Sara Mills

The field of cell and gene therapy (CGT) is maturing at a rapid rate. Manufacturing remains a major challenge and manufacturing failures and limitations are a notable source of CGT products not meeting specification or being held back from regulatory approvals. To ensure that products remain compliant and competitive throughout their lifecycle, CGT process development requires both ongoing advancement of fit-for-purpose technologies to allow for and support well-designed development studies… Show more

The field of cell and gene therapy (CGT) is maturing at a rapid rate. Manufacturing remains a major challenge and manufacturing failures and limitations are a notable source of CGT products not meeting specification or being held back from regulatory approvals. To ensure that products remain compliant and competitive throughout their lifecycle, CGT process development requires both ongoing advancement of fit-for-purpose technologies to allow for and support well-designed development studies, and a methodology that enables these studies to occur effectively during focused product development campaigns. We describe a framework for ongoing innovation in CGT process development, manufacturing, and clinical testing, based on the quality by design (QbD) approach. We propose use of the concepts of process discovery, process characterization, and process development in an iterative way to refine the design space as a product matures. This strategy is enabled by the early implementation of broad and robust analytics, and a modular approach to accelerate optimization. With these strategies, CGT developers can prospectively plan for comparability studies and develop in a stage-appropriate manner, to allow for ongoing innovation and improvements from discovery through to commercialization. Show less

Human induced pluripotent stem (iPS) cells are remarkably similar to embryonic stem (ES) cells, but recent reports indicate that there may be important differences between them. We carried out a systematic comparison of human iPS cells generated from hepatocytes (representative of endoderm), skin ?broblasts (mesoderm) and melanocytes (ectoderm). All low-passage iPS cells analysed retain a transcriptional memory of the original cells. The persistent expression of somatic genes can be partially… Show more

Human induced pluripotent stem (iPS) cells are remarkably similar to embryonic stem (ES) cells, but recent reports indicate that there may be important differences between them. We carried out a systematic comparison of human iPS cells generated from hepatocytes (representative of endoderm), skin ?broblasts (mesoderm) and melanocytes (ectoderm). All low-passage iPS cells analysed retain a transcriptional memory of the original cells. The persistent expression of somatic genes can be partially explained by incomplete promoter DNA methylation. This epigenetic mechanism underlies a robust form of memory that can be found in iPS cells generated by multiple laboratories using different methods, including RNA transfection. Incompletely silenced genes tend to be isolated from other genes that are repressed during reprogramming, indicating that recruitment of the silencing machinery may be inefficient at isolated genes. Knockdown of the incompletely reprogrammed gene C9orf64 (chromosome 9 open reading frame 64) reduces the ?efficiency of human iPS cell generation, indicating that somatic memory genes may be functionally relevant during reprogramming. Show less

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess… Show more

Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression. Show less