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The UK has been a global leader in the development and regulation of biobanks and bio-databases that facilitate clinical and laboratory access to tissue, blood samples, DNA and data. Yet the persistent barrier to mobilise non- White communities into actively contributing to and, subsequently benefiting from structural and scientific advantages that the UK can offer constitutes a ‘Silent Crisis’. This paper builds on ongoing research on stem cell donations carried out by the authors in the UK. We underline the centrality of the concept of ‘relatedness’ in donor recruitment, and the tricky role it has played, both as a uniting and an alienating force within and between different ethnic communities. We argue that the building of a thick societal relatedness or what we term as ‘polyphonic relatedness’ offers a constructive guidance to overcome the racial disparity in biomaterial donations.

Genome-scale technologies are increasingly adopted by the stem cell research community, because of thepotential to uncover the molecular events most informative about a stem cell state. These technologies also presentenormous challenges around the sharing and visualisation ofdata derived from different laboratories or under differentexperimental conditions. Stemformatics is an easy to use, publicly accessible portal that hosts a large collection ofexemplar stem cell data. It provides fast visualisation of gene expression across a range of mouse and human datasets, withtransparent links back to the original studies. One difficulty in the analysis of stem cell signatures is the paucity of publicpathways/gene lists relevant to stem cell or developmental biology. Stemformatics provides a simple mechanism tocreate, share and analyse gene sets, providing a repository of community-annotated stem cell gene lists that areinformative about pathways, lineage commitment, and common technical artefacts. Stemformatics can be accessed atstemformatics.org.

Down syndrome (DS) is the most frequent cause of humancongenital mental retardation. Cognitive deficits in DSresult from perturbations of normal cellular processesboth during development and in adult tissues, but themechanisms underlying DS etiology remain poorly under-stood. To assess the ability of induced pluripotent stemcells (iPSCs) to model DS phenotypes, as a prototypicalcomplex human disease, we generated bona fide DS andwild-type (WT) nonviral iPSCs by episomal reprogram-ming. DS iPSCs selectively overexpressed chromosome 21genes, consistent with gene dosage, which was associatedwith deregulation of thousands of genes throughout thegenome. DS and WT iPSCs were neurally converted at>95% efficiency and had remarkably similar lineage po-tency, differentiation kinetics, proliferation, and axonextension at early time points. However, at later timepoints DS cultures showed a twofold bias toward glial line-ages. Moreover, DS neural cultures were up to two timesmore sensitive to oxidative stress-induced apoptosis, andthis could be prevented by the antioxidant N-acetylcysteine.Our results reveal a striking complexity in the genetic alter-ations caused by trisomy 21 that are likely to underlie DSdevelopmental phenotypes, and indicate a central role fordefective early glial development in establishing develop-mental defects in DS brains. Furthermore, oxidative stresssensitivity is likely to contribute to the accelerated neurode-generation seen in DS, and we provide proof of concept forscreening corrective therapeutics using DS iPSCs and theirderivatives. Nonviral DS iPSCs can therefore model fea-tures of complex human disease in vitro and provide arenewable and ethically unencumbered discovery platform.

Genome-scale technologies are increasingly adopted by the stem cell research community, because of thepotential to uncover the molecular events most informative about a stem cell state. These technologies also presentenormous challenges around the sharing and visualisation ofdata derived from different laboratories or under differentexperimental conditions. Stemformatics is an easy to use, publicly accessible portal that hosts a large collection ofexemplar stem cell data. It provides fast visualisation of gene expression across a range of mouse and human datasets, withtransparent links back to the original studies. One difficulty in the analysis of stem cell signatures is the paucity of publicpathways/gene lists relevant to stem cell or developmental biology. Stemformatics provides a simple mechanism tocreate, share and analyse gene sets, providing a repository of community-annotated stem cell gene lists that areinformative about pathways, lineage commitment, and common technical artefacts. Stemformatics can be accessed atstemformatics.org.

Genome-scale technologies are increasingly adopted by the stem cell research community, because of thepotential to uncover the molecular events most informative about a stem cell state. These technologies also presentenormous challenges around the sharing and visualisation ofdata derived from different laboratories or under differentexperimental conditions. Stemformatics is an easy to use, publicly accessible portal that hosts a large collection ofexemplar stem cell data. It provides fast visualisation of gene expression across a range of mouse and human datasets, withtransparent links back to the original studies. One difficulty in the analysis of stem cell signatures is the paucity of publicpathways/gene lists relevant to stem cell or developmental biology. Stemformatics provides a simple mechanism tocreate, share and analyse gene sets, providing a repository of community-annotated stem cell gene lists that areinformative about pathways, lineage commitment, and common technical artefacts. Stemformatics can be accessed atstemformatics.org.

Down syndrome (DS) is the most frequent cause of humancongenital mental retardation. Cognitive deficits in DSresult from perturbations of normal cellular processesboth during development and in adult tissues, but themechanisms underlying DS etiology remain poorly under-stood. To assess the ability of induced pluripotent stemcells (iPSCs) to model DS phenotypes, as a prototypicalcomplex human disease, we generated bona fide DS andwild-type (WT) nonviral iPSCs by episomal reprogram-ming. DS iPSCs selectively overexpressed chromosome 21genes, consistent with gene dosage, which was associatedwith deregulation of thousands of genes throughout thegenome. DS and WT iPSCs were neurally converted at>95% efficiency and had remarkably similar lineage po-tency, differentiation kinetics, proliferation, and axonextension at early time points. However, at later timepoints DS cultures showed a twofold bias toward glial line-ages. Moreover, DS neural cultures were up to two timesmore sensitive to oxidative stress-induced apoptosis, andthis could be prevented by the antioxidant N-acetylcysteine.Our results reveal a striking complexity in the genetic alter-ations caused by trisomy 21 that are likely to underlie DSdevelopmental phenotypes, and indicate a central role fordefective early glial development in establishing develop-mental defects in DS brains. Furthermore, oxidative stresssensitivity is likely to contribute to the accelerated neurode-generation seen in DS, and we provide proof of concept forscreening corrective therapeutics using DS iPSCs and theirderivatives. Nonviral DS iPSCs can therefore model fea-tures of complex human disease in vitro and provide arenewable and ethically unencumbered discovery platform.

Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken strand-specific RNA sequencing of multiple cellular RNA fractions (>20 Gb) to uncover the transcriptional complexity of human embryonic stem cells (hESCs). We have shown that human embryonic stem (ES) cells display a high degree of transcriptional diversity, with more than half of active genes generating RNAs that differ from conventional gene models. We found evidence that more than 1000 genes express long 5′ and/or extended 3′UTRs, which was confirmed by “virtual Northern” analysis. Exhaustive sequencing of the membrane-polysome and cytosolic/untranslated fractions of hESCs was used to identify RNAs encoding peptides destined for secretion and the extracellular space and to demonstrate preferential selection of transcription complexity for translation in vitro. The impact of this newly defined complexity on known gene-centric network models such as the Plurinet and the cell surface signaling machinery in human ES cells revealed a significant expansion of known transcript isoforms at play, many predicting possible alternative functions based on sequence alterations within key functional domains.

Background: Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for these molecules. Results: To assess the biological relevance of isomiRs, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline called miRNA-MATE to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. A large proportion of isomiRs potentially derive from AGO2 cleavage independent of Dicer. We isolated polyribosome-associated mRNA, captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies allow us to experimentally determine genome-wide mRNA targets, and these experiments showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Conclusions: Together, these results find isomiRs to be biologically relevant and functionally cooperative partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur when the specificity of miRNA targeting is mediated by only 6 to 11 nucleotides.

Human embryonic stem cells (hESCs) replicate in vitro by the process of self-renewal, whilst maintaining their pluripotency. Understanding the pathways involved in the regulation of this process will assist in developing fully-defined conditions for the robust proliferation of hESCs necessary for therapeutic applications. We previously demonstrated that sphingosine-1-phosphate (S1P) plays an important role in survival and proliferation of hESCs, and here the key signaling pathways and downstream targets of S1P were investigated in a representative cell line (Shef 4). A significant rise in ERK1/2 activation with S1P treatment was witnessed in hESCs maintained on murine embryonic fibroblasts (MEFs) exhibiting significantly higher levels of active ERK1/2 than those grown on Matrigel. RT-PCR and microarray analysis of micro-dissected, non-differentiated hESC revealed 1049 differentially expressed genes in S1P treated preparations compared with controls (n = 3). S1P regulated apoptosis through several BCL-2 family members, including BAX and BID, with increased expression of cell cycle progression genes associated with proliferation of hESC cultures. S1P treatment also increased expression of cell adhesion genes specifically cadherins and integrins. However, gene expression associated with pluripotency was decreased with S1P treatment indicating that an increased rate of hESC turnover (higher proliferation and lower apoptosis) may be balanced by an increased susceptibility to differentiate.

Human embryonic stem cells (hESCs) replicate in vitro by the process of self-renewal, whilst maintaining their pluripotency. Understanding the pathways involved in the regulation of this process will assist in developing fully-defined conditions for the robust proliferation of hESCs necessary for therapeutic applications. We previously demonstrated that sphingosine-1-phosphate (S1P) plays an important role in survival and proliferation of hESCs, and here the key signaling pathways and downstream targets of S1P were investigated in a representative cell line (Shef 4). A significant rise in ERK1/2 activation with S1P treatment was witnessed in hESCs maintained on murine embryonic fibroblasts (MEFs) exhibiting significantly higher levels of active ERK1/2 than those grown on Matrigel. RT-PCR and microarray analysis of micro-dissected, non-differentiated hESC revealed 1049 differentially expressed genes in S1P treated preparations compared with controls (n = 3). S1P regulated apoptosis through several BCL-2 family members, including BAX and BID, with increased expression of cell cycle progression genes associated with proliferation of hESC cultures. S1P treatment also increased expression of cell adhesion genes specifically cadherins and integrins. However, gene expression associated with pluripotency was decreased with S1P treatment indicating that an increased rate of hESC turnover (higher proliferation and lower apoptosis) may be balanced by an increased susceptibility to differentiate.