Periodic Reporting for period 1 - AiPSC (AI-powered platform for autologous iPSC manufacturing)
Periodo di rendicontazione: 2022-09-01 al 2023-08-31
In 2006 Shinya Yamanaka and Kazutoshi Takahashi published the discovery of four transcriptional factors, the Oct3/4, Sox2, c-Myc, and Klf4 (1) (OSKM factors), which can induce the reprogramming of adult somatic cells into an embryonic-like state. The reprogrammed cells were designated the name of induced pluripotent stem cells (iPSCs), due to their morphological and growth resemblance to embryonic stem cells (ESCs) and their pluripotent capabilities (the capacity of iPSCs to differentiate in any cell of the body). The discovery of the OSKM factors revolutionized the field of regenerative medicine, the field which focuses on the development of novel therapies with the aim to restore or regenerate organs or tissues that have been compromised due to diseases. The importance of the OSKM factors discovery lies in the lift of the ethical and political barriers opposed to the use of ESCs, which are derived from the destruction of human embryos. The potential of iPSCs to cure health problems including degenerative diseases, cancer, and defective tissues, is unprecedented in history. Despite the significant efforts of the scientific and clinical communities to employ iPSCs in clinical therapies, their efforts are hindered by a lack of standardization and high manufacturing costs. Clinical iPSC-based therapies can be categorized into two groups, the allogeneic and the autologous approach. The allogeneic approach refers to the use of cells derived from one patient to treat other patients. Whereas the autologous approach refers to the treatment of a patient with the patient’s own cells. The allogeneic approach offers various benefits over autologous therapies, but it also has notable drawbacks and limitations. The main advantage of allogeneic therapies is that they can be produced as an “off-the-shelf” solution, which translates to more cost-effective, easily automated, and scalable therapies. Despite these advantages, allogeneic therapies are constrained by the risk of graft rejection or the occurrence of "graft-versus-host" disease, limiting their application. Cells exhibit surface proteins known as histocompatibility antigens or human leukocyte antigens (HLA), which can trigger an immune response when incompatible with the recipient, potentially leading to graft rejection by the recipient's immune system (2,3). The “graft-versus-host” disease results from the opposite reaction, with donor cells rejecting and attacking the host cells (2,3). To overcome the histocompatibility challenges, various methods can be deployed including the use of immunosuppressive drugs, HLA matching (2), or the development of hypoimmunogenic cells (4). HLA matching refers to the assessment of the compatibility of host-recipient antigens (2) but all have significant health concerns. Hypoimmunogenic cells are genetically modified cells engineered to not present any antigens on their surface that can trigger an immune response (4). Immunosuppressive drugs reduce the capacity of immune cells to react to foreign antigens (6). Autologous cell therapies can lift any risks of transmission of infections, graft rejection, or “graft-versus-donor” disease. The major drawback is the high manufacturing costs for developing a personalised therapy which can exceed the €500.000 which makes it inaccessible for most patients.
The AiPSC seeks to develop a new technology that will enable the mass production of personalized iPSC-based therapies. The consortium will for the first time create an artificial intelligence (AI) guided microfluidic device that standardizes the GMP production of autologous iPSCs fast and at a fraction of the current cost. Moreover, it will conduct cutting-edge cell genomics and bioinformatics research on iPSCs to identify clones of the highest quality and develop a database that will be the basis for AI software to select clones that meet clinical standards. The consortium comprises experts in microfluidics engineering process automation for cell therapies, stem cell molecular biology and bioinformatics, GMP production, and AI modeling. Altogether, we propose to create revolutionary technology for low-cost, fast, and standardized automated mass production of autologous iPSCs, which holds the potential to enable numerous new therapies and make them accessible to the public.
References:
1 Takahashi, K. et al. Cell 126, 663–676 (2006)
2 Chinen, J. et al. J. Allergy Clin. Immunol. 125, S324 (2010)
3 Caldwell, K. J. et al. Front. Immunol. 11, 618427 (2021)
4 Zhao, W. et al. (2020)
5 Caldwell, A. et al. (2018)
6 Rossi, S. J. et al. Drug Saf. 9, 104–131 (1993)
The AiPSC seeks to develop a new technology that will enable the mass production of personalized iPSC-based therapies. The consortium will for the first time create an artificial intelligence (AI) guided microfluidic device that standardizes the GMP production of autologous iPSCs fast and at a fraction of the current cost. Moreover, it will conduct cutting-edge cell genomics and bioinformatics research on iPSCs to identify clones of the highest quality and develop a database that will be the basis for AI software to select clones that meet clinical standards. The consortium comprises experts in microfluidics engineering process automation for cell therapies, stem cell molecular biology and bioinformatics, GMP production, and AI modeling. Altogether, we propose to create revolutionary technology for low-cost, fast, and standardized automated mass production of autologous iPSCs, which holds the potential to enable numerous new therapies and make them accessible to the public.
References:
1 Takahashi, K. et al. Cell 126, 663–676 (2006)
2 Chinen, J. et al. J. Allergy Clin. Immunol. 125, S324 (2010)
3 Caldwell, K. J. et al. Front. Immunol. 11, 618427 (2021)
4 Zhao, W. et al. (2020)
5 Caldwell, A. et al. (2018)
6 Rossi, S. J. et al. Drug Saf. 9, 104–131 (1993)
In the first year of the project, the AiPSC consortium members, MIDA Biotech, KVentures, Leiden University, and MIRCOD have collaborated to pursue the overarching goal of standardizing and automating the creation of autologous iPSCs. The consortia partners during the course of the first reporting period have made the following progress:
MIDA established the basis for the generation of iPSCs in microfluidic devices:
-Developed and validated GMP-translated protocols for the generation and maintenance of autologous iPSCs.
-Developed a plan for iPSC quality assessment.
-Successfully downscaled the fibroblast reprogramming protocols to suit low-volume culture vessels such as microfluidic chips.
-Created an annotated dataset of more than 4000 reprogramming images for training the AI models for iPSC colony detection and selection.
KVentures in order to initiate the development of the AI algorithms for the software designed for determining iPSC colony quality has:
-Developed an annotation platform for securely depositing and annotating reprogramming datasets.
-Develop and train supervised and unsupervised AI models for iPSC colony detection and the morphological selection of high-quality colonies
-Introduced a scheduler command line for enabling time-lapse imaging of reprogramming experiments
-Established two distinct stitching approaches for the analysis of whole slide images.
Leiden University in order to expand and refine the quality standards for iPSCs, will during the course of the project create a new colony quality index based on next-generation sequencing and ATAC-seq. During the reporting period, they have:
-Curated an extensive compilation of next-generation sequencing datasets obtained from iPSCs generated through various methodologies, utilizing diverse cell sources and donors, including primary cells and cancer cell lines.
-Acquired cell lines from the same donor originating from different cell sources such as blood, urine, and skin.
-Devised comprehensive protocols for differentiating these cells from the same donor and plans to employ single-cell RNA and ATAC sequencing techniques to extract valuable insights into the differentiation potential of iPSCs.
MIRCOD has developed the first designs of microfluidic automation for iPSC production:
-Designed the first AiPSC reprogramming microfluidic chips
-Designed the automatic liquid handling of the microfluidic chips
MIDA established the basis for the generation of iPSCs in microfluidic devices:
-Developed and validated GMP-translated protocols for the generation and maintenance of autologous iPSCs.
-Developed a plan for iPSC quality assessment.
-Successfully downscaled the fibroblast reprogramming protocols to suit low-volume culture vessels such as microfluidic chips.
-Created an annotated dataset of more than 4000 reprogramming images for training the AI models for iPSC colony detection and selection.
KVentures in order to initiate the development of the AI algorithms for the software designed for determining iPSC colony quality has:
-Developed an annotation platform for securely depositing and annotating reprogramming datasets.
-Develop and train supervised and unsupervised AI models for iPSC colony detection and the morphological selection of high-quality colonies
-Introduced a scheduler command line for enabling time-lapse imaging of reprogramming experiments
-Established two distinct stitching approaches for the analysis of whole slide images.
Leiden University in order to expand and refine the quality standards for iPSCs, will during the course of the project create a new colony quality index based on next-generation sequencing and ATAC-seq. During the reporting period, they have:
-Curated an extensive compilation of next-generation sequencing datasets obtained from iPSCs generated through various methodologies, utilizing diverse cell sources and donors, including primary cells and cancer cell lines.
-Acquired cell lines from the same donor originating from different cell sources such as blood, urine, and skin.
-Devised comprehensive protocols for differentiating these cells from the same donor and plans to employ single-cell RNA and ATAC sequencing techniques to extract valuable insights into the differentiation potential of iPSCs.
MIRCOD has developed the first designs of microfluidic automation for iPSC production:
-Designed the first AiPSC reprogramming microfluidic chips
-Designed the automatic liquid handling of the microfluidic chips
No results beyond the state of the art yet.