Periodic Reporting for period 2 - STACCATO (European Industrial Doctorate for enhancing upstream biopharmaceutical manufacturing process development through single cell analysis)
Okres sprawozdawczy: 2021-01-01 do 2022-12-31
Biopharmaceuticals have revolutionised the treatment of chronic diseases such as cancer and inflammatory disorders, with 350 million patients benefiting from biological medicines worldwide. The discovery of biopharmaceutical candidates continues at a staggering pace encompassing >50% of all new medicines in drug discovery pipelines. There are tremendous opportunities to improve human health and contribute to economic growth and sustainability in the years to come.
Of the more than 6,300 biopharmaceuticals in development, ~70% have the potential to be designated “first-in-class medicines”. The sheer number, diversity and increasing sophistication of emerging biopharmaceuticals (e.g. designer proteins as well as gene and whole cell therapies) in drug discovery pipelines is putting the industry under considerable pressure to produce these medicines in a cost-effective and safe manner. If Europe’s biopharmaceutical sector is to grow, the industry urgently requires not only new analytical approaches that enable rapid design of efficient bioprocesses to produce new biological medicines but also excellent scientists to pioneer the development of innovative solutions as new challenges emerge.
The consortium of the European Industrial Doctorate STACCATO was united by a shared vision - to contribute to delivering life-changing medicines to as many people as possible in the years to come. The STACCATO consortium has achieved its overall goal and has delivered on the research and training objectives proposed at the beginning of the project. Through the immersion of the STACCATO ESRs in an extensive industry-focussed training programme (9 of the 11 ESRs were employed at non-academic partners), we have equipped the students with the scientific, business and entrepreneurial skills required to become the next generation of leaders in the sector. The consortium has also developed ground-breaking approaches for understanding biopharmaceutical manufacturing processes and demonstrated that single cell analysis is a powerful approach for characterising the cell populations used for biopharmaceutical manufacturing.
Of the more than 6,300 biopharmaceuticals in development, ~70% have the potential to be designated “first-in-class medicines”. The sheer number, diversity and increasing sophistication of emerging biopharmaceuticals (e.g. designer proteins as well as gene and whole cell therapies) in drug discovery pipelines is putting the industry under considerable pressure to produce these medicines in a cost-effective and safe manner. If Europe’s biopharmaceutical sector is to grow, the industry urgently requires not only new analytical approaches that enable rapid design of efficient bioprocesses to produce new biological medicines but also excellent scientists to pioneer the development of innovative solutions as new challenges emerge.
The consortium of the European Industrial Doctorate STACCATO was united by a shared vision - to contribute to delivering life-changing medicines to as many people as possible in the years to come. The STACCATO consortium has achieved its overall goal and has delivered on the research and training objectives proposed at the beginning of the project. Through the immersion of the STACCATO ESRs in an extensive industry-focussed training programme (9 of the 11 ESRs were employed at non-academic partners), we have equipped the students with the scientific, business and entrepreneurial skills required to become the next generation of leaders in the sector. The consortium has also developed ground-breaking approaches for understanding biopharmaceutical manufacturing processes and demonstrated that single cell analysis is a powerful approach for characterising the cell populations used for biopharmaceutical manufacturing.
The STACCATO project was comprised of three scientific work packages:
The WP1 team, focussed on the development of experimental and computational methods for single cell RNA sequencing (scRNA-seq) using the BD Rhapsody platform, single cell mtDNA sequencing and the measurement of protein abundance in individual cells. The activities of WP1 enabled the first single cell studies of biopharmaceutical cell factories. The Rhapsody system was also successfully applied to chimeric antigen receptor (CAR)-T cell therapies and to human embryonic stem cell derived pancreatic aggregates. To study mtDNA mutations, a method was developed to detect mitochondrial heteroplasmy in individual CHO cells The consortium was also able to measure protein abundance for CHO cells and CAR-T cell therapies using BD’s AbSeq system.
WP2 centred on the analysis of cell factories used to produce recombinant proteins, gene therapies, vaccines, and oncolytic viruses. Over the course of the project the first-ever single cell study of CHO cells was accomplished. Additional experiments were carried out to investigate additional phenotypes and probe the correlation between gene expression and recombinant protein abundance in two mAb producing CHO cell lines. The 10X Genomics Chromium platform was also used to capture chromatin accessibility profiles in CHO cells for the first time. Further experiments in CHO cells focused on uncovering the relationship between the cell specific perfusion rate (CSPR) in high cell density perfusion culture (HCDP) and a high throughput platform for media screening has been designed. In addition the BD Rhapsody whole transcriptome analysis (WTA) was also used to capture scRNA-seq data for A549 producing oncolytic viruses. WP2 researchers working with insect cell systems developed customised cell culture strategies to increase titer for enhancing virus like particle (VLP) and recombinant adeno-associated virus (AAV). This work enabled the successful application of the Rhapsody system for the Sf9 and Hi5 insect cell lines, which allowed transcriptional heterogeneity to be captured at single cell resolution for the first time.
The third STACCATO work package focussed on the application of single cell technology for the analysis of exciting new therapies where living cells are utilised for treatment. For instance, STACCATO generated new knowledge that has the potential to improve the manufacture of CAR T cells by understanding heterogeneity introduced during the manufacturing process. STACCATO completed a range single cell analyses of CAR T-cells. STACCATO partners have also developed an efficient pancreatic differentiation protocol resulting in an increased yield of insulin-positive cells and functional glucose-stimulated insulin secretion.
Overcoming the inherent variability of cells grown in vitro to deliver effective, uniform and safe biological medicines is one of the most significant challenges faced by the industry today. The STACCATO research programme developed advanced experimental and computational methods to characterise manufacturing systems used in the biopharmaceutical industry with an unprecedented level of detail. During the project, the STACCATO ESRs contributed in total to 34 scientific publications comprising 11 published papers with a further 23 manuscripts in preparation for submission to peer-reviewed journals. STACCATO also contributed to 22 conferences. To further disseminate the knowledge gained throughout the project, we have created the STACCATO website, which includes a dedicated STACCATO Wiki, a searchable online platform hosted on the STACCATO website, that contains a collection of various terms related to the project. In addition, a series of podcasts were developed to communicate the research finding and experience to a broad audience.
The WP1 team, focussed on the development of experimental and computational methods for single cell RNA sequencing (scRNA-seq) using the BD Rhapsody platform, single cell mtDNA sequencing and the measurement of protein abundance in individual cells. The activities of WP1 enabled the first single cell studies of biopharmaceutical cell factories. The Rhapsody system was also successfully applied to chimeric antigen receptor (CAR)-T cell therapies and to human embryonic stem cell derived pancreatic aggregates. To study mtDNA mutations, a method was developed to detect mitochondrial heteroplasmy in individual CHO cells The consortium was also able to measure protein abundance for CHO cells and CAR-T cell therapies using BD’s AbSeq system.
WP2 centred on the analysis of cell factories used to produce recombinant proteins, gene therapies, vaccines, and oncolytic viruses. Over the course of the project the first-ever single cell study of CHO cells was accomplished. Additional experiments were carried out to investigate additional phenotypes and probe the correlation between gene expression and recombinant protein abundance in two mAb producing CHO cell lines. The 10X Genomics Chromium platform was also used to capture chromatin accessibility profiles in CHO cells for the first time. Further experiments in CHO cells focused on uncovering the relationship between the cell specific perfusion rate (CSPR) in high cell density perfusion culture (HCDP) and a high throughput platform for media screening has been designed. In addition the BD Rhapsody whole transcriptome analysis (WTA) was also used to capture scRNA-seq data for A549 producing oncolytic viruses. WP2 researchers working with insect cell systems developed customised cell culture strategies to increase titer for enhancing virus like particle (VLP) and recombinant adeno-associated virus (AAV). This work enabled the successful application of the Rhapsody system for the Sf9 and Hi5 insect cell lines, which allowed transcriptional heterogeneity to be captured at single cell resolution for the first time.
The third STACCATO work package focussed on the application of single cell technology for the analysis of exciting new therapies where living cells are utilised for treatment. For instance, STACCATO generated new knowledge that has the potential to improve the manufacture of CAR T cells by understanding heterogeneity introduced during the manufacturing process. STACCATO completed a range single cell analyses of CAR T-cells. STACCATO partners have also developed an efficient pancreatic differentiation protocol resulting in an increased yield of insulin-positive cells and functional glucose-stimulated insulin secretion.
Overcoming the inherent variability of cells grown in vitro to deliver effective, uniform and safe biological medicines is one of the most significant challenges faced by the industry today. The STACCATO research programme developed advanced experimental and computational methods to characterise manufacturing systems used in the biopharmaceutical industry with an unprecedented level of detail. During the project, the STACCATO ESRs contributed in total to 34 scientific publications comprising 11 published papers with a further 23 manuscripts in preparation for submission to peer-reviewed journals. STACCATO also contributed to 22 conferences. To further disseminate the knowledge gained throughout the project, we have created the STACCATO website, which includes a dedicated STACCATO Wiki, a searchable online platform hosted on the STACCATO website, that contains a collection of various terms related to the project. In addition, a series of podcasts were developed to communicate the research finding and experience to a broad audience.
The STACCATO research programme has developed and applied a range of experimental and computational methods to characterise manufacturing systems used in the biopharmaceutical industry with an unprecedented level of detail. These methods have enabled the consortium to progress beyond the current state of the art by allowing the measurement of variations in DNA sequence and the abundance of RNA and protein molecules in thousands of individual cells and correlating these measurements with the performance of the manufacturing process. The approaches developed during STACCATO provide a new route to allow biopharmaceutical companies understand their manufacturing systems at an unprecedented level of detail. Ultimately, these tools will contribute to improving the production of existing drugs and accelerating the delivery of new medicines to patients.