Team:Paris Bettencourt/Human Practices
Quaranskin - Integrated Human Practices
Introduction
Quaranskin, a combination of quarantine and skin, is an ambitious research project, combining science and societal 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 behavioral traits.
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 rationale surrounding the synthesis of this project. We start from our initial context being confined due to the pandemic and our limited possibilities. Then we head to the formation of our objectives and finally to the elements of response that we have proposed, thanks to the input of numerous stakeholders alongside our own investigations.
(Legend) Lockdown, its impact on human health, the interest for citizen science, those are the three starting pillars of our project. These led us to define the following objectives: work on the skin microbiome, comply with health precautions, and ensure data privacy protection. Concrete choices have been made to meet these objectives: the use of the Open Humans platform, Framaforms, the Personal Protection Committee, and the dissemination of kits through the post.
In order to understand the general scheme of Quaranskin 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 corynebacteria and staphylococci in moist skin regions or propionibacteria 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,sebaceous,and dry 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.
Data Analysis
From the composition, we note three pieces of information: the genus (e.g. Staphiloccocus, propionibacteria etc.), the abundance for each site, and the diversity of the site.
At the same time, we send out a questionnaire in which we collect four types of information. First about skin health, then asking personal information (age, sex, location, etc.), hygiene issues, and finally about the level of sanitary restrictions. From these last three groups, we want to construct three index, ranking between 1 and 5 (IP,IH,IS). This index should then enable us to group and treat data.
How to deal with these two sets of information?
1. Diversity analysis by index of hygiene, personal information, level of sanitary restriction
First, we are interested in the alpha diversity between genus within an individual's microbiome.
To do this, the microbiomes in the generated database are grouped by index value in each of the three categories. Then by setting two indices, we can study the impact of the third element on the diversity of the microbiome.
For example, we want to test hygiene. The groups of microbiomes corresponding to the indices of personal information IP1 and level of sanitary restrictions IS1 are fixed; then, for the groups of microbiomes with a hygiene index ranging from 1 to 5, the average of the diversities is calculated for each index. If the diversity values for each index are far apart, then hygiene (as defined here) has a significant impact on the microbiome.
2. Proportion of Staphylococcus and environmental factors
Staphylococcus bacteria are the most abundant, among the sites tested, at the elbow bend. We are looking for which environmental factors influence the proportion of its population. To do this, we define an interesting propotion threshold, then we identify all the people who present a population of Staphylococcus beyond this threshold. Once this group of microbiomes has been formed, we look for parameters common to these individuals, with the aim of identifying potentially determining factors.
3. Researching existing microbiome composition among our data set
The literature gives typical compositions for certain pathologies related to the cutaneous microbiome. Notably for eczema. We therefore want to compare a typical composition of eczematic microbiome, to our data. For data that are close to this composition, we want to question the possible symptoms or the lifestyle of the person, in order to correlate it or not to an eczema pathology.
4. Analysis of data based on common symptoms
We want to analyze the microbiome of people with skin symptoms. When a significant number of people present the same symptom, independently of the environment and lifestyle, we want to make a synthesis of the typical composition of the microbiome for this symptom.
Questionnaire
KIT - Participant actions
One of the biggest challenges of this project was to make people participate in our study from their home since we were all confined. Hopefully delivery companies were still working, so in collaboration with La Poste, national delivery company of France, we developed a pipeline in which we send to the participant deliverable kits containing all the materials needed to sample microbiome from 4 body sites following a given protocol. This kit is composed of 6 sterile cotton swabs, a prepaid letter allowing to send back the sample by mail, some labels to annotate the tubes and a Handbook.
The handbook is giving to the participant all the information about the procedure they have to follow as a Quaranskin participant, which are summarized in 3 main steps : 1. The creation of an Open Humans account 2. The microbiome sampling 3. The Questionnaire answering.
Step 1. Create an Open Humans account
Open human is a platform that allows the sharing of personal data in complete security. It is often used for studies that require the collection of personal information from participants while respecting their anonymity. Indeed, this platform allows each participant, by creating an account, to obtain an identification number to which the collected data will be linked. The files associating the identification numbers to the collected data are stored securely on the Open Humans servers, so the organizers do not have access to them. More information about Open Humans and our commitment to the protection of our participants' data is described below in the Open Humans section.
When creating their account, the participants receive an 8-digit code that they must keep until the end of the study. In order to respect the anonymity of our participants, from the moment their account is created, we only communicate with them through this platform and no longer by email.
Step 2. Sampling the Microbiome
Each participant will have to sample their microbiome from 4 body sites : the palm hand, the forearm, the antecubital fossa, and the retroauricular fold. To do so they will have to follow the detailed protocol contained in the handbook which consists of rubbing for 50 round trips the swab on a surface of 16cm2 of the area to be sampled.
As our study is based on participatory science, 70 participants will perform this protocol on themselves and not just one trained medical person. This raises the question of the variability in the protocol realization and its impact on the results. To verify that this variability does not have a significant impact on the results, we carried out a control test: One member of our team, who will be the reference for thegoodconduct of the protocol will sample all the other members of the team who will also have to sample themselves by exaggerating abadconduct of the protocol (rubbing the skin with too little pressure or rubbing the skin for only 25 round trips). If no significant difference is found between the two samples from the same member (sampled by the reference member or by himself), it will mean that making participants sample their microbiome isolated from home during the confinement can be concidered.
Step 3. Answering the Questionnaire
In parallel to the microbiome sampling, the participants have to fill out a questionnaire with information that should enable us to interpret the raw sequencing data. It would be pointless to collect data on the microbiome without knowing which individual it relates to and in what context. The aim of such a study is to generate a database in order to then question certain correlations, for example between lifestyle and diversity of the cutaneous microbiome.
During our research, we have identified four main areas of interest:
1. General information
The first criteria to be taken into account are related to the identity of the interviewee. Studies show that age and gender are important intrinsic parameters. We also ask in the questionnaire the city of residence to study the microbiome according to geographical distributions
2. Potential skin disorder
As we look at the microbiome at the microscopic scale, we think it’s important to link what we observe to effects at a macroscopic scale. We hope that we could see some trend that emerges as a sign of an imbalance anomaly which would be associated with a skin disorder. That’s why we ask the participants if they have some skin anomalies. We distinguished between so-called diagnosed anomalies (e.g., eczema, psoriasis, acne) and symptoms that are not related to an identified disease. They can be redness, irritation, pimples, oily, wet or dry skin. We also ask them if these symptoms are present on one of the four body sites analyzed (palm of the hand, forearm, antecubital fossa, retroauricular fold). In addition to that, we include a temporal notion, we want to know how these symptoms have evolved over a period of time.
3. Hygiene
In the set of changes in lifestyles brought about by the pandemic, we wanted to detail the influence of hygiene. More specifically, we ask about the frequency of thorough washing (shower) and hand washing because soap obviously alters the microbiome and its regeneration. Too many washes can have a negative impact, especially for some sensitive people.
(In this case, the washes are for the destruction of the virus, absolute priority, without regard for the health of the microbiome.)
4. The level of confinement
This last part aims to quantify the level of confinement of a person based on qualitative data. The state of isolation is judged according to the number of people encountered on average daily, and during the last 24 hours, with a certain level of proximity. Secondly, it is assessed in relation to the number of places frequented (homes, workplaces); then the transport used (metro, bicycle, etc.). Finally, the last criterion takes into account a person's activities (going out in enclosed areas - cinema, bars - etc.).
In addition, we want these last three criteria to be quantified in the form of an index.
Ethical Considerations and Administrative Authorizations
CPP Introduction
As Quaranskin is a collection of data extracted from human derived samples (skin microbiome) and personal information (answer to the questionaire), it was important for us to learn about the ethical rules that govern research in Europe in order to respect the protection of the participants in our study.
In France, Research Involving Human Being (RIPH) has to be approved and framed by the Committees for the Protection of Persons (CPP).
The CPP are approved by the Minister in charge of health for a period of 6 years and have a regional competence. The members are appointed by the Director General of the Regional Health Agency for a renewable period of 3 years.
The CPP are responsible for issuing a prior opinion on the conditions of validity of any research involving the human person. The favorable opinion of a CPP is essential to be able to start a research. The Committees give their opinion on the conditions under which the promoter of the research ensures the protection of persons and in particular participants, the merits and relevance of the research project, and its methodological quality.
To get the approval before starting our Quaranskin study we had to submit a file presenting the project for reviewing by z CPP.The documents include a research protocol, information note and consent form, authorization of research site, letter requesting notification, GCP certificate, CNIL declaration, and a summary.
Research Protocol
The most important element of the administrative file is surely the research protocol. This is what the committee first judges in order to give its opinion on the merits and sufficient conditions to enter into legality and respect the rights of individuals. This implies making a detailed description of all the stakeholders, their different roles, the methodology used, the criteria used, etc.
Such a protocol must follow a well-defined framework.
Firstly, we needed to provide administrative information, where the notions of promoter and investigator are fundamental. The promotor is the natural person initiating the research involving the human being; the latter must have a permanent research position in a European country. The investigators supervise and direct the carrying out of the research: they must have a certificate of Good Clinical Practice. We therefore had to obtain it.
Secondly, we had to present the context of the research, the starting points, our inspirations, and almost all thestate of the art of the study.
Then, the objectives, main and secondary, must be detailed. These must be justified by a specific context and judgmental criteria that make them achievable.
Finally, the protocol must include the organization of the study: the steps, the timetable, the methodology, and the analysis.
Information Note
This document is for the attention of the participants. This is the doucment that informed them about the precise execution of the study, their task, their constrains and their rights. It's the document that allows them to take the decision to take part or not in the study before signing the consent form.
1. In the note of information several points must be informed:
2. The objective of the study
3. Inclusion and Exclusion Criteria
4. Key steps in the study, data processing and storage
5. Potential risks and side effects
6. Cost and financing
7. Contacts in case of problems
8. Privacy and data protection
9. The rights of participants
The briefing note must be both the clearest and the most detailed, requiring a formative work of synthesis and explanation.
Open Humans
Discussions with Bastian Greshake Tzovaras and Mad Price Ball
After discussions with several experts, we realized the importance of a robust anonymization and data protection system. This is how we discovered Open Humans, and got in touch with platform administrators Bastian Greshake Tzovaras and Mad Price Ball.
Open Humans is a source-based software program that is one of the programs of the Open Human Foundation, a non-profit organization based in the United States. This organization provides digital tools that allow individuals or communities to use and share their personal data for educational, health or research purposes. It is the organization that operates and manages Open Humans, whose project is to facilitate the participation of individuals, citizens, in scientific research or "citizen science" projects.
The servers used by Open Humans for data storage use state-of-the-art security measures; they are protected by a firewall, and operate with high-level encryption to ensure data confidentiality and security. Data processing complies with US and European Union data protection regulations.
For those reasons, we were enthusiastic to start collaborating on the platform.
Human Practices
Introduction
We have set up a large-scale project for the collection and analysis of the cutaneous microbiome involving many citizens, along with partnering with an open science initiative and complying with French ethical standards for such work.We had many exchanges with several actors, which set up our pipeline to include the following actors: the Open Humans platform, a questionnaire on Framaforms, a file submitted to the Committee for the Protection of Persons.
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 overall project. Synthetic biology researchers with expertise in the 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. The procedure for the approval of our study has illuminated the complexity surrounding personal data and its collection. In an era where metagenomics and genomics increasingly involve lay people, the question of the safety of one's sequence data is increasingly relevant.
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. The link between health and social behaviours, exacerbated or altered by the health crisis, stands at the core of the Quaranskin project. In the continuity of the project, we keep in mind the potential implementation of SynDerma, which consists of opening new avenues for skin therapies. 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 health care 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 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 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 wasimportant to meet a skin expert in
the
medical sphere, to learn more aboutpatient feedback during lockdown. Which
populations
were the most vulnerable? And on the other hand, what wasthe 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
verylittle 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 alsoenvironmental 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 backgroundafter 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 and getting sponsoring
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!
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.