experts we met
Methodology:
Context:
Who? Béatrice Jalenques-Vigouroux: lecturer in ethics and sciences of information and communication at INSA Toulouse, researcher in environmental communication.
Why? We wanted to adopt an ethical approach to design and define our project. That is why we asked for guidance in this field.
Rationale:
Subjects and raised issues:
Ethics: we discussed the main notions of ethics and how they would apply to our project. Béatrice Jalenques-Vigouroux summed up the main kinds of ethics and explained the ethical process to apply to an engineering project with some examples.
Persons to contact:she agreed that we should contact as many stakeholders as possible to collect their opinions about our project. She recommended we contact Emmanuelle Rial-Sebbag from INSERM, Michel Clanet from the ethics committee of the Toulouse university hospital, and Vincent Grégoire-Delory, specialist of bioethics at TWB.
Conclusion: We decided to look deeper into ethics and follow the ethical process she introduces us to. We contacted the persons she recommended.
Portraits of the experts we met
Methodology:
Context:
Who? Emmanuelle Rial-Sebbag: research director in bioethics and health law at INSERM. She is also a lecturer in bioethics and health law at the Toulouse medicine faculty of Purpan. Her studies focus on biobanks, innovative therapies, production, and the use of medical data.
Why? Béatrice Jalenques-Vigouroux recommended us to meet Emmanuelle Rial-Sebbag. We were questioning some ethical aspects of our project and wanted to discuss them.
Rationale:
Subjects and raised issues:
Advice about stakeholders: Emmanuelle Rial-Sebbag advised us to expose in separate ways the advantages of our technique for patients, medical laboratories, and allergists. She recommended that we ask allergists if they would agree to be trained to use our technique.
DAISY’s App:we thought about creating an app helping allergic people to live with their allergies. The goal is to give them their test results after the allergist's confirmation, as well as a pollen map, a tool to detect allergens in food composition. Their allergy profile would be personalized. They would receive notifications to take their desensitization treatment if they choose to take one, to know if their test results are available if there is a pollen alert. We discussed it with Emmanuelle Rial-Sebbag. She told us that this app would need to be approved in France by the National Health Insurance for data protection. This app would need to be very innovative with a new feature because the ones we thought about already exist.
Production of health personal data: one of the project perspectives is that we would be able to screen a very high number of allergens, and therefore know almost all the allergies and predispositions of a patient. We were concerned about data protection, as well as observing the patient’s wishes, and wanted to discuss it with Emmanuelle Rial Sebbag. We concluded that there is a possibility that the patient does not want to know everything he is or could be allergic to. In every case, the extent of the test should be openly explained to the patient for him to consent. Doctor-patient confidentiality must be observed, as well as data protection. We then thought that offering different ranges of allergens to do a screening could be a good alternative.
Use of blood:as a perspective, we wanted to test our technique on human blood to ensure its efficiency. We discussed it with Emmanuelle Rial-Sebbag. In the R&D phase, this requires special authorization. In the commercialization phase, taking a blood sample requires medical prescriptions. There should not be a particular ethical problem about this apart from personal believings.
Desensitization:according to Emmanuelle Rial-Sebbag, there is no particular ethical problem with our desensitization technique if we cleave allergens from bacteria, to administer them with adjuvants in gastro-resistant capsules. Even if the cells are empty of any DNA and intracellular content, an ethical concern could rise if we use probiotic strains displaying allergens for desensitization. We should evaluate the risk-benefit ratio of both techniques with allergists and health professionals.
Perspectives of our project:she recommended that we explore more about further developments and perspectives of our project. An important point is to study the economic aspect of our project to compare it to other tests. We should also search for information about tests on human blood and clinical essays, given that these would be mandatory steps in the development of DAISY. She agreed that the increasing allergy prevalence is a major public health issue and our project could have a huge societal impact. She thought that our technique could help detect earlier allergies and obtain better care and treatment thanks to customized desensitization.
Conclusion: Thanks to this meeting, we decided to get more information about the stakeholders’ points of view. We agreed that we have to find an innovative feature for our DAISY App.
Portraits of the experts we met
Methodology:
Context:
Who? Jasper Kamphuis: postdoctoral researcher at Infinity INSERM.
Why? His work on food allergies naturally led us toward him to have his point of view about our project, its relevance, and its design.
Rationale:
Subjects and raised issues:
Use of antibodies: he advised us about the use of antibodies and marked antibodies.
Choice of chassis: he confirmed the recommendation of Chloé Beuraud regarding the strain to use in our system.
Signalization: his remarks on our system gave us the idea to search for interactions between different microorganisms. The aim would be to have a signalization caused by the extreme physical proximity of two different organisms.
Conclusion: we kept in touch with Jasper Kamphuis during our project for specifications about the antibody to use, and to explore the field of signalization via microorganisms’ interactions.
Portraits of the experts we met
Methodology:
Context:
Who? Chloé Beuraud: researcher in immuno-oncology at Evotec, former researcher at Stallergenes Greer.
Why? She did her Ph.D. in respiratory allergies and worked with antibodies. We contacted her to have her thoughts about our first design, more information about current detection methods, and the relevance of our project.
Rationale:
Subjects and raised issues:
Chassis for desensitization: she recommended that we choose a probiotic strain such as lactic bacteria to induce a better tolerance and desensitization when administering the allergen to the patient.
Displaying of allergens: she also proposed using yeast instead of bacteria to produce allergens with better glycosylation and folding. This would help to better recognize the allergen in the human body.
Detection methods: Chloé Beuraud advised us about detection methods of the agglomerate through FRET, and FACS approaches.
Risks:she also warned us of the risks of using a patient serum with anticoagulant in our system, given that we want to observe an aggregation of bacteria.
Conclusion:Her encouraging feedback led us to choose the DAISY project as our final project among other project ideas. We kept in mind her remarks about the chassis for an extension of our project once first fully developed with E. coli.
Portraits of the experts we met
Methodology:
Context:
Who? Yvan Canitrot: researcher at LBCMCP (Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération) and expert of FACS (Fluorescent Activated Cell Sorter).
Why? We planned to use fluorescent proteins to detect the aggregation by FACS.
Rationale:
Subjects and raised issues:
FACS: he explained to us how FACS works and advised us on the process to use it with our system. He advised against the sorting of cells and recommended working with microplates with 96 wells.
Fluorescence proteins: he advised us to look for the fluorescent proteins with the highest brightness for both of the colors that we will use.
Autofluorescent balls: he recommended using autofluorescent balls of the size of bacteria single or clamped together to calibrate the device.
Suspension concentrations: Yvan Canitrot advised us to use diluted suspensions because the bacterial cells doublet can be hard to detect with SSC (side scatter) and FSC (forward scatter).
Conclusion: We determined together the important parameters to obtain the best results with FACS and had recommendations about the process.
Portraits of the experts we met
Methodology:
Context:
Who? Delphine Lestrade: manager of the flux cytometry platform at TWB, worked at Infinity INSERM on immunology and antibodies.
Chloé Habouzit: research engineer at the flux cytometry platform of TWB, worked on microbiota and probiotics.
Why? We needed to have more information about flux cytometry and its use to detect bacterial aggregation in our project.
Rationale:
Subjects and raised issues:
Flux cytometry at TWB: at TWB, six populations can be sorted, while in our project we have three. It is possible to mark the cells at TWB, which is the goal we wanted to achieve. We need to be careful with the size of the aggregates to not clog the tube. Delphine Lestrade told us that it is possible to use a cellular sieve before using flux cytometry.
Modeling: it would be useful to have a model of aggregation to obtain the estimated size and time of aggregation.
Spectral cytometer: Delphine Lestrade recommended the use of the TWB Spectral cytometer. This would allow access to the “purified” specter of the bacteria without any autofluorescence.
Coloration of bacteria: Delphine Lestrade and Chloé Habouzit suggest coloring the bacteria that display allergens using dyes. One allergen would correspond to one color. This would allow identifying allergens displayed by the bacteria without sequencing. The dyes are expensive and in a limited number, so this would only be an alternative during our experimentations.
Cytometers are common: cytometers and cell sorters are common in laboratories according to Delphine Lestrade and Chloé Habouzit. It means that our techniques do not require the purchase of new equipment.
Conclusion: Thanks to this meeting, we had a better understanding of what is possible or not with flux cytometry. Delphine Lestrade and Chloé Habouzit reinforced our conviction that the use of flux cytometry is a very relevant idea for our project. Delphine Lestrade and Chloé Habouzit helped us to conduct FACS experiments to test our method.
Portraits of the experts we met
Methodology:
Context:
Who? Emmanuelle Trevisiol: deputy director of TBI (Toulouse Biotechnology Institute) and researcher.
Why? She worked on biochips to detect patients’ specific IgE in the case of food allergies. This technology was used by the firm Innopsys.
Rationale:
Subjects and raised issues:
Biochips for IgE detection: this system allows for using smaller volumes than the ELISA test, but is still expensive.
IgE volumes: 10µL IgE is used for biochips.
Conclusion: Meeting Emmanuelle Trevisiol gave us a wider view of current detection methods of allergies. We ask her for advice about the use of IgE. We learned that the price of the test as well as the required IgE volume is two parameters that can impact the utilization and promotion of an allergy detection test by allergists.
Portraits of the experts we met
Methodology:
Context:
Who? Gabrielle Potocki-Veronese: researcher and manager of the microfluidic platform at TBI. Sophie Lajus: resercher at TBI using the microfluidics platform.
Why? We met Gabrielle Potocki-Veronese at a presentation of our project to obtain sponsorship from her laboratory. She explained to us the technology that her team was developing and we agreed that it would be of interest to us.
Rationale:
Subjects and raised issues:
New technology: she exposed the operation of microfluidic techniques, their characteristics, and their potential for our system. The technology is called CultissimDrop and is aiming to find new functions of microorganisms through metagenomic and culturomic with high throughput screening. She presented the patent that her team was working on and proposed to help us to adapt this innovative technique to our project.
How does it work: only small amounts of substrate and reagent are needed, lowering the costs. She said that because we use natural antigens, we are less exposed to false positives and negatives. In a microreactor, oil microdroplets are encapsulated with a single cell, the natural substrate, and an activatable fluorescent tag. For each microdroplet, there is one single cell according to Poisson’s law. It means that 90% of the microdroplets are empty. The microdroplets marking is done by a laser controlled by a trained Artificial Intelligence. Microscopy images are taken to train the AI. We can train the AI to recognize aggregates for our project. If an aggregate is recognized, the microdroplet is marked by activating the fluorescent tag by laser. FACS then sorts the microdroplets. A big advantage of the fluorescent protein used (Dendra2) is that it doesn't leak. AI has very low percentages of false positives and negatives (0,16 and 1,7%).
Low percentages of false positives and negatives: the low percentages of false positives and negatives are due to the precision of the laser used to activate the fluorescent tag. These results are very low, especially for microfluidic techniques.
Limiting factor: the limiting factor for the high throughput is the microdroplet observation and marking.
Conclusion: Following this meeting, we decided to integrate the use of this microfluidic technique into the DAISY project. Gabrielle Potocki-Veronese connected us with Sophie Lajus at TWB (microfluidic part), Rémi Flores-Flores at I2MC (microscopy and AI part), and Delphine Lestrade at TWB (FACS part). Sophie Lajus helped us to conduct microfluidics experiments to test our method.
Portraits of the experts we met
Methodology:
Context:
Who? Alain Liné: process engineering teacher, specializing in mixing for aggregation control. Jérôme Morchain: lecturer in fluid mechanics, research engineer
Why? We needed a specialist in fluid mechanics to consider our aggregation modeling, so the modeling tutor first contacted Arnaud Cockx and he redirected us to Alain Liné and Jérôme Morchain
Rationale:
Subjects and raised issues:
Population Balance Equation (PBE): Alain Liné explained to us how to build a population balance equation for our study case, characterized the main terms of this equation, and how to obtain them through experiments or modeling.
PBE Solving method: Alain Liné showed us how to solve a PBE, with his favorite software: Matlab. He proposed that we use the DQMOM method to solve the PBE, and helped us to implement it. Jérôme Morchain added a proposition of an equation used on the PBE to be accurate with the duality of bacteria and explained to us how to conduct a modeling strategy.
Matlab program: He supplied us with his program to solve bivariate PBE, in that way we had just to change the equation and the initial parameters and that helped us to save a lot of time coding.
Conclusion: they helped us a lot by directing our modeling strategy and giving us resources to better understand the problem requested.
Portraits of the experts we met
Methodology:
Context:
Who? Pascal Lebourgeois: professor at UPS and researcher at TBI, specialist of Lactococcus lactis.
Why? After meeting Chloé Beuraud and Jasper Kamphuis, we wanted to have more information about probiotic strains for the desensitization phase.
Rationale:
Subjects and raised issues:
Chassis for desensitization: we wanted to know if we could use a Lactococcus lactis strain as a chassis for our constructions, knowing that this microorganism is a probiotic and would make the desensitization easier and more efficient. Indeed, these lactic bacteria are used for vaccinal vectors and are classed as GRAS in the USA.
Displaying of allergens: we agreed that using L. lactis in our project would be too complicated for a proof of concept given the short period that we had. The main problem would have been to display allergens and DARPins at the bacteria surface. That is why we choose to set on E. coli as chassis to do our proof of concept.
Conclusion: We will keep in mind the use of Lactococcus lactis as a perspective for the future of our project.
Portraits of the experts we met
Methodology:
Context:
Who? Julien Durand: co-founder and CEO of Sweetech, a start-up that produces oligosaccharides using innovative fermentation processes.
Why? We wanted to benefit from its experience in start-up foundations and entrepreneurship.
Rationale:
Subjects and raised issues:
Business model: we talked about our business plan and especially about the following aspects: market segmentation, value proposal, incomes…
IVDR regulation: Julien Durand told us about laws and regulations regarding in-vitro diagnostic and medical devices.
Outsourcing: we learned that in a deep tech start-up, a lot of steps are outsourced, especially regulation and intellectual property.
Location: thanks to this conversation we learned that it is common for a start-up to rent space in laboratories at the beginning, before having private investors. A lot of financing solutions exist for deep tech start-ups.
Conclusion: This meeting was a great occasion to learn more about how to create a start-up and gave us many tools for our entrepreneurship part.
Portraits of the experts we met
Methodology:
Context:
Who? Marianne Lefèvre: she is an Intellectual Property consultant from the Adamante consulting firm. She is a specialist in patents in microbiological products and processes.
Why? We wanted information on intellectual property and patents, as it is a common step for a deep tech start-up.
Rationale:
Subjects and raised issues:
Patents: she gave us information about how to patent an invention and what steps to follow, as well as the prices of patents.
Concurrent patents: she helped to search for concurrent patents to our method.
Conclusion: We had a lot of information on intellectual property that was truly useful for the entrepreneurship section.
Portraits of the experts we met
Methodology:
Context:
Who? Le Catalyseur: a pre-incubator in Toulouse that offers to guide project promoters through the process of creating a start-up. We especially had several meetings and workshops with Colette Schenker, who was our main advisor at Le Catalyseur.
Why? Le Catalyseur is a specialist in supporting new projects and has very interesting tools and advice to offer.
Rationale:
Subjects and raised issues:
Aims and missions of the company: we defined together the aims and missions of our company.
SWOT canvas: Le Catalyseur provided us with a SWOT canvas and explains how to use it.
Business model canvas: Le Catalyseur provided us with a business model canvas and explained to us how to use it.
Entrepreneurial profile: we defined together the entrepreneurial profile of our team members to find what skills we had and which ones we needed.
Project diagnostic: we did a project diagnostic with the Catalyseur to evaluate the project progress and what was still to be done.
Conclusion: Meetings with Colette Schenker and Le Catalyseur were very useful in our project implementation, as well as for our supporting entrepreneurship part.