Team:Paris Bettencourt/Human Practices
Quaranskin - Integrated Human Practices
Introduction
Quaranskin, contraction of quarantine and skin, is an ambitious research project, combining science and society issues, which we wanted to promote as an integrated Human Practices project. The project is based on the collection and analysis of skin microbiome samples, collected from participants across Europe. The analysis and the answers to an online questionnaire should allow us to correlate the composition of the cutaneous microbiome to certain lifestyles.
Although the project has undergone its first phase of construction and preparation from the end of April to October, Quaranskin still has its future ahead of it, with the analysis of the samples by a sequencing company, subject to the approval of an ethics committee, which is still pending.
The map below gives a representation of the three logical steps that allowed us to build our project, starting from our initial context related to the pandemic and our limited possibilities, to the formation of our objectives, to the elements of response that we have proposed, thanks to the light of numerous research and stakeholders.
(Legend) Lockdown, its impact on human health, the interest for citizen science, those are the three starting pillars of our project. These fundamentals then led us to define objectives: work on the skin microbiome, compliance with health precautions, maximum levels of data protection. Concrete choices have been made to meet these objectives: the use of the Open Humans platform, Framaforms, the Personal Protection Committee, the postable system of kits, and others.
In order to apprehend the general scheme of Quaranski as we have organized it, here is the procedure from a participant's point of view.
For more information on the genesis of the Quaranskin project, its conception as a Human Practices project in the middle of lockdown, how we have involved citizens, the challenges that have arisen, and the future of Quaranskin, click on the PDF below!
Relevance of the Quaranskin project in skin microbiome research
The project Quaranskin serves to add to the body of work on the skin microbiome. The human skin microbiome refers to the microorganisms that occupy the human skin at the level of the hypodermis, dermis and epidermis. Existing literature has revealed the human skin microbiome to be highly particular to the individual in relation to the specific composition of the bacteria that reside at particular body sites, however, there is an established trend into the taxonomic specificity for various body sites such as Coryne bacteria and Staphylococci in moist skin regions or Propioni bacteria in sebaceous regions1.
The analysis of bacterial composition of the skin microbiome has been revealed to be an important consideration in the context of skin health. For instance, individuals presenting with acne vulgaris, tend to have less diversity in their microbiome profile as opposed to their unafflicted counterparts. Another feature in acne flares is an overrepresentation of certain strains of Cutibacterium acnes which is a family of bacteria that normally resides on the skin in a non-pathogenic manner2.
In atopic dermatitis a similar phenomenon occurs where there is a decrease in overall microbial diversity at skin lesions and high representation of Staphylococcus aureus. The term for deleterious alterations of the microbial flora is a dysbiosis, however, there is little understanding of the factors that cause dysbiosis3.
The current understanding of the skin microbiome, sampled from human volunteers suggests that in general the microbial composition and diversity of the skin microbiome is temporally stable4. These studies are based on sample sizes from 10 to 40 people, and many are based on North American subjects. Summarily, current evidence suggests a greater microbial diversity to be a beneficial trait, however there is a need for greater diversity in the participant pools from which this data is derived.
In our work, we aim to understand if there are correlations between behavioral characteristics that involve activity, hygiene and human interaction, and the diversity and composition of skin microbes at four body sites. The general rationale is that if these behaviors alter the physical conditions of the skin they could change how favorable the skin environment is to the organisms that reside there, thus causing a change in the relative diversity of some species over others.
To investigate this we will take advantage of the current global environment wherein a significant number of people are minimizing their interactions with other people, and recruit volunteers residing in Europe, to swab their skin microbiomes for metagenomic analysis. We selected four body sites to sample which represent different physiological “biomes”, namely moist,sebaceousanddry areas of the skin. Using 16S sequencing (to be performed by an external company), we will be able to assess the general bacterial composition of each site within individuals as well as the relative diversity within each skin site.
Human Practices
Introduction
On the one hand, our values, our resources, everything that made our project responsible.
On the other hand, the integrated Human Practices part, in which we have set up a large-scale project for the collection and analysis of the cutaneous microbiome involving many citizens and other stakeholders.
This complex part, we had many exchanges with several actors, which led us to make choices: the Open Humans platform, a questionnaire on Framaforms, a dossier to be submitted to the Committee for the Protection of Persons.
On this page: our values, a responsible project for the world; our exchanges with stakeholders.
Through our project, we called upon health professionals, who spoke to us from a medical perspective, who encouraged us to probe certain aspects, and from which we designed main ideas of our Quaranskin project. Synthetic biology researchers with expertise in cutaneous microbiome also helped us validate the relevance of our laboratory project and helped us build a trajectory for the wet lab.
Since an important part of SynDerma is based on Human Practices, we have had numerous contacts with stakeholders from the safety, ethics and legal fields, which have enabled us to understand the issues raised by research involving human beings and to respond to them using the best tools. This has led us in particular to put together a dossier and to convene a Committee for the Protection of Persons(CPP), which delivers an assessment of the validity and ethics of the study.
Team Positioning
The values and positioning that we defend through SynDerma are both scientific and societal, with an emphasis on the implementation of our ideas in practice. The choice to study the skin microbiome is first and foremost a reflection of our interest in human health, and more specifically in the link between health and social interactions, exacerbated by the health crisis, and at the heart of the Quaranskin project. In the continuity of the project, we keep in mind the potential implementation of SynDerma, which consists in opening new avenues for clinical research around eczema. The work on the cutaneous microbiome is particularly interesting, in that it is necessary to apprehend the whole entity within a complex ecosystem, an approach that we think is essential today in many areas of research.
At the same time, our approach is in line with the development of technology as a progress in the service of the living, and the use of bioengineering to solve tomorrow's problems. It is in this spirit that we have developed the project to build a MoClo kit for S. epidermidis and the SynBio projects EpiGrow, EpiFlex, EpiGlow. Such a project contains at the same time the will to produce useful and safe to use tools for research.
Finally, both the Synbio and Quaranskin projects demonstrate our willingness to contribute to synthetic biology research on the cutaneous microbiome, by means of biological engineering, or the creation and processing of data collected from individuals.
Reaching out to legal experts for Data Protection
Given the security and ethical issues raised by the Quaranskin project, we wanted to get in touch with several people with expertise in this field.
Piers Millett, iGEM Security and Safety Committee
By the end of May, we met Dr. Piers Millett from iGEM Security and Safety Committee. Our first inquiry was whether such a project was possible under iGEM framework, which he immediately confirmed. He brought us to make the distinction between ethics and safety, and highlighted the need to have an agreement from an ethics committee, at least at the level of our institution, as well as the importance of communicating in a transparent way on our protocol and our intentions.
During this discussion, the idea emerged to focus on French and European teams and to develop real partnerships, where several iGEM teams would work on Quaranskin at the same time and equally. This would have allowed us to obtain more diversified data, and it was a unique opportunity to create a multi-national iGEM team during this generalized confinement to almost every country! Unfortunately, we were unable to find a team that was willing to work with us on this project. Perhaps this is a new prospect for 2021?
Christine Dosquet and Benoît Marin
At the end of May we also reached out with Dr. Christine Dosquet, President of the INSERM's Ethical Evaluation Committee, and Pr. Benoît Marin, from the Ministry of Health and Solidarity. These exchanges enabled us to learn which legal categories our project referred to and which procedures we had to follow.
Jean-Christophe Thalabard
Finally, we met Jean-Christophe Thalabard, a former member of the INSERM ethics committee. He gave us clues to constitute a file to be submitted to the Committee for the Protection of Persons (CPP). How to set up a system for collecting personal information that respects the anonymity of individuals with a sufficient level of security, what questions can be asked, what procedures respect French and European law, are all questions for which Mr. Thalabard has provided us with guidance.
Reaching out to Healthcare Professionals
Interview with a pharmacologist, Céline Couteau
At the beginning of June, we had the opportunity to get in touch with Mrs. Céline Couteau, working in an industrial pharmacology and cosmetology laboratory in Nantes, and specialized in cutaneous microbiome. During this interview, we were able to better define the stakes of the Quaranskin project; in particular the importance of hygiene, of the aspetized interior.
Soap washes impact on skin microbiome
This is a problem that existed long before the health crisis, but which has been amplified considerably by the injunction to respect "barrier gestures". It is a problem insofar as soap sanitizes the skin; by washing the hands, the cutaneous microbiome of the hands can be damaged.This is why we developed the idea of taking the microbiome from the palm of the hand, which should be particularly affected in these times of COVID-19 spread, and asked detailed questions about the frequency of washing (hands and body).
In addition, not all soaps have the same action on the skin: syndet, hydroalcoholic gel, different types of common soaps. One idea proposed by Ms. Couteau was to study the impact of the soap used (with the brand of the product) on the skin flora, by noting the cutaneous microbiome of the hand before and after use.This is why we developed the idea of taking the microbiome from the palm of the hand, which should be particularly affected in these times of COVID-19 spread, and asked detailed questions about the frequency of washing (hands and body).
In addition, not all soaps have the same action on the skin: syndet, hydroalcoholic gel, different types of common soaps. One idea proposed by Ms. Couteau was to study the impact of the soap used (the brand of the product) on the skin flora, by noting the cutaneous microbiome of the hand before and after use.This was not feasible; however, as a result of this exchange, a distinction was made between washing with soap and hydroalcoholic gel in the Quaranskin project questionnaire, and the use of moisturizers.
Time spent in sanitized interiors impacts on skin microbiome
Another aspect discussed during this interview, which influenced our approach to Quaranskin, was the impact of cleaning products and the atmosphere in the home. Indeed, the various confinements and sanitary restrictions push people to spend much more time inside their homes. The use of cleaning products of various qualities and proportions, air conditioning in the summer, clothing, or other elements of the modern home, can lead to damage to the microbiome balance. This led us to ask participants about the number of homes or workplaces they attended, and the time spent indoors. This aspect is particularly important for vulnerable people with allergies, or eczematous people for example.
One possible solution was to design a probiotic cream adapted to fragile people. This was a first step towards our Synbio project, in which we are engineering a bacterium involved in numerous imbalances in the skin microbiome: S.epidermidis
Interview with a dermatologist, Stéphanie Leclerc-Mercier
In mid-June, we met a dermatologist from Necker Hospital in Paris, working in the field of laboratory analysis of skin-related pathologies. We contacted her following an article published in theExpressdealing with the cutaneous microbiome during confinement. Through our SynDerma project, we thought it was important to meet a skin expert in the medical sphere, to learn more about patient feedback during lockdown. Which populations were the most vulnerable? And on the other hand, what was the status of probiotic use in medical skin care and clinical research.
The cutaneous microbiome in dermatology
Despite its known involvement in many skin-related pathologies, the microbiome is very little studied in dermatology
The most widespread pathologies are acne, psioriasis, eczema - the latter surely gathering the most data on skin flora. Many factors are recognized as impacting these diseases, such as stress or hypersensitivity. Some populations are therefore more at risk than others. This observation led us to reflect on the role of the cutaneous microbiome. The fragility of certain individuals in the face of these pathologies could be correlated to a poor balance of the microbiome ecosystem, and this by intrinsic factors, but also environmental and behavioral factors. Hence the idea of studying the composition of the cutaneous microbiome in relation to geographical location, people's activities, time spent in confined spaces or interactions with a person's entourage.
Use of probiotics in medical care
According to Stéphanie Leclerc-Mercier, probiotics were used about ten years ago in dermatology, before being relegated to the background after a few years of enthusiasm. Their ineffectiveness was due to the resilience of the skin microbiome preventing the action of the probiotic. The discussion that followed allowed us to identify two important concepts for SynDerma. The first, if we want to eventually apply probiotic care, it is imperative to study the global ecosystem. It is in this sense thatwe developed an artificial skin model part of the EpiGrow project, which we unfortunately did not have time to implement. Such a support could be an interesting way to study population dynamics between certain bacteria of the microbiome.
The second key idea that shaped the SynDerma project is the use of synthetic biology to address the issue of probiotics in medical care. By developing the Quaranskin project on the one hand, and the EpiFlex and EpiGlow projects on the other, we are building tools to meet a current clinical need that has remained unresolved over the past few years.
Reaching out to commercial companies
The keystone of the Quaranskin project is the sequencing of microbiome samples by a company.
Finding a company that could perform DNA extraction and sequencing of the 16S region from swabs at affordable prices has been an arduous task.Finding a company to sponsor the project
The challenge was to find a company that could perform DNA extraction and sequencing from mailed swabs. From a technical point of view, our constraints are important: the sampling is carried out and stored dry. From a financial point of view, the price of such a treatment, for nearly 300 swabs (60 participants, 4 body sites), is out of reach for our team. It was therefore necessary to negotiate a discount. For this reason, we had to contact many companies and discuss the conditions with each one. This work lasted several months, from the beginning of May to the end of July. Through the Lyon-based company Biofidal, via Dr. Agnès Nguyen, we were first able to have four samples tested to test our pipeline. This taught us the basics of doing business with this kind of company. Unfortunately, Biofidal being too small a structure, it could not sponsor our project. We then went in search of other companies! We found the company LC Sciences, based in Texas; talking to Dr. Chris Hebel, responsible commercial manager, even though he offered us the best prices, the transportation and uncertainty about the opening of the borders discouraged us. Then we met Dr. Axel Strittmater from the Swiss company Fasteris, which could unfortunately only offer sponsorship for sequencing and not for extraction. Finally, through Dr. Valérie Antonio, we were able to enter into a partnership with the company Genewiz, which gives us a 50% discount on all processes, for a price of about 25,000€!
During all these discussions, we were able to refine our protocol, by asking questions about the shelf life of the swabs, storage conditions, extraction and sequencing protocol.
Shipping company
In the meantime, we have been looking for a partnership with a postal system. The challenge is to be able to send shipments throughout Europe, which contains a prepaid return shipment. We finally made a contract with La Poste, through Mrs. Céline Munoz.