OptogenEYEsis is a multifaceted project dedicated to vision restoration. Our objectives encompass identifying novel opsins, enhancing their properties through directed evolution, and creating a specialized tool for opsin characterization. Our innovative, cost-effective hardware and software combination automates experiments on a plate, while our commitment to human practices revolves around considering the impact on all stakeholders, especially the patients. Our approach is organized into three key axes:
The OptogenEYEsis project is driven by a set of core values that encompass environmental, social, moral, and scientific considerations. At its heart, the project is inspired by a commitment to healthcare and improving the lives of individuals with vision disabilities.
The values that underpin the project include:
The OptogenEYEsis project takes responsibility seriously in various aspects of its work. This includes:
The project embodies responsiveness in multiple ways:
Important and inspiring sources which guided us to build our project and rethink our project human practices aspects:
According to World Health Organization (WHO) statistics, 2.2 billion people worldwide suffer from blindness or visual impairments. The primary causes of these conditions are refractive errors and cataracts. These visual impairments not only result in a colossal loss of productivity on a global scale but also significantly impact the daily lives of affected individuals, particularly affecting their sense of direction.
Numerous organizations, such as the Valentin Haüy Association and the French Federation of the Blind, have implemented initiatives to restore and enhance the independence of these individuals, allowing them to reintegrate into society. These efforts encompass teaching them to prevent falls and, for example, to learn Braille.
Furthermore, a range of tools and technologies have been developed to facilitate the lives of visually impaired individuals. For instance, Ceciaa offers reading pens, and SonarVision has created a highly precise Google Maps-like system to guide the visually impaired with precision down to the centimeter.
When considering authorized medical treatments, it becomes evident that there are limitations. In France, surgery, sometimes accompanied by grafts, is the most commonly used method, as practiced at institutions like the Rothschild Foundation. In the United States, surgery is often complemented with artificial tissue implants, such as intraocular artificial lenses, for procedures aimed at removing cataracts or correcting refractive errors [6]. However, these interventions do not provide solutions for rare or severe eye diseases, highlighting the necessity of ongoing research in this field. The Retina Foundation, for instance, is actively working on various fronts, including gene therapy, cell therapy, and intra-vitreal injections.
Gene therapy is gaining traction worldwide. While it was first authorized in China in 2003 with the medication Gendicine, it was only accepted in Europe in 2016 with Strimvelis. Gene therapy has not yet been authorized in France, however the FDA in the United States recently approved gene therapy for a retinal disease, marking a significant step toward the broader use of such practices [7].
In this context, the gene therapy project we are working on, aiming to produce modified opsin proteins capable of being placed in retinal cells to restore vision for patients suffering from blindness or vision loss due to a loss of photoreceptor cells, appears to align with promising research in the field.
In discussions with the communication department of the Valentin Haüy Association, among others, it became clear that in France, even individuals sympathetic to the cause of the blind and visually impaired are not fully informed about the latest developments in this field. The focus remains primarily on assisting and managing the challenges faced by these individuals rather than on their complete recovery. It's worth noting that opinions on gene therapies, in particular, are mixed, as they represent expensive, novel treatments still in the research stage, and although results are promising, they may not yet be entirely convincing. In the clinical trial known as "Reverse," which involved 37 patients, researchers demonstrated the effectiveness of this approach by measuring substantial clinical improvement. Specifically, they found that injecting the gene therapy vector into one eye led to bilateral vision improvement in over three-quarters of the patients [8].
Optogenetics is a method that allows the manipulation of neuronal activity through light exposure. This technique relies on the use of photosensitive proteins, which are inserted into cells that are not naturally light-sensitive, especially in the human retina. By incorporating light-sensitive proteins into such cells, it becomes feasible to control their activity by exposing them to specific light sources. Consequently, optogenetics holds promising avenues for research and treatment of various neurological diseases and vision impairments.
By definition, optogenetic therapy is a gene therapy: this means one should be very careful about what exactly is the pursued aim, who would benefit from it, and what risks they encounter. Moreover, the potential for misuse, or harmful second use, must be thoroughly examined to ensure that the benefit-to-risk ratio justifies the development of this critical medical technology.
The tool we build is designed to firstly facilitate the identification of natural opsins in a quick and straightforward manner and secondly characterize their potential for optogenetics applications. The opsins showing particular potential are thus considered for potential vision restoration.
As a group, our initial intention has always been to help people with vision disability, because of the day-to-day handicap it represents for so many people. The construction of our project has been done through internal reflections and expert stakeholder consultations, to finally arrive at our current work. The path of thoughts we followed and the questions that were raised along the way is described in this section.
The first spark of the project emerged to find applications and extend the work of our iGEM Evry Paris-Saclay 2021 team. Our work was centered on directed evolution, a method in protein engineering that mimics natural selection to steer genes towards desired outcomes. Inspired by this work [9,10], we incorporated specific domains to facilitate mutation insertions.
At the heart of our system, named Evolution.T7, is the innovative fusion of two enzymes: the T7 RNA polymerase (T7RNAP) and base deaminase (BD). While T7RNAP transcribes DNA into RNA, the base deaminase modifies DNA bases.
Together, they collaboratively introduce random but controlled in space DNA mutations, ensuring these changes occur specifically between the T7 promoter and its terminators. This year, we aim to further use this system to discover opsins that are not only more sensitive to light but also shift towards the red spectrum, approaching the 700 nm wavelength. Having such a powerful genetic tool in our hands, we naturally desired to use it for good.
This first idea was complemented by two consultations with professors, who helped us refine our problem. The first interview was done in person with Professor Sylvain Fisson, researcher in neuroimmunology, ophthalmology and genic therapy and professor of immunology at University of Evry Paris-Saclay. This consultation helped us explore ideas, constraints, opportunities and risks associated with the project, and resulted in the following key points:
This discussion led us to the reevaluation of initial methods and goals, and to take good care of keeping the patient’s health and safety in mind.
The second interview was done remotely by video-call, with Professor Christelle Monville, biology professor at University of Evry Paris-Saclay and team leader of the Retinopathies team at I-Stem Institute. Retinopathies is working on the development of innovative therapies for the treatment of genetic pathologies that affect the retina. The discussion centered on the team's optogenetics research project, focusing on the integration of stem cells and opsins:
This exchange strengthened our faith in the potential of our method, and allowed us to precise the orientation of our project.
Having such experts assessing and validating the quality of our method has been a crucial point of the project, at which we could project ourselves further in the development.
As we developed our project, a crucial question came: who will benefit from our discovery? To answer this, we looked at advanced vision therapies and the key challenge they share: their often high cost, which puts them out of reach for many people, especially in developing countries.
In thinking about accessibility, it's essential to consider how these therapies fit into the different stages of vision loss. For example, gene therapy shows promise when used early on when cells are still present but not functioning correctly due to genetic issues. It involves the injection of a functional copy of a specific gene into the retina, aiming to repair the damaged photoreceptors. The associated causes of disease are various, and many genetic mutations may be the source of this impairment, some of them being congenital. But, gene therapy's potential is limited by its high price and limited availability: each injection can cost several hundreds of thousands of dollars (which is covered by social security in some countries).
On the other hand, as we reach later stages of vision loss when photoreceptors have mostly or entirely stopped working, we turn to alternative therapies like optogenetics or cell transplantation. These approaches aim to restore vision by introducing light-sensitive proteins or replacing damaged cells. For example, the company Pixium Vision develops the Prima implant which allows patients affected by age-related macular degeneration (AMD) to recover about 1/20th of their visual acuity which allows them to read (an estimated 200 million people are estimated to have AMD [11]). As explained on the Institut de la Vision website, patients wear glasses with a camera that sends images to a microcomputer in their pocket. The visual information is converted to electrical signals and transmitted to a chip, which sends these signals to nerve cells of the retina that relay them to the brain. This solution is still in late development and no official cost was disclosed, yet it is expected to be high, though potentially reimbursed by social securities as there exist currently no treatment for sight restoration of AMD.
It is estimated that 700 million people affected by vision impairment in the world could benefit from treatments [12]. Statistics also reveal that many people, particularly in developing areas, suffer from "preventable blindness", with 80% of blindness being avoidable [13]. Our project aims to address these disparities and advocate for better global access to affordable advanced vision therapies. We strive for a future where these life-changing treatments are accessible to everyone, no matter where they live or their economic circumstances, allowing more people to regain their sight.
The OptogenEYEsis project aligns with the innovations mentioned above, aiming to restore color vision, something currently not possible given that current opsins are sensitive to blue, yellow, and violet light, but not red. In this sense, it suffers the same drawbacks as existing solutions, but we are convinced that more research and publication of more results will transfer into lesser cost in time.
As a matter of fact, drug development is structured in such a way that initial research is extremely expensive due to its high uncertainty [14]. When an actual treatment is found, its initial cost is often colossal, for a variety of reasons: it amortizes part of the research and development cost invested, but it also reflects a monopoly or oligopoly situation due to technical superiority, or due to patents. For this reason, continuing research allows other companies to have a better understanding of the treatment, and therefore diminish the cost for patients (and/or states that have social security) in the long run. Far from being reserved to a minority, we hope that our findings will serve and improve future treatments against vision impairment, a situation that affects a large portion of the world population.
As we propose to improve current vision restoration methods, our method inherits from the ethical debates that naturally arise from genetic therapy. In particular, it is crucial to understand what border separates actual deficiency and human augmentation. This question is well developed in “At the risk of the human: the suicidal promises of transhumanists”, written by Agnès Rousseaux, journalist specialized in technosciences, and Jacques Testart, physician and researcher behind the first in vitro fertilization baby. While restorative medicine seeks to ensure the proper functioning of the human body, human augmentation raises the spectrum of a separation between non-augmented humans that we know and a new (kind of) species: the augmented ones. This implies blurring the symbolic boundary of the human body, in particular if technologies become connected to the human brain: humans become a sort of patchwork of components, a mix of organs and electronics. On top of this, one can argue that augmenting humans while others suffer from a lack of some basic senses is outrageous.
While the concerns about the potential creation of augmented humans is critical, we must keep in mind the immense potential for good that genetic therapy offers [15]. It has the power to alleviate the suffering of individuals affected with devastating genetic diseases and to prevent the transmission of such conditions to future generations [16]. This leaves us with an ethical responsibility to use this technology to its fullest extent, as long as it is employed with informed consent and stringent regulatory oversight. Genetic therapy could moreover contribute to reducing healthcare costs in the long run, diminishing treatment costs by solving genetic issues early enough not to have to treat patients afterwards. In our societies relying ever more on screens, videos, and texts, it is more fundamental than ever to help the excluded ones.
More specifically about our project, while our aim is to restore an accurate color vision, our findings could be reused to produce opsins that capture different wavelengths than a typical human, allowing for new perceptions of colors. Although real, this risk needs to be put in perspective with the cost of development, and the risk and unknown consequences it implies for potential subjects, most of whom would have a functional vision. Compared with the tremendous amount of visually impaired people, the risk of augmenting vision to a restricted amount of people seems very limited: we as a team are convinced that the potential of misuse is low, and will not exist in the near future, with a high degree of certainty.
While we navigate the ethical questions of genetic therapy, we insist on the need to keep in mind the balance between benefits and risks, to foster dialogue with experts, and engage a diverse array of stakeholders to make sure the treatments are parsimoniously used.
In the realm of synthetic biology, experimental procedures have traditionally been synonymous with tedious pipetting, high-precision operations, and countless hours of human intervention. These practices can introduce room for errors, increase labor time in often uncomfortable positions [17], and therefore slow down research progress. Our iGEM team recognized these challenges and has developed an innovative solution to address them. With a vision of creating a more efficient and user-friendly experimental environment, our digital microfluidics hardware is designed to replace traditional test-tube-based procedures.
When one thinks about technological disruptive innovations, the immediate image is that of groundbreaking change, a paradigm shift that redefines how the whole field functions. However, the consequence of such rapid innovation often involves the potential obsolescence of existing technology and methodologies [18]. This not only poses economic challenges but also rings environmental alarms. For instance, transitioning labs across the globe to adopt new instruments could result in significant waste and environmental burdens, as older equipment becomes redundant. Nonetheless, our innovation also holds the promise of democratizing access to scientific tools and knowledge. Our digital microfluidics hardware is not just a new tool reserved for wealthy and large corporations. We believe that, due to its cheap design and high modularity, it will help researchers, especially in emerging countries.
The cost barrier in science is, unfortunately, a significant obstruction to progress [19]. Researchers with bright ideas in regions where financial resources are constrained often find themselves unable to partake in global scientific discussions purely because of a lack of access to affordable lab equipment. By introducing low-cost, efficient solutions like our digital microfluidics hardware, we are leveling the playing field. This democratization means that more people, regardless of their economic background or geographical location, can contribute to scientific advancements.
Democratization does not merely amplify the number of voices in the scientific community; it diversifies them. By allowing individuals from underrepresented backgrounds and emerging countries to participate, this could, for instance, help to reduce the predominance of caucasian patients in clinical trials [20]. Furthermore, as more people gain access to research tools, there's potential for solutions that are tailor-made for local challenges and communities.
Environmental implications of technological shifts are undeniable and must be addressed responsibly [21]. However, by reducing barriers to entry in scientific research, the hope is to contribute to the democratization of biological science as a collective endeavor.
Acceleration in the field of research has a two-fold outcome. On one hand, rapid advancements can lead to breakthroughs that address critical issues and help the development of life-saving treatment. On the other, the pace of innovation and increased accessibility could lead to potential misuse, with new tools possibly finding their way into the hands of those with malicious intentions.
To harness the advantages while mitigating the risks, the proposed hardware/software solution includes the establishment of a community website. This platform will allow individuals to share their experiment designs and findings, similar to protocol.io. However, it won't be a complete free-for-all: the shared "experiment recipes" will undergo review by the community to ensure adherence to ethical guidelines and no undue risks. This moderation process will involve volunteers, similar to Wikipedia, with experts stepping in for severe conflicts. This ensures that only scientifically sound and ethical experiments are shared with the wider community.
Having an open tool with accessible experiments can help improve reproducibility in biology [22]. Firstly, by minimizing human error during manual procedures, experimental precision is increased. Secondly, by maintaining an open platform, one can share their procedures and receive corrections from others, benefiting everyone. Thirdly, as the proposed digital microfluidics hardware is affordable, many teams can reproduce the same experiments, ensuring consistent research results.
It's crucial to note that the risks associated with misuse in an accelerated research environment aren't fundamentally different from those in traditional research methodologies. Even with classic biology tools, misuse has always been a potential concern. The key lies in rigorous checks and balances. By using a combination of community and expert moderation, and imposing ethical guidelines on the community website, the aim is to equalize or even reduce the risks of misuse compared to traditional biology. The vision is to foster responsible innovation, ensuring that speed doesn't compromise safety or ethics.
Like countless other fields that have been deeply modified by mechanization, the world of biological experimentation is no exception [23]. With the advent of generative AI, even more tasks that once required a human touch can now be automated [24]. It raises the looming question: Are we making certain roles obsolete?
While automation might seem like a threat to human employment, it is crucial to consider the tangible benefits it brings to the experimenter. In wet labs, researchers often find themselves manipulating hazardous biological materials, a task fraught with risks, and which can result in dramatic consequences [25]. By delegating such tasks to machines, we're not just making processes faster; we're making them also safer. Moreover, the physical demands of a wet lab are often understated: researchers sometimes stand up for more than 10 hours a day, and often in wrong positions. This can lead to a myriad of health issues over time, from musculoskeletal problems to fatigue-related errors [17]. Automation, in this context, is not just about efficiency but also the well-being of the scientists.
It's important to emphasize that while our digital microfluidics hardware automates many processes, it doesn't put a cap on human responsibility and creativity. Automation tools, like our hardware, provide a consistent and efficient way to perform standard tasks on top of which researchers can test their hypotheses and experimental tweaks. The flexibility of our hardware allows experimenters to adjust parameters and explore new experimental settings: by taking care of the repetitive and tedious tasks, our hardware gives researchers the time and mental space to test new ideas, think critically about their results, and delve deeper into creative problem-solving. On top of this, we make the deliberate design choice to never take the power from the researcher, even when the hardware is used with our software. More details are available in the following section.
In academic life science labs, manual protocols dominate due to funding structures, protocol variability, and a culture of investing in people over equipment. While automation offers reproducibility and efficiency, it poses challenges such as obsolescence and reduced innovation. To enhance automation adoption, more flexible, cost-effective designs are needed, considering environmental and financial constraints. Future scientists should possess engineering, programming and biology skills to harness laboratory automation's potential in addressing research questions [24].
One of the key benefits of employing a vocal assistant like Thalia, the one we developed in our project, is that researchers no longer require extensive programming abilities to automate their experiments. Historically, lab machinery suffered from a lack of an intuitive interface and restricted modularity. Without programming skills, it was difficult to personalize the procedures that were hard-coded by manufacturers. Therefore, an assistant that comprehends natural language allows biologists without coding expertise to engage in research that leverages automation.
Moreover, our research assistant Thalia can help scientists with physical disabilities actively engage in laboratory tasks. Traditional laboratory experiments often have physical demands, such as pipetting, handling samples, and operating instruments. These can be difficult or even impossible for those with certain disabilities. The combination of our digital microfluidics hardware and our software Thalia facilitates these individuals in conducting experiments, operating lab tools, and gathering data. This not only makes their tasks easier but also grants them more independence, enabling them to make significant contributions to scientific breakthroughs.
The topic of responsibility becomes paramount with assisted software, drawing parallels with debates in areas like automated vehicles. It's crucial to understand that even though AI-assisted systems can vastly enhance the user experience, they don't necessarily relieve researchers of their duties. For instance, even with an autopilot engaged, drivers must remain attentive to the road and regain control in potentially hazardous situations. This topic is indeed controversial and entails ethical considerations [26].
For our synthetic biology research software, it was our intent to prioritize responsibility. We integrated a safety mechanism necessitating a researcher's confirmation prior to initiating any experiment. This step acts as a verification point, even amidst intricate and automated experiment setups, which might encompass AI-driven decisions and automated actions. Researchers are obligated to actively affirm the experiment's purpose and parameters, ensuring alignment between intended objectives and their actual execution.
In addition, we crafted multiple safety features that experimenters can activate at any stage of the experiment.
The droplet movement on the digital microfluidics hardware can be stopped at any time with the "instant stop" button. This simply stops all current movements, and keeps the droplet where they are.
The droplet movement can be stopped and put in a neutral position, with the "neutral stop" button. This function freezes all current tasks, and moves as quickly as possible all droplets on neutral squares, such that no droplet remains on a heating, freezing, or any other function zone.
The digital microfluidics hardware can be wiped out as quickly as possible with the "wipe stop" button. As its name indicates, this means throwing aways all droplets from the plate, to remove all components from it. We intend to complement this with a cleaning function that automatically moves a droplet of alcohol (or any relevant chemical) to remove any remaining trace of any biological component from the plate.
This human oversight is a pivotal aspect of maintaining control and accountability in the research process when interacting with our assistant.
Complementary to the previous points, as creators of the software, our responsibility extends beyond merely providing a functional tool. We are committed to ensuring that our program operates safely. This will involve rigorous testing and validation to prevent unintended breaches or deviations from the intended behavior. We are dedicated to upholding the highest standards of software quality, security, and reliability to safeguard the integrity of the research conducted using our platform.
Integrating artificial intelligence and automation in academic life science labs brings significant benefits and challenges. It enhances reproducibility and inclusivity but requires managing obsolescence and preserving innovation. To ensure broad adoption, cost-effective, environmentally friendly solutions are essential. Vocal assistants, like Thalia, make automation accessible to non-programmers and researchers with physical disabilities. Responsible software design, with safety mechanisms and human oversight, maintains accountability. This empowers future scientists with interdisciplinary skills and fosters inclusivity, diversity, and ethical responsibility in research.