This project employs synthetic biology technology to construct an engineered yeast that can identify biomarkers related to intestinal Alzheimer's disease. Through the "AND" Gate judgment, it initiates butyric acid production and can colonize the intestinal tract to continuously provide benefits over a long period. This project utilizes the key pathway of the brain-gut axis and, from a new perspective of inhibiting neuroinflammation, achieves prevention and innovative treatment of Alzheimer's disease.

Brief background

Alzheimer's disease (AD), as a very common and severely harmful neurodegenerative disorder, imposes a heavy burden on patients and their families. Its main clinical features include progressive cognitive impairment and significant decline in memory ability. Patients will experience continuous deterioration of learning and memory functions, dementia, forgetfulness, aphasia, and difficulty concentrating. Although extensive research has been conducted on the pathogenesis of Alzheimer's disease, proposing various theories such as the free radical theory, calcium overload theory, metabolic disorder theory, and synaptic theory, the exact mechanism of the disease remains unclear.

In terms of treatment, existing drugs such as those that regulate neurotransmitters (such as donepezil, a cholinesterase inhibitor) and glutamate function regulators (such as NMDA receptor antagonists, neurotrophic factors, etc.) can only alleviate the symptoms of patients to a certain extent and cannot fundamentally prevent and cure Alzheimer's disease, nor can they effectively control the progression of the disease.In contrast, the antibody agent, Lecanemab, which targets and cleaves soluble amyloid β (Aβ) fibrils, is considered to have moderate efficacy in slowing cognitive decline and is associated with common adverse events, including cerebral edema and hemorrhage (ARIA).

In recent years, an increasing number of studies have revealed a close connection between the gut microbiota and the brain, and the concept of the brain-gut axis has gradually gained widespread attention. The brain-gut axis is a complex two-way interactive system existing between the central nervous system and the gut microbiota. It regulates the state of the gut to a certain extent, which also affects mental health. The gut microbiota can synthesize and release various neuroactive substances, such as short-chain fatty acids (SCFAs), biogenic amines, and neurotransmitters, etc. These substances can reach the brain through various pathways and thereby affect the activity of neurons. Studies have found that the gut microbiota of patients with neurological diseases such as autism, Alzheimer's disease, and depression are all disordered. Butyric acid, as one of the main metabolic products of the gut microbiota, plays a key role in human physiological functions. Its lack may be closely related to the deterioration of neurodegenerative diseases.

In addition to some official data, our team also collected further statistics and information on the understanding of Alzheimer's disease and its research prospects among different social individuals through questionnaires, expert interviews, etc. Due to issues such as previous research oversights, there is still a significant research gap in drug development and disease mechanism analysis for Alzheimer's disease. Moreover, most social surveys believe that due to its slow and irreversible progression, there are significant oversights in the prevention aspect in the early stages.

Project Inspiration and Enlightening

A New Perspective on the Brain-Gut Axis: After noticing the current lack of effective treatment methods for Alzheimer's disease, which imposes a heavy burden on society and families, we turned our attention to emerging research fields. When we learned about the certain connection between the gut microbiota and the brain - the brain-gut axis, as well as the crucial role of short-chain fatty acids, especially butyric acid, in regulating intestinal health, we were deeply inspired. Previous studies have shown that the abundance of butyric acid-producing strain is lower in patients with autism, Alzheimer's disease, and Parkinson's disease, and there is a disorder of the microbiota accompanied by gastrointestinal disorders. Therefore, we wondered whether supplementation of butyric acid-producing yeast could balance the concentration of fatty acids in the gut, thereby regulating brain neuroinflammation through the brain-gut axis.

The Analysis and Inspiration of the Full Synthesis Pathway of Butyrate: In 2024, a team from Tianjin University solved the full synthesis pathway of butyric acid that can be realized in yeast and made a preliminary attempt to construct the related gene ( Wu J, et al. 2024 ). Based on the design ideas in the references, combined with the design of relevant factors (such as TMA concentration, ROS level, etc.) and the introduction of relevant plasmids, the microorganisms were purposefully modified and designed to provide technical support for the construction of engineered yeast that produce butyric acid. These factors collectively inspired us to carry out this project. By using synthetic biology techniques to construct engineered that produce butyric acid and colonize the intestinal tract, and using the brain-gut axis to transfer butyric acid, a new approach for the treatment of Alzheimer's disease was opened up.

Research target

Therefore, our project aims to use a yeast strain as a chassis, introduce detection elements and butyric acid synthesis genes into it, and thereby develop a preventive health care product.

Constructing biological elements for identifying early AD biomarkers:
Based on our research and the solid conclusions of the dry experimental model, we have determined TMA as an effective biomarker. Then we designed biological elements that can sense TMA: the modified human TAAR5 fusion protein + the modified yeast GPA1 fusion protein, which can activate downstream signaling pathways. Biological elements that can sense ROS ( The second guarantee ): the pTRR1 promoter.

Ensure that the engineered yeast can effectively colonize:
We introduced the adhesion protein LcGC into the yeast, enabling it to colonize near the colon.

Construction of butyric acid-producing engineered yeast:
Based on our research and the solid conclusions of the dry experimental model, we have determined TMA as an effective biomarker. Then we designed biological elements that can sense TMA: the modified human TAAR5 fusion protein + the modified yeast GPA1 fusion protein, which can activate downstream signaling pathways. Biological elements that can sense ROS ( The second guarantee ): the pTRR1 promoter.

Exploring clinical application potential:
Based on the results of previous studies, we want to explore the potential and feasibility of using engineered yeast that produce butyric acid in clinical applications. Assess the safety and stability of the engineered yeast, as well as how to achieve large-scale production and effective delivery, to lay the foundation for the development of new biological therapies for Alzheimer's disease in the future.

Innovation Strategies

1. Calibration method of kinetic model based on parameter confidence grading

We have innovatively proposed a kinetic model calibration method based on parameter confidence grading. Traditional modeling often directly uses parameters with mixed sources in the literature (human, rat, calculation, etc.), while our method first differentiated all parameters according to their sources of confidence, kept the high confidence parameters unchanged, set a reasonable range for the low confidence parameters and allowed them to fluctuate within the range, and made the model output reach the physiological values measured in the literature through optimization. Thus, the parameter calibration was completed. After the physiological calibration, we further applied the method to pathological states: variable ranges of different parameters were set according to the disease mechanism, optimized to the target values of pathological states, and the disease mechanism was inferred by observing the changes of parameters. This double-calibration strategy effectively avoids the problem of over-fitting the model to a few data points. More importantly, it combines parameter source reliability with disease mechanism research to ensure that the parameters are not only numerically reasonable but also biologically meaningful, making the mathematical model both mechanistically based and in turn a tool for studying the mechanism.

2. Preventive Early Intervention

Traditional AD medications are usually initiated after the onset of significant cognitive symptoms. Our engineered yeast enables real-time monitoring of disease-related early pathological signals (TMA and ROS elevation) in the gut environment (Rath S. et al. 2017 & Das TK. Et al. 2023), enabling the initiation of therapeutic interventions before significant clinical symptoms such as neurological damage and memory loss occur. This "yeast knows the risk before you" preventive strategy provides a window of time to delay or stop disease progression.

3. Sustained Release Overcoming First-Pass Effect

Oral butyrate supplements face a serious first-pass effect problem - according to the model simulation results of the dry experimental group, about 95% of butyrate is metabolized in the colonic epithelial cells, and it is difficult to enter the circulation system and reach the brain. Our engineered yeast achieves in situ continuous production by intestinal colonization, resulting in a significant increase in bioavailability. Combined with its long-term colonization ability, the system can provide a steady, sustained release of therapeutic molecules without frequent drug administration.

4. Intelligent Dual-Signal Logic Gating System

Unlike traditional drugs with static dosing regimens or single-biomarker diagnostics suffering from high false-positive rates due to physiological noise, our system implements a synthetic biology "AND-gate" logic circuit. The engineered yeast functions as a "smart diagnostic-therapeutic unit" requiring simultaneous presence of two independent disease markers (elevated TMA and ROS) to activate therapeutic butyrate production. By requiring concordant elevation of both TMA (indicating gut dysbiosis) and ROS (indicating oxidative stress and inflammation), the system dramatically improves disease specificity, distinguishing true pathological states from normal physiological variations, enabling autonomous, real-time, and on-demand precision therapeutic regulation.

5. Humanistic and Economic Advantages

Our products are essentially engineered probiotics rather than "drugs" in the traditional sense, and patients have a higher psychological acceptance, getting rid of the dependence on hospital and invasive treatment. The long-term intestinal colonization property of engineered yeast greatly reduces the frequency of drug administration and improves patient compliance. At the same time, the cost of production based on microbial fermentation is much lower than that of existing monoclonal antibody drugs (annual cost $26,000-$56,000) ( Hering H. et al. 2025), and it is expected to achieve broader patient access.

Reference

Details

Das, T. K., & Ganesh, B. P. (2023). Interlink between the gut microbiota and inflammation in the context of oxidative stress in Alzheimer's disease progression. Gut Microbes, 15(1), Article 2206504.

Hering, H., Bussiere, T., Liu, C. C., Glajch, K. E., Weihofen, A., Grogan, J., & Walsh, D. M. (2025). A manifesto for Alzheimer's disease drug discovery in the era of disease-modifying therapies. Molecular Neurodegeneration, 20(1), Article 88.

Rath, S., Heidrich, B., Pieper, D. H., & Vital, M. (2017). Uncovering the trimethylamine-producing bacteria of the human gut microbiota. Microbiome, 5(1), Article 54.

Wu, J., Huang, H., Wang, L., Gao, M., Meng, S., Zou, S., Feng, Y., Feng, Z., Zhu, Z., Cao, X., Li, B., & Kang, G. (2024). A tailored series of engineered yeasts for the cell-dependent treatment of inflammatory bowel disease by rational butyric acid supplementation. Gut Microbes, 16(1), Article 2316575.