Integrative genomic and functional analyses reveal neuronal subtype differentiation bias in human embryonic stem cell lines

Abstract

The self-renewal and differentiation potential of human embryonic stem cells (hESCs) suggests that hESCs could be used for regenerative medicine, especially for restoring neuronal functions in brain diseases. However, the functional properties of neurons derived from hESC are largely unknown. Moreover, because hESCs were derived under diverse conditions, the possibility arises that neurons derived from different hESC lines exhibit distinct properties, but this possibility remains unexplored. To address these issues, we developed a protocol that allows stepwise generation from hESCs of cultures composed of Ϸ70 -80% human neurons that exhibit spontaneous synaptic network activity. Comparison of neurons derived from the well characterized HSF1 and HSF6 hESC lines revealed that HSF1-but not HSF6-derived neurons exhibit forebrain properties. Accordingly, HSF1-derived neurons initially form primarily GABAergic synaptic networks, whereas HSF6-derived neurons initially form glutamatergic networks. microRNA profiling revealed significant expression differences between the two hESC lines, suggesting that microRNAs may influence their distinct differentiation properties. These observations indicate that although both HSF1 and HSF6 hESCs differentiate into functional neurons, the two hESC lines exhibit distinct differentiation potentials, suggesting that they are preprogrammed. Information on hESC line-specific differentiation biases is crucial for neural stem cell therapy and establishment of novel disease models using hESCs.microRNA ͉ neural differentiation ͉ neural stem cells ͉ synapse formation H uman embryonic stem cells (hESCs) are thought to be capable of unlimited proliferation (i.e., self-renewal), and of in vitro and in vivo differentiation into cell types originating from all three germ layers including neurons, in short, to be pluripotent (1-3). This makes hESCs perhaps the only stable and genetically tractable source of human neurons, which, besides being potentially useful for therapeutic purposes, could be invaluable for studying the function of neurological disease genes in a human genetic background (4). However, different hESC lines were established under diverse culture conditions from embryos with distinct genetic backgrounds which might endow the hESCs and their derivative neurons with distinct epigenetic and cellular properties, with obvious implications for their use in regenerative medicine. The relative properties of neurons derived from different hESC lines, however, are unknown, prompting the present study.Here, we have developed methods that allow for controlled, stepwise conversion of hESCs into cultures that contain Ͼ95% human neural stem/progenitor cells (hNPCs). The hNPCs are in turn differentiated into cultures containing 70-80% human neurons that form functional synaptic networks when cocultured with astrocytes. Using such methods, we compared neuronal sublineage differentiation and network properties of neurons derived from two NIH-registered hESC lines, HSF6 [XX, 46, National Institutes o...

Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration

“…We established and modified procedures for high-throughput studies to expand hESCs and induce a nearly uniform differentiation of these cells into NESTIN, SOX2, PAX6, and polysialylated neural cell adhesion molecule (PSA-NCAM)-positive neural precursors (NPCs) using the bone morphogenic protein antagonist, noggin, and fibroblast growth factor 2 (FGF2) (1,13). We used a commercial, pooled wholegenome lentiviral shRNA library developed by the Broad Institute [The RNA1 Consortium (TRC)/Mission LentiPlex; Sigma] to search for genes that promoted or limited neural commitment and differentiation of hESCs (Fig.…”

Retinoic Acid and Bone Morphogenetic Protein Signaling Synergize to Efficiently Direct Epithelial Differentiation of Human Embryonic Stem Cells

“…Although recent evidence suggests that the propensity of individual cell lines to differentiate toward certain lineages may differ [37,38], it seems unlikely that the signaling mechanisms regulating differentiation to particular lineages are different. Thus, our findings in two cell hESC lines should be applicable to other lines, although relative levels of differentiation may vary.…”

Specification of functional neurons and glia from human pluripotent stem cells

“…Propensity also exists when subtype of cells are differentiated from a specific lineage. For instance, HSF1 primarily form forebrain neurons whereas HSF6 predominantly produce hindbrain, cervical and thoracic neurons (Wu et al, 2007). The bias of neural differentiation seems getting much more significant in hiPSCs, regardless of how the hiPSCs was derived (Hu et al, 2010).…”