Snapshots of Pluripotency

Mammalian Germ Cell Development: From Mechanism to In Vitro Reconstitution

The germ cell lineage gives rise to totipotency and perpetuates and diversifies genetic as well as epigenetic information. Specifically, germ cells undergo epigenetic reprogramming/programming, replicate genetic information with high fidelity, and create genetic diversity through meiotic recombination. Driven by advances in our understanding of the mechanisms underlying germ cell development and stem cell/reproductive technologies, research over the past 2 decades has culminated in the in vitro reconstitution of mammalian germ cell development: mouse pluripotent stem cells (PSCs) can now be induced into primordial germ cell-like cells (PGCLCs) and then differentiated into fully functional oocytes and spermatogonia, and human PSCs can be induced into PGCLCs and into early oocytes and prospermatogonia with epigenetic reprogramming. Here, I provide my perspective on the key investigations that have led to the in vitro reconstitution of mammalian germ cell development, which will be instrumental in exploring salient themes in germ cell biology and, with further refinements/extensions, in developing innovative medical applications.

Organization of the Pluripotent Genome

In the past several decades, the establishment of in vitro models of pluripotency has ushered in a golden era for developmental and stem cell biology. Research in this arena has led to profound insights into the regulatory features that shape early embryonic development. Nevertheless, an integrative theory of the epigenetic principles that govern the pluripotent nucleus remains elusive. Here, we summarize the epigenetic characteristics that define the pluripotent state. We cover what is currently known about the epigenome of pluripotent stem cells and reflect on the use of embryonic stem cells as an experimental system. In addition, we highlight insights from super-resolution microscopy, which have advanced our understanding of the form and function of chromatin, particularly its role in establishing the characteristically "open chromatin" of pluripotent nuclei. Further, we discuss the rapid improvements in 3C-based methods, which have given us a means to investigate the 3D spatial organization of the pluripotent genome. This has aided the adaptation of prior notions of a "pluripotent molecular circuitry" into a more holistic model, where hotspots of co-interacting domains correspond with the accumulation of pluripotency-associated factors. Finally, we relate these earlier hypotheses to an emerging model of phase separation, which posits that a biophysical mechanism may presuppose the formation of a pluripotent-state-defining transcriptional program.

100 Years of phenogenetics: Valentin Haecker and his examination of the phenotype

Following the 'rediscovery' of Mendel's work around 1900 the study of genetics grew rapidly and multiple new inheritance theories quickly emerged such as Hugo de Vries' "Mutation Theory" (1901) and the "Boveri-Sutton Chromosome Theory" (1902). Mendel's work also caught the attention of the German geneticist Valentin Haecker, yet he was generally dissatisfied the simplicity of Mendelian genetics as he believed that inheritance and the expression of various characteristics appeared to be much more complex than the proposed "on-off hypotheses". Haecker's primary objection was that Mendelian-based theories still failed to bridge the gap between hereditary units and phenotypic traits. Haecker thus set out to bridge this gap in his research program, which he called Phänogenetik ("phenogenetics"). He outlined his work in a special study "Entwicklungsgeschichtliche Eigenschaftsanalyse (Phänogenetik)" in 1918. 2018 thus marks the 100th anniversary of Haecker's seminal publication, which was devoted to the analysis of the phenotype and highlighted the true complexity of heredity. This article takes a specific look at Haecker and his work, while also illustrating how this often forgotten scientist influenced the field of genetics and other scientists.

Advances in translational inner ear stem cell research

Stem cell research is expanding our understanding of developmental biology as well as promising the development of new therapies for a range of different diseases. Within hearing research, the use of stem cells has focused mainly on cell replacement. Stem cells however have a broad range of other potential applications that are just beginning to be explored in the ear. Mesenchymal stem cells are an adult derived stem cell population that have been shown to produce growth factors, modulate the immune system and can differentiate into a wide variety of tissue types. Potential advantages of mesenchymal/adult stem cells are that they have no ethical constraints on their use. However, appropriate regulatory oversight seems necessary in order to protect patients from side effects. Disadvantages may be the lack of efficacy in many preclinical studies. But if proven safe and efficacious, they are easily translatable to clinical trials. The current review will focus on the potential application on mesenchymal stem cells for the treatment of inner ear disorders.

Vitamin C and l-Proline Antagonistic Effects Capture Alternative States in the Pluripotency Continuum

Metabolites and cofactors are emerging as key regulators of cell plasticity and reprogramming, and their role in the control of pluripotency is just being discovered. Here we provide unprecedented evidence that embryonic stem cell (ESC) pluripotency relies on the relative levels of two physiological metabolites, namely ascorbic acid (vitamin C, VitC) and l-proline (l-Pro), which affect global DNA methylation, transcriptional profile, and energy metabolism. Specifically, while a high VitC/l-Pro ratio drives ESCs toward a naive state, the opposite condition (l-Pro excess) captures a fully reversible early primed pluripotent state, which depends on autocrine fibroblast growth factor and transforming growth factor β signaling pathways. Our findings highlight the pivotal role of metabolites availability in controlling the pluripotency continuum from naive to primed states.

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Global DNA methylation is modulated by l-Pro and VitC availability in ESCs

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l-Pro and VitC relative levels induce naive and reversible primed pluripotency

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High l-Pro/low VitC levels induce metabolic reprogramming in ESCs

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l-Pro induces and sustains autocrine FGF and TGF-β signaling in ESCs

Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling

The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies. We conclude that sample heterogeneity masks DNA methylation signatures in subpopulations of cells and thus believe that beside a genetic evaluation, extensive epigenomic screening should become a standard procedure to ensure hiPSCs state before they are used for genome editing and differentiation into neurons of interest. In particular, we suggest that exploitation of the single-cell composition of the epigenome will provide important insights into heterogeneity within hiPSCs subpopulations to fast forward development of reliable hiPSC-based analytical platforms in neurological disorders modelling and before completed hiPSC technology will be implemented in clinical approaches.