Our Integrated Human Practices (iHP) work aimed to ensure that our project evolved with both scientific depth and real-world relevance. From initial design to application refinement, we consistently sought feedback from clinicians, molecular biologists and industry professionals. Their insights guided us to balance innovation with safety and practicality.
Through continuous communication and reflection, we identified key issues in biosafety, clinical translation, and experimental feasibility. These findings helped us refine our aptamer–riboswitch system and align it more closely with potential medical applications.
Rather than being a parallel effort, iHP functioned as an ongoing dialogue between science and society — allowing our project to grow through evidence, responsibility, and meaningful engagement.
Associate Chief Physician of a community hospital in Shenzhen
Research Interest
Chronic disease management
Result
we gained a clearer understanding of the shortcomings and unmet needs in current cirrhosis management. While existing therapies focus on protecting the liver, the key—according to the clinician—is to reactivate it. Therefore, our team has decided to focus our development efforts on a hepatoprotective therapy that directly targets hepatocyte metabolism and functional restoration. The goal is to reactivate liver metabolism at the cellular level, promote repair and regeneration, reduce medication burden and side effects, enhance patient quality of life, and ensure feasibility for broad adoption in community healthcare settings.
Background
Our team is currently exploring new therapeutic approaches for liver cirrhosis. During research, we observed that while existing hepatoprotective and anti-fibrotic drugs can reduce inflammation and slow disease progression, they have limited ability to repair hepatocyte metabolism and restore liver function. Many patients continue to suffer from fatigue, bloating, and poor appetite even after long-term medication, with little improvement in quality of life. With these questions in mind, we approached a frontline community physician to better understand the real challenges in treatment, identify the limitations of current therapies, and seek professional insight into which therapeutic direction could truly address patients' unmet clinical needs.
Process
the physician highlighted several major issues with current cirrhosis treatments: most existing drugs protect rather than repair, focusing on reducing damage rather than restoring hepatocyte function; patients often take multiple medications long-term, leading to high burden and side effects, yet with limited improvement in lab results; poor efficacy reduces treatment adherence and makes community follow-up difficult. The doctor explained that the fundamental problem lies in impaired hepatocyte metabolism and mitochondrial dysfunction. A therapy that directly targets metabolic and functional repair could restart hepatocyte activity, not only improving test results but also helping patients regain energy, appetite, and reduce ascites. The physician recommended focusing on a combined hepatoprotective and metabolic repair approach, viewing it as an innovative and differentiated direction beyond current treatments.
Before Engineering
Prof. Yunlong Zhang (Academic)
Associate Professor of the Department of Biological Science and Technology, Donghua University
Research Interest
Metabolic engineering modification and application of functional microorganisms
Result
We adopted the suggestion of retaining the P0 loop and verified the plasmid system in HEK293T cells. Given the significant differences in composition and complexity between the in vitro experimental environment and the intracellular environment, and considering that our previous experiments have already demonstrated that the components have the function of self-cutting, we are more inclined to seek experimental conditions that can alter the intracellular SAM concentration.
Background
During the first engineering cycle, we encountered problems in the functional verification of SAM aptamer enzymes in HEK293T cells: After fusing the aptamer region of SAM VI riboswitch with HDV riboenzyme, we expected that its binding to SAM should induce structural transformation and activate inactive HDV to complete self-cleavage. However, the experimental results show that the self-cleavage level of the fused SAM aptamer enzyme has no correlation with the SAM concentration. For this purpose, we reviewed the relevant studies on conformational changes of SAM-VI ribose switches. Particular attention was paid to the work Bifidobacterium bifidum SAM-VI Riboswitch Conformation Change Requires published by Dr. Xiao Wenwen and Professor Lu Changrui's team in Biomolecules Peripheral Helix Formation. This research focuses on the cross-disciplinary direction of SAM riboswitch structure-function and aging metabolite imaging, systematically applying methods such as SAXS, SHAPE, and ITC to analyze the conformational regulation mechanism of SAM VI riboswitch. The inspirations for our project mainly lie in the following two aspects: The decisive role of the peripheral helix (such as the P1 stem) in conformational transformation: Research has revealed through various experimental methods that the formation of the P1 stem is the key for the SAM-VI ribose switch to complete ligand recognition and conformational locking. M1 mutants lacking P1 completely lose their SAM response ability, while M2 mutants with shortened P1 partially regain function, but their binding affinity significantly decreases. This suggests that when designing eukaryotic SAM-responsive RNA devices, we cannot merely focus on the core binding sites. It is necessary to rationally design and stabilize the peripheral helical structure to ensure that the conformational changes induced by ligands can be effectively transmitted to the functional modules. Thermodynamic controllability of conformational transition and functional output: This study quantitatively analyzed the binding free energy (ΔG) of different P1 length mutants with SAM and found that P1 length was positively correlated with binding affinity, and the degree of conformational compression was directly related to functional output (such as translation inhibition). This provides a theoretical basis for us to optimize the response threshold and dynamic range of the SAM-ribozyme coupling system, that is, through the control, the self-cutting activity of the ribozyme can be finely regulated without modifying the core recognition area.
Process
First, we introduced the design and conception of this iGEM project and raised the question: Should we try other types of SAM ribose switches besides SAM-I, SAM-VI, and SAM-III? Dr. Xiao pointed out that types such as SAM-II and SAM-IV have relatively long lengths. Combined with the complex conformational changes before and after SAM, they may not be suitable for the HDV ribozyme system. Meanwhile, she suggested retaining the P0 ring of SAM-VI, which plays an important auxiliary role in aptamer folding. Regarding the screening strategy, she mentioned that methods such as IVT, in vitro incubation and RNA electrophoresis could be considered for in vitro validation to better control the ligand concentration.
Engineer 1
Prof. Zhen Xi (Academic)
Professor of the College of Chemistry, Nankai University
Research Interest
Nucleic acid chemical biology
Result
His perspective underscores the need to improve screening methodologies while maintaining a function-oriented mindset. This direction is highly relevant for our SAM project, where the identification of effective and novel RNA elements is essential for precise metabolic control.
Background
The development of regulatory elements for metabolite control, such as SAMe, remains constrained by the incomplete understanding of RNA regulatory mechanisms. This has made systematic, mechanism-driven design difficult to achieve.
Process
Professor Xi highlighted that most regulatory elements have been discovered through functional screening rather than rational design. He stressed that true innovation should focus on developing elements with novel and robust functions, rather than minor modifications of existing strategies.
Engineer 2
Dr. Shan Gao (Industry)
Senior Vice President and Chief Scientific Officer of Ruibo Biotech
Research Interest
RNA modification and delivery technology platform
Result
Engineered small-molecule–responsive RNA elements offer a promising direction for improving control and reducing risk. For our SAM project, this insight reinforces the importance of developing elements capable of precise and dynamic regulation to maintain the physiological balance of SAM.
Background
Metabolites such as S-adenosylmethionine (SAM) require strict homeostatic regulation, since both deficiency and excess can trigger severe diseases. This makes RNA-based safety mechanisms and tunable expression strategies highly relevant to metabolic therapeutic design.
Process
Dr. Gao emphasized safety as the primary bottleneck for RNA therapeutics. He noted that delivery via lipid nanoparticles often lacks tissue specificity, and that the inherent multi-targeting nature of miRNAs further compounds safety risks. These limitations highlight the difficulty of achieving predictable therapeutic outcomes.
Engineer 2
Dr. Yanqiu Shao (Industry)
Director of Artificial Intelligence at Xunjing Biotech
Research Interest
Research and development of small molecule drugs targeting RNA
Result
The method provides valuable technical support for the rational design of SAMe-responsive elements, though it cannot yet capture RNA allostery and dynamic conformational shifts. This limitation points to future research directions crucial for enabling precise metabolic regulation.
Background
Understanding RNA–small molecule interactions is a key step toward designing RNA elements responsive to metabolites like SAM. However, the structural complexity of RNA makes accurate prediction of such interactions a major challenge.
Process
Dr. Shao introduced an integrated dry–wet workflow in which fluorescent probes capture structural signals experimentally, and these data are combined with large-scale computational models to refine predictions of RNA secondary and tertiary structures. This hybrid strategy improves reliability and accuracy over purely computational or experimental approaches.
Engineer 2
Prof. Fengmin Lu (Academic)
Professor at the School of Basic Medical Sciences, Peking University
Research Interest
New indicators and technologies for hepatitis B virus and related liver diseases
Result
Professor Lu Fengmin strongly endorsed our strategic selection of cycloleucine as a specific inhibitor targeting MAT2A, affirming the scientific rationale behind this approach. He further emphasized the profound clinical value and societal significance of developing innovative therapeutics for challenging liver cirrhosis. Professor Lu spoke highly of the scientific merit and translational potential of our project, expressing confidence that our research direction holds promise for achieving breakthrough progress in the field.
Background
In the initial phase of this study, our team designed siRNA targeting MAT1A and transfected it into HepG2 cell lines with the objective of establishing a cellular model characterized by low MAT1A expression. However, through in-depth consultations with domain experts and comprehensive literature review, we came to understand that cirrhotic and hepatocellular carcinoma cells intrinsically exhibit basal low expression levels of MAT1A, while MAT2A demonstrates compensatory upregulation. This revelation indicated a divergence between our experimental approach of MAT1A gene silencing in HepG2 cells and the actual pathological conditions of the disease.
Process
When our research encountered obstacles, we proactively engaged in thorough academic discussions with Professor Lu Fengmin. By systematically analyzing published literature and through iterative validation, we elucidated the specific overexpression pattern of MAT2A in cirrhotic and hepatocellular carcinoma cells. Building upon this finding, we implemented cycloleucine as a specific inhibitor, which successfully guided the development of a cellular model that more accurately reflects clinical pathological characteristics.
Engineer 3
Prof. Lei Miao (Academic)
Researcher at the School of Pharmaceutical Sciences, Peking University
Research Interest
Targeted gene drug delivery systems
Result
Prof. Lei Miao confirmed the innovation of self-regulated SAM control, particularly the selective activation in diseased hepatocytes, and emphasized this pathological–normal distinction as the project's conceptual core. Technical recommendations included exploring more durable expression systems or controlled-release strategies and minor delivery improvements through LNP modification or exocytosis-enhancing ligands. Delivery itself is not the limiting factor; the project's strength lies in system-level regulation. Overall, the SAM regulatory circuit demonstrates strong biological relevance and innovation potential, and with optimized delivery and expression stability, it could provide a new therapeutic framework for liver fibrosis.
Background
Our team aims to address a major challenge: efficient liver delivery, as fibrotic barriers can impede nanoparticle entry and optimizing delivery while maintaining selective activation in diseased cells.
Process
During the discussion, Prof. Lei Miao addressed the biological significance of switch regulation in mRNA, noting that mRNA's short half-life raises questions about its practical impact. The team clarified that the riboswitch is intended to distinguish diseased from healthy hepatocytes, being active in pathological states while silent in normal cells. This selective activation was recognized as a key innovation with translational relevance. The discussion also covered delivery strategies. Liver delivery via lipid nanoparticles (LNPs) is generally efficient, though fibrotic barriers can impede entry. Prof. Lei Miao highlighted potential optimization strategies, including matrix-degrading enzyme decoration, sequential dosing to weaken the extracellular matrix, reducing particle size for enhanced penetration, and leveraging transcytosis or exocytosis mechanisms. Animal models were reviewed, including CCl₄-induced, high-fat diet, and hamster models, each with advantages and limitations. Due to biosafety constraints, experiments so far used human hepatocellular carcinoma lines; mouse primary hepatocytes and cross-species enzyme homology were suggested for future validation.
Shenzhen Bay Laboratory Institute of Systems and Physical Biology
Research Interest
Structural bioinformatics, AI-driven biomolecule prediction and design, focusing on RNA 3D structure prediction and optimization in recent years, and developed tools such as RNA-BRiQ energy function.
Result
We established that Mg2+ must be accounted for in chemical kinetics simulations, while Tris+/Cl- can be omitted as needed to strike the optimal balance between accuracy and computational efficiency. Secondly, RNA's inherent polyconformational nature is common. Although functional states may exist as unique configurations, they can not be predetermined from existing data. Only by introducing conformational ensembles during simulations—rather than relying on single structures—can prediction reliability be significantly enhanced. Finally, we validated the feasibility of transferring rational protein design methodologies to RNA research while recognizing RNA's data scarcity bottleneck. This necessitates future efforts to strengthen secondary and tertiary structural features specific to RNA through data augmentation, thereby addressing sample insufficiency challenges.
Background
In the process of RNA structure prediction and rational design, we discuss how to trade off the accuracy and cost of solvent ions in molecular dynamics simulation, how a single crystal structure cannot represent the actual state of multiple conformational coexistence in solution, and how the migration design concept is questionable due to the fact that the high quality RNA samples available for training are far less than those for protein.
Process
Professor Zhou emphasized that Mg²⁺ significantly impacts the stability and free energy calculations of RNA frameworks, requiring explicit consideration, while Tris can be omitted as needed. He further noted that experiments have demonstrated the structural stability of certain RNAs (e.g., tRNA), yet physiological environments still contain numerous “utilized but not deciphered” structures. Regarding tertiary structures, he observed that usually only one structure typically functions effectively, though current method training datasets are insufficient to determine which structure truly performs the required function. When asked whether rational protein design principles could be directly applied to RNA design, Professor Zhou acknowledged the feasibility of this approach but cautioned thatRNA structural data remains scarce, making rapid breakthroughs unlikely in the short term.
Prof. Qiangfeng Zhang (Academic)
Associate professor, School of Life Sciences, Tsinghua University
Research Interest
RNA structure genomics, AI structure prediction and viral RNA mechanism research
Result
We used Smrt Net software to predict the docking of SAM riboswitch system, and the results showed that the interaction between index 3 and SAM was the most significant, which was highly consistent with the results obtained in wet experiments, providing a strong verification for wet experiments.
Background
In the rational design of RNA, we are puzzled about how to use computational methods to optimize the conformational stability and binding specificity of nucleic acid sequences, and we need to refer to existing computational frameworks or software tools for learning.
Process
Dr. Ma Jianbo and Dr. Huang Wenze systematically introduced the “RNA Structure-Function-Dynamics” one-stop platform proposed by Professor Zhang Qiangfeng's research group: using experimentally resolved samples as the training set, the deep learning model directly outputs three-dimensional coordinates and automatically generates Amber/GROMACS topology, achieving a full-chain closed loop of “structure prediction → molecular docking → MD sampling → free energy analysis.” In addition, they highly recommended the latest internal tool Smrt Net, which can quickly predict RNA-small molecule binding sites and affinities.
In the process of promoting inclusive work, our team not only compiles guidelines and norms for science popularizers but also continuously explores how to more effectively assist special groups. Epidemiological data shows that China remains one of the countries with the largest number of blind and visually impaired patients in the world. There are approximately 17.31 million visually impaired people, with about 450,000 new blind people and 1.35 million new low-vision patients added each year. Meanwhile, the overall resources for low vision diagnosis, treatment and rehabilitation in China are insufficient and unevenly distributed. Based on this reality, we have decided to focus our support on the visually impaired community and be committed to addressing the practical problems they face in their daily lives.
In the recent "N Ways to Touch Light" event we participated in, our team further personally experienced the obstacles and psychological challenges that visually impaired people encounter in their daily lives. For this reason, we plan to launch a practical tool development project for the visually impaired community. To ensure that the plan truly meets the needs of users and is technically feasible, we specially visited the well-known Beijing visually impaired public welfare organization "Golden Cane", and had in-depth exchanges with the organization's director, Xin Ming, the director of the "Independent Travel Training Camp", and Huang Weixin, the technical director, focusing on discussing the real pain points of the visually impaired group and feasible support paths.
Figure 1. The first visit to the Golden Cane Organization
During the communication, we focused on inquiring about the main difficulties that the visually impaired group encounters in their daily lives. Xinming and Huang Weixin pointed out that travel obstacles and difficulty in obtaining information are the two most common problems, and the inconvenience of operating smart home appliances is also quite common. Specifically, in the context of going out, they find it difficult to independently obtain public information such as bus stop signs, which not only affects travel efficiency but also brings safety hazards. In home Settings, there are also obstacles in daily tasks such as drug instructions and home appliance operations. Since not all visually impaired people are proficient in Braille, merely adding Braille labels to the packaging has limited effect. More and more smart home appliances that rely on touch screens, due to the lack of clear tactile identification, further increase the difficulty of use.
Figure 2. Have in-depth exchanges with two teachers
In addition, we have learned that currently, applications serving the visually impaired are highly dependent on two technologies: image recognition and network services, but both have obvious limitations. In terms of image recognition, the recognition accuracy of existing models drops significantly in scenarios such as insufficient light, stacked objects, or complex layouts, seriously affecting practicality and user experience. In terms of network services, the smoothness of voice interaction and remote recognition is constrained by network latency. Slow response is not only an efficiency issue but also directly related to users' sense of security and independence.
Based on the feedback obtained from this exchange, our team, after discussion, has decided to develop an intelligent tag system based on NFC technology, aiming to build an accessible interaction environment that is responsive and reliable in feedback from the bottom up. This system will be prioritized for deployment in three types of scenarios: kitchen usage, office and study, and pharmaceutical and health care. Through digital barrier-free interaction methods, visually impaired people can obtain key information more conveniently and safely, thereby effectively enhancing their autonomy in life and social participation.
