Periodic Reporting for period 2 - PRIME (A Personalised Living Cell Synthetic Computing Circuit for Sensing and Treating Neurodegenerative Disorders)
Reporting period: 2022-02-01 to 2023-07-31
There remain urgent and unmet needs for the treatment of neurological diseases. Epilepsy is a serious, chronic brain disease characterized by recurrent seizures, being one of the most common serious neurological condition, affecting about 1% of the population, i.e. about 60M people globally (6M in Europe). The end result of PRIME is a software design tool for designing engineered cells that compute, diagnose, and produce therapeutic molecules capable of preventing seizures. The design tool is governed by AI integrated with Molecular Communication simulations that utilise Biophysical and Statistical Mechanics modelling. This trans-disciplinary project aims to approach a serious neurological problem through a solution bringing together synthetic biology, computer science, communication engineering, nanomedicine, bioengineering and material science. This vision of implanting programmable synthetic cells that mimic electronic computing circuits is not limited to managing epileptic seizures but may extend to many other neurological diseases.
Obj1: Developing molecular communication simulation and modeling design tool.
Obj2: Engineering cells to sense, perform logic computing and release GDNF.
Obj3: Developing an encapsulated implantable device that integrates three-dimensional (3D) constructs of the cells from Objective 2 grown in hybrid biomaterial scaffolds.
Obj4: Experimental testing and validation of device in vivo.
Obj1: Developing molecular communication simulation and modeling design tool.
Obj2: Engineering cells to sense, perform logic computing and release GDNF.
Obj3: Developing an encapsulated implantable device that integrates three-dimensional (3D) constructs of the cells from Objective 2 grown in hybrid biomaterial scaffolds.
Obj4: Experimental testing and validation of device in vivo.
During the first year of the project, the consortium partners worked towards the biological and technological goals of PRIME:
During the second year of the project up to M30, the project has made substantial advancements across key WPs, driving innovation in molecular communication, cell engineering, biomaterial development, and preclinical validation.
WP2 has continued to work on developing state-of-the-art mathematical models and computational tools to simulate end-to-end molecular communication systems, supporting the functionality of the cell-based biosensor. RCSI has tested the tsRNAsearch bioinformatics tool on multiple RNA datasets, identifying significant tsRNA alterations in epilepsy models and performing functional studies on 5’tRFs for integration into simulation and modeling tools.
WP3 made progress in engineering mammalian cells with molecular computing functions. AU optimized RNA loading into extracellular vesicles (EVs) and live monitoring of EV-cell interactions. UniFE successfully determined GDNF expression and secretion pathways in ARPE-19 and rMC-1 cells, examining the role of intracellular Ca2+ in GDNF regulation. Furthermore, RCSI developed assays for detecting extracellular 5’-tRFs and GDNF, facilitating the validation of engineered cells.
For WP4, significant strides have been made in designing implantable cell encapsulation structures. EPOS optimized hybrid scaffolds incorporating collagen hydrogels and laminin-functionalized nanorods to mimic the brain's extracellular matrix. TAU developed an encapsulation method for ARPE-19 cells and introduced a porous PDMS hollow tube for cell containment, alongside investigating kainic acid-induced in vitro seizure models.
In WP5, RCSI and UniFE have established epilepsy models for validating in vivo studies of the biocomputing cell insert. Efforts have focused on optimizing epilepsy modeling with telemetry, conducting long-term recordings, behavioral assessments, and validating tRNA fragment detection following tissue extraction.
WP6 has been instrumental in dissemination and communication efforts. The project has achieved high-impact presentations, publications, and follow-up proposals, engaging a diverse audience, including the scientific and medical community, industry, patient groups, and the general public. Strategic exploitation planning ensures technology transfer, intellectual property management, and industry collaboration to maximize the project’s impact.
During the second year of the project up to M30, the project has made substantial advancements across key WPs, driving innovation in molecular communication, cell engineering, biomaterial development, and preclinical validation.
WP2 has continued to work on developing state-of-the-art mathematical models and computational tools to simulate end-to-end molecular communication systems, supporting the functionality of the cell-based biosensor. RCSI has tested the tsRNAsearch bioinformatics tool on multiple RNA datasets, identifying significant tsRNA alterations in epilepsy models and performing functional studies on 5’tRFs for integration into simulation and modeling tools.
WP3 made progress in engineering mammalian cells with molecular computing functions. AU optimized RNA loading into extracellular vesicles (EVs) and live monitoring of EV-cell interactions. UniFE successfully determined GDNF expression and secretion pathways in ARPE-19 and rMC-1 cells, examining the role of intracellular Ca2+ in GDNF regulation. Furthermore, RCSI developed assays for detecting extracellular 5’-tRFs and GDNF, facilitating the validation of engineered cells.
For WP4, significant strides have been made in designing implantable cell encapsulation structures. EPOS optimized hybrid scaffolds incorporating collagen hydrogels and laminin-functionalized nanorods to mimic the brain's extracellular matrix. TAU developed an encapsulation method for ARPE-19 cells and introduced a porous PDMS hollow tube for cell containment, alongside investigating kainic acid-induced in vitro seizure models.
In WP5, RCSI and UniFE have established epilepsy models for validating in vivo studies of the biocomputing cell insert. Efforts have focused on optimizing epilepsy modeling with telemetry, conducting long-term recordings, behavioral assessments, and validating tRNA fragment detection following tissue extraction.
WP6 has been instrumental in dissemination and communication efforts. The project has achieved high-impact presentations, publications, and follow-up proposals, engaging a diverse audience, including the scientific and medical community, industry, patient groups, and the general public. Strategic exploitation planning ensures technology transfer, intellectual property management, and industry collaboration to maximize the project’s impact.
The end result of PRIME is a software design tool for designing engineered cells that compute, diagnose, and produce therapeutic molecules capable of preventing seizures. The tool is governed by AI integrated with Molecular Communication simulations that utilize Biophysical and Statistical Mechanics modelling. This trans-disciplinary project aims to approach a serious neurological problem through a solution bringing together synthetic biology, computer science, communication engineering, nanomedicine, bioengineering and material science. This vision of implanting programmable synthetic cells that mimic electronic computing circuits is not limited to managing epileptic seizures but may extend to many other neurological diseases.
Significant progress has been achieved in the initial 30 months of the PRIME project, with key developments spanning molecular communication simulation, cell engineering, and implantable device design. Advanced modelling tools have been established to enhance the understanding and design of interactions within the biocomputer system. Partners have successfully engineered mammalian ARPE-19 cells with molecular computing functions capable of detecting seizure-related signals (tsRNAs) and triggering the release of a therapeutic molecule (GDNF). This work includes the exploration of innovative cell circuit designs utilizing L7Ae/kink-turn technology to optimize gene regulation and signal amplification.
Efforts are also focused on the development of an encapsulated, implantable device to house these engineered cells. Research is being conducted into biocompatible materials that support the diffusion of critical molecules (tsRNAs and GDNF), incorporating hybrid biomaterial scaffolds designed to replicate the brain’s extracellular matrix. Porous membrane structures, including PDMS hollow tubes and coaxial electrospun nanofibers, are being developed to facilitate cell encapsulation. To support preclinical validation, in vitro epilepsy models are being established to assess the PRIME concept prior to in vivo studies. Significant progress has been made in identifying and characterising tsRNAs as potential biomarkers and sensors for seizure detection, reinforcing the personalised and responsive nature of the proposed therapy. Collectively, these advancements in cell engineering, biomaterial science, and molecular sensing represent a substantial step forward beyond current state-of-the-art treatments for neurodegenerative disorders.
Significant progress has been achieved in the initial 30 months of the PRIME project, with key developments spanning molecular communication simulation, cell engineering, and implantable device design. Advanced modelling tools have been established to enhance the understanding and design of interactions within the biocomputer system. Partners have successfully engineered mammalian ARPE-19 cells with molecular computing functions capable of detecting seizure-related signals (tsRNAs) and triggering the release of a therapeutic molecule (GDNF). This work includes the exploration of innovative cell circuit designs utilizing L7Ae/kink-turn technology to optimize gene regulation and signal amplification.
Efforts are also focused on the development of an encapsulated, implantable device to house these engineered cells. Research is being conducted into biocompatible materials that support the diffusion of critical molecules (tsRNAs and GDNF), incorporating hybrid biomaterial scaffolds designed to replicate the brain’s extracellular matrix. Porous membrane structures, including PDMS hollow tubes and coaxial electrospun nanofibers, are being developed to facilitate cell encapsulation. To support preclinical validation, in vitro epilepsy models are being established to assess the PRIME concept prior to in vivo studies. Significant progress has been made in identifying and characterising tsRNAs as potential biomarkers and sensors for seizure detection, reinforcing the personalised and responsive nature of the proposed therapy. Collectively, these advancements in cell engineering, biomaterial science, and molecular sensing represent a substantial step forward beyond current state-of-the-art treatments for neurodegenerative disorders.