Jeanne F. Loring

The northern white rhinoceros (NWR; Ceratotherium simum cottoni ) is functionally extinct, with only two nonreproductive females alive. Efforts to rescue the NWR from its inevitable demise have inspired the exploration of unconventional conservation methods, including the development of induced pluripotent stem cells (iPSCs) for the in vitro generation of artificial gametes. The integrity of iPSC genomes is critical for in vitro gametogenesis to be used for assisted reproductive technologies using NWR iPSCs. We generated a chromosome-level NWR reference genome that meets or exceeds the metrics proposed by the Vertebrate Genome Project, using complementary sequencing and mapping methods. The genome represents 40 autosomes, an X and a partially resolved Y chromosome, and the mitochondrial genome. Using comparative FISH mapping, we confirmed a general gene order conservation between the NWR and horse genomes. We aligned the NWR genome with that of the southern white rhinoceros (SWR; Ceratotherium simum simum ), a population that has been physically separated from the NWR for tens of thousands of years, and we found that the two subspecies are very similar on the chromosome level. Comparing long-read data from NWR iPSC lines and the fibroblast cultures used for reprogramming, we identified copy number variations that were likely to have been introduced during in vitro iPSC expansion. The NWR reference genome allows for efficient, rapid, and accurate assessment of the genomic integrity of iPSC lines to direct their differentiation. This will assist in strategies to rescue the NWR through extraordinary measures like cloning and the generation of embryos from iPSC-derived gametes.

Research conducted on the International Space Station (ISS) in low-Earth orbit (LEO) has shown the effects of microgravity on multiple organs. To investigate the effects of microgravity on the central nervous system, we developed a unique organoid strategy for modeling specific regions of the brain that are affected by neurodegenerative diseases. We generated 3-dimensional human neural organoids from induced pluripotent stem cells (iPSCs) derived from individuals affected by primary progressive multiple sclerosis (PPMS) or Parkinson’s disease (PD) and non-symptomatic controls, by differentiating them toward cortical and dopaminergic fates, respectively, and combined them with isogenic microglia. The organoids were cultured for a month using a novel sealed cryovial culture method on the International Space Station (ISS) and a parallel set that remained on Earth. Live samples were returned to Earth for analysis by RNA expression and histology and were attached to culture dishes to enable neurite outgrowth. Our results show that both cortical and dopaminergic organoids cultured in LEO had lower levels of genes associated with cell proliferation and higher levels of maturation-associated genes, suggesting that the cells matured more quickly in LEO. This study is continuing with several more missions in order to understand the mechanisms underlying accelerated maturation and to investigate other neurological diseases. Our goal is to make use of the opportunity to study neural cells in LEO to better understand and treat neurodegenerative disease on Earth and to help ameliorate potentially adverse neurological effects of space travel.

The motor symptoms of Parkinson’s disease (PD) are caused by the progressive loss of dopamine neurons from the substantia nigra. There are currently no treatments that can slow or reverse the neurodegeneration. To restore the lost neurons, international groups have initiated clinical trials using human embryonic or induced pluripotent stem cells (PSCs) to derive dopamine neuron precursors that are used as transplants to replace the lost neurons. Proof-of-principle experiments in the 1980s and 1990s showed that grafts of fetal ventral mesencephalon, which contains the precursors of the substantial nigra, could, under rare circumstances, reverse symptoms of the disease. Improvements in PSC technology and genomics have inspired researchers to design clinical trials using PSC-derived dopamine neuron precursors as cell replacement therapy for PD. We focus here on 4 such first-in-human clinical trials that have begun in the US, Europe, and Japan. We provide an overview of the sources of PSCs and the methods used to generate cells for transplantation. We discuss pros and cons of strategies for allogeneic, immune-matched, and autologous approaches and novel methods for overcoming rejection by the immune system. We consider challenges for safety and efficacy of the cells for durable engraftment, focusing on the genomics-based quality control methods to assure that the cells will not become cancerous. Finally, since clinical trials like these have never been undertaken before, we comment on the value of cooperation among rivals to contribute to advancements that will finally provide relief for the millions suffering from the symptoms of PD.

Exposure to microgravity in low-Earth orbit (LEO) has been shown to affect human cardiovascular, musculoskeletal, and immune systems. Post-flight brain imaging indicates that reports about astronauts and mouse models suggest that microgravity may cause intracranial fluid shifts and possibly alter white and gray matter of the brain [1]. To focus on the effects of microgravity on the brain, we used induced pluripotent stem cells (iPSCs) to produce three-dimensional (3D) human neural organoids as models of the nervous system. We studied iPSCs derived from four individuals, including people with the neurological diseases primary progressive multiple sclerosis (PPMS) and Parkinson’s disease (PD) and non-symptomatic controls. We patterned the organoids toward cortical and dopaminergic fates representing regions of the brain affected by MS and PD, respectively. Microglia were generated from the same cell lines and integrated into a portion of the organoids. The organoids were maintained for 30 days in a novel static culture system on the International Space Station (ISS) and live samples were returned to Earth. The post-flight samples were evaluated using histology, transcriptome and secretome analysis. Microglia-specific genes and secreted proteins were detectable in the microglia-containing organoid cultures. The gene expression analyses of individual organoids cultured in LEO and on Earth suggest that cell proliferation was lower and neural cells were more mature in samples that were cultured in LEO. These experiments lay the groundwork for further studies, including long term studies to investigate the effects of microgravity on the brain. With two more missions using similar cells, we are determining whether this effect of microgravity is consistent in separate experiments. Such studies may ultimately aid in developing countermeasures for the effects of microgravity on the nervous systems of astronauts during space exploration and suggest novel therapeutic interventions for neurological diseases on Earth.

Transplantation of human induced pluripotent stem cell-derived dopaminergic (iPSC-DA) neurons is a promising therapeutic strategy for Parkinson's disease (PD). To assess optimal cell characteristics and reproducibility, we evaluated the efficacy of iPSC-DA neuron precursors from two individuals with sporadic PD by transplantation into a hemiparkinsonian rat model after differentiation for either 18 (d18) or 25 days (d25). We found similar graft size and dopamine (DA) neuron content in both groups, but only the d18 cells resulted in recovery of motor impairments. In contrast, we report that d25 grafts survived equally as well and produced grafts rich in tyrosine hydroxylase-positive neurons, but were incapable of alleviating any motor deficits. We identified the mechanism of action as the extent of neurite outgrowth into the host brain, with d18 grafts supporting significantly more neurite outgrowth than nonfunctional d25 grafts. RNAseq analysis of the cell preparation suggests that graft efficacy may be enhanced by repression of differentiation-associated genes by REST, defining the optimal predifferentiation state for transplantation. This study demonstrates for the first time that DA neuron grafts can survive well in vivo while completely lacking the capacity to induce recovery from motor dysfunction. In contrast to other recent studies, we demonstrate that neurite outgrowth is the key factor determining graft efficacy and our gene expression profiling revealed characteristics of the cells that may predict their efficacy. These data have implication for the generation of DA neuron grafts for clinical application.

Fragile X Syndrome (FXS), the leading monogenic cause of intellectual disability and autism spectrum disorder, is caused by expansion of a CGG trinucleotide repeat in the 5ʹ-UTR of the Fragile X Mental Retardation-1 (FMR1) gene. Epigenetic silencing of FMR1 results in loss of the Fragile X Mental Retardation Protein (FMRP). Although most studies to date have focused on excitatory neurons, recent evidence suggests that GABAergic inhibitory networks are also affected. To investigate human GABAergic neurogenesis, we established a method to reproducibly derive inhibitory neurons from multiple FXS and control human pluripotent stem cell (hPSC) lines. Electrophysiological analyses suggested that the developing FXS neurons had a delay in the GABA functional switch, a transition in fetal development that converts the GABA_A channel’s function from depolarization to hyperpolarization, with profound effects on the developing brain. To investigate the cause of this delay, we analyzed 14 400 single-cell transcriptomes from FXS and control cells at 2 stages of GABAergic neurogenesis. While control and FXS cells were similar at the earlier time point, the later-stage FXS cells retained expression of neuroblast proliferation-associated genes and had lower levels of genes associated with action potential regulation, synapses, and mitochondria compared with controls. Our analysis suggests that loss of FMRP prolongs the proliferative stage of progenitors, which may result in more neurons remaining immature during the later stages of neurogenesis. This could have profound implications for homeostatic excitatory-inhibitory circuit development in FXS, and suggests a novel direction for understanding disease mechanisms that may help to guide therapeutic interventions.

Summary: Transplantation of human pluripotent stem cell-derived dopaminergic (DA) neurons is an emerging therapeutic strategy for Parkinson’s disease (PD). In this study, we demonstrate, for the first time, that that functional recovery after DA neuron transplant is critically dependent on graft-host integration, and not dependent on graft size or DA neuron content. Specifically, in anticipation of an autologous DA neuron transplant strategy, we studied two human induced pluripotent stem cell lines derived from people with idiopathic PD. We confirmed the cells’ ability to differentiate into mature DA neurons in vitro by assessing electrophysiology and depolarization-induced neurotransmitter release. To evaluate efficacy, we transplanted DA neuron precursors into a hemiparkinsonian rat model. We differentiated the cell lines for either 18 (d18) or 25 days (d25) to investigate the effect of cell maturity on efficacy. We found comparable graft survival in d18 and d25 groups from both cell lines, but behavioral analysis revealed that only d18 preparations, from both cell lines, resulted in recovery of motor impairments. Immunohistochemical analysis did not reveal any DA neuron-associated markers that correlated with efficacy. However, we found striking and consistent differences in graft neurite outgrowth between the two culture timepoints. The functional grafts from d18 cells had more outgrowth than non-functional d25 grafts. A time course of gene expression during differentiation of the cell lines revealed differences in genes associated with DA neuron development and neurite plasticity. These results are the first to demonstrate that graft-host integration, and not DA neuron content, is key to graft-induced functional recovery. The gene expression profiling may offer insight into the optimal developmental stage for graft efficacy.

Aim: This study aimed to determine knowledge and attitudes toward induced pluripotent stem cell technology and biobanking. Methods: A survey instrument was developed to determine individuals’ knowl... Plain language summary Stem cell biobanks have few samples from minorities for genomic studies. We conducted an online survey to understand knowledge and attitudes toward stem cell biobanks and tec...

Extinction rates are rising, and current conservation technologies may not be adequate for reducing species losses. Future conservation efforts may be aided by the generation of induced pluripotent stem cells (iPSCs) from highly endangered species. Generation of a set of iPSCs from multiple members of a species can capture some of the dwindling genetic diversity of a disappearing species. We generated iPSCs from fibroblasts cryopreserved in the Frozen Zoo ^® : nine genetically diverse individuals of the functionally extinct northern white rhinoceros ( Ceratotherium simum cottoni ) and two from the closely related southern white rhinoceros ( Ceratotherium simum simum ). We used a nonintegrating Sendai virus reprogramming method and developed analyses to confirm the cells' pluripotency and differentiation potential. This work is the first step of a long-term interdisciplinary plan to apply assisted reproduction techniques to the conservation of this highly endangered species. Advances in iPSC differentiation may enable generation of gametes in vitro from deceased and nonreproductive individuals that could be used to repopulate the species.