Genetic Signatures of Evolution of the Pluripotency Gene Regulating Network across Mammals

Advancing stem cell technologies for conservation of wildlife biodiversity

Wildlife biodiversity is essential for healthy, resilient and sustainable ecosystems. For biologists, this diversity also represents a treasure trove of genetic, molecular and developmental mechanisms that deepen our understanding of the origins and rules of life. However, the rapid decline in biodiversity reported recently foreshadows a potentially catastrophic collapse of many important ecosystems and the associated irreversible loss of many forms of life on our planet. Immediate action by conservationists of all stripes is required to avert this disaster. In this Spotlight, we draw together insights and proposals discussed at a recent workshop hosted by Revive & Restore, which gathered experts to discuss how stem cell technologies can support traditional conservation techniques and help protect animal biodiversity. We discuss reprogramming, in vitro gametogenesis, disease modelling and embryo modelling, and we highlight the prospects for leveraging stem cell technologies beyond mammalian species.

Complex regulatory networks influence pluripotent cell state transitions in human iPSCs

Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines.

Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis

After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency to give rise to embryonic stem cells, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that pervasive regulatory remodeling has shaped the earliest stages of development. Here, we show that maternal homologs of mammalian pluripotency reprogramming factors OCT4 and SOX2 divergently activate the two subgenomes of Xenopus laevis, an allotetraploid that arose from hybridization of two diploid species ~18 million years ago. Although most genes have been retained as two homeologous copies, we find that a majority of them undergo asymmetric activation in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in predicted enhancer architecture between the subgenomes, which likely arose through genomic disruptions as a consequence of allotetraploidy. However, comparison with diploid X. tropicalis and zebrafish shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the core vertebrate pluripotency transcriptional program, amid genomic instability following hybridization.

Bat pluripotent stem cells reveal unusual entanglement between host and viruses

Bats are distinctive among mammals due to their ability to fly, use laryngeal echolocation, and tolerate viruses. However, there are currently no reliable cellular models for studying bat biology or their response to viral infections. Here, we created induced pluripotent stem cells (iPSCs) from two species of bats: the wild greater horseshoe bat (Rhinolophus ferrumequinum) and the greater mouse-eared bat (Myotis myotis). The iPSCs from both bat species showed similar characteristics and had a gene expression profile resembling that of cells attacked by viruses. They also had a high number of endogenous viral sequences, particularly retroviruses. These results suggest that bats have evolved mechanisms to tolerate a large load of viral sequences and may have a more intertwined relationship with viruses than previously thought. Further study of bat iPSCs and their differentiated progeny will provide insights into bat biology, virus host relationships, and the molecular basis of bats' special traits.

Pluripotent Stem Cells of Order Carnivora: Technical Perspective

Human and mouse induced pluripotent stem cells (PSCs) are widely used for studying early embryonic development and for modeling of human diseases. Derivation and studying of PSCs from model organisms beyond commonly used mice and rats may provide new insights into the modeling and treating human diseases. The order Carnivora representatives possess unique features and are already used for modeling human-related traits. This review focuses on the technical aspects of derivation of the Carnivora species PSCs as well as their characterization. Current data on dog, feline, ferret, and American mink PSCs are summarized.

Generation and gene expression profiles of Grevy's zebra induced Pluripotent Stem Cells

Induced pluripotent stem cells (iPSCs) can serve as a biological resource for functional and conservation research for various species. This realisation has led to the generation of iPSCs from many species, including those identified as endangered. However, the understanding of species variation in mammalian iPSCs remains largely unknown. To gain insight into species variation in iPSCs, we generated iPSCs from a new species Grevy's zebra (Equus grevyi; gz-iPSCs), which has been listed as endangered in the IUCN (International Union for Conservation of Nature) Red List. We isolated primary fibroblast cells from an individual and successfully reprogrammed them into iPSCs. The generated gz-iPSCs continued to grow under primed-type culture condition and showed pluripotency and differentiation potential. To describe the molecular characteristics of gz-iPSCs, we performed RNA sequencing analysis. The gz-iPSC transcriptome showed robust expression of pluripotency associated genes reported in human and mouse, suggesting evolutionary conservation among the species. This study provides insight into the iPSCs from a rare species and helps the understanding of the gene expression basis underlying mammalian PSCs.

Cytology, function and dynamics of stem and progenitor cells in decapod crustaceans

Stem cells play key roles in development, tissue homeostasis, regeneration, ageing and diseases. Comprehensive reviews on stem cells are available for the determinately growing mammals and insects and some lower invertebrates like hydra but are rare for larger, indeterminately growing invertebrates that can live for many decades. This paper reviews the cytology, function and dynamics of stem and progenitor cells in the decapod crustaceans, a species-rich and ecologically and economically important animal group that includes mainly indeterminate growers but also some determinate growers. Further advantages of decapods for stem cell research are almost 1000-fold differences in body size and longevity, the regeneration of damaged appendages and the virtual absence of age-related diseases and tumours in the indeterminately growing species. The available data demonstrate that the Decapoda possess a remarkable variety of structurally and functionally different stem cells in embryos and larvae, and in the epidermis, musculature, haematopoietic tissue, heart, brain, hepatopancreas, olfactory sense organs and gonads of adults. Some of these seem to be rather continuously active over a lifetime but others are cyclically activated and silenced in periods of days, weeks and years, depending on the specific organ and function. Stem cell proliferation is triggered by signals related to development, moulting, feeding, reproduction, injury, infection, environmental enrichment and social status. Some regulatory pathways have already been identified, including the evolutionarily conserved GATA-binding and runt-domain transcription factors, the widespread neurotransmitter serotonin, the arthropod-specific hormone 20-hydroxyecdysone and the novel astakine growth factors. Knowledge of stem cells in decapods primarily refines our picture on the development, growth and maintenance of tissues and organs in this animal group. Cultured decapod stem cells have good potential for toxicity testing and virus research with practical relevance for aquaculture. Knowledge of stem cells in decapods also broadens our understanding of the evolution of stem cells and regeneration in the animal kingdom. The stem cells of long-lived, indeterminately growing decapods may hold the key to understanding how stem and progenitor cells function into old age without adverse side effects, possibly evoking new ideas for the development of anti-ageing and anti-cancer treatments in humans.