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Induced pluripotent stem cells (iPSCs) and their derivatives have been described to display epigenetic memory of their founder cells, as well as de novo reprogramming-associated alterations. In order to selectively explore changes due to the reprogramming process and not to heterologous somatic memory, we devised a circular reprogramming approach where somatic stem cells are used to generate iPSCs, which are subsequently re-differentiated into their original fate. As somatic founder cells, we employed human embryonic stem cell-derived neural stem cells (NSCs) and compared them to iPSC-derived NSCs derived thereof. Global transcription profiling of this isogenic circular system revealed remarkably similar transcriptomes of both NSC populations, with the exception of 36 transcripts. Amongst these we detected a disproportionately large fraction of X chromosomal genes, all of which were upregulated in iPSC-NSCs. Concurrently, we detected differential methylation of X chromosomal sites spatially coinciding with regions harboring differentially expressed genes. While our data point to a pronounced overall reinstallation of autosomal transcriptomic and methylation signatures when a defined somatic lineage is propagated through pluripotency, they also indicate that X chromosomal genes may partially escape this reinstallation process. Considering the broad application of iPSCs in disease modeling and regenerative approaches, such reprogramming-associated alterations in X chromosomal gene expression and DNA methylation deserve particular attention. [ABSTRACT FROM AUTHOR]

Background: NOS2 expression is mostly found in bacteria-exposed or cytokine-treated tissues and is mostly connected to innate immune reactions. There are three isoforms of NOS2 (NOS2-1 to -3). In RNA-seq data sets, analyzing inflammatory gene expression, only expression of the NOS2-1 mRNA isoform is detected. However, the expression of NOS2 in differentiating human pluripotent stems (hPSCs) has not been analyzed yet. Methods: Public available RNA-seq databases were screened for data of hPSCs during differentiation to different target cells. An isoform specific algorithm was used to analyze NOS2 mRNA isoform expression. In addition, we differentiated four different human iPSC cell lines toward cortical neurons and analyzed NOS2 mRNA expression by qRT-PCR and 5′-RACE. The functionality of the NOS2-2 protein was analyzed by transient transfection of expression clones in human DLD1 cells and nitrate measurement in the supernatant of these cells. Results: In RNA-seq databases we detected a transient expression of the NOS2 mRNA during the differentiation of hPSCs to cardiomyocytes, chondrocytes, mesenchymal stromal cells, neurons, syncytiotrophoblast cells, and trophoblasts. NOS2 mRNA isoform specific analyses showed, that the transiently expressed NOS2 mRNA in differentiating hPSC (NOS2-2; "diff-iNOS") differ remarkably from the already described NOS2 transcript found in colon or induced islets (NOS2-1; "immuno-iNOS"). Also, analysis of the NOS2 mRNA- and protein expression during the differentiation of four different hiPSC lines towards cortical neurons showed a transient expression of the NOS2 mRNA and NOS2 protein on day 18 of the differentiation course. 5′-RACE experiments and isoform specific qRT-PCR analyses revealed that only the NOS2-2 mRNA isoform was expressed in these experiments. To analyze the functionality of the NOS2-2 protein, we transfected human DLD-1 cells with tetracycline inducible expression clones encoding the NOS2-1- or -2 coding sequence. After induction of the NOS2-1 or -2 mRNA expression by tetracycline a similar nitrate production was measured proofing the functionality of the NOS2-2 protein isoform. Conclusions: Our data show that a differentiation specific NOS2 isoform (NOS2-2) is transiently expressed during differentiation of hPSC. 1uj3Epc_eyJHiftngx9Qfc Video Abstract [ABSTRACT FROM AUTHOR]

Transcription factor-based forward programming enables the efficient generation of forebrain excitatory and inhibitory neurons from human pluripotent stem cells (hPSCs). This provides an opportunity to study stimulation-response patterns in highly defined neuronal networks in a controlled and customizable in vitro environment. Cell populations composed of defined ratios of excitatory and inhibitory neurons were generated by forward programming genome-edited human hPSCs carrying the inducible transcription factors NGN2 and ASCL1/DLX2, respectively. These populations were cultured on multi-electrode arrays (MEAs), and population responses elicited by distinct spatial and temporal stimulation patterns were analyzed. In parallel, in silico network models fed with neuronal parameters obtained from the in vitro cultures were developed to explore potential mechanisms underlying experimental observations. Neuronal cultures developed network-level electrophysiological activities with pronounced synchronized network bursts (NBs), which responded to synaptic modulators. Interestingly, local electrical pulse stimulation at frequencies ≤ 0.2 Hz reliably elicited NBs, while frequencies of ≥ 1 Hz yielded no homogeneous responses, but only sporadic NBs. In contrast, multi-site stimulation at the same frequency could elicit NBs robustly. Data from computational models suggest that this phenomenon can be explained by exhaustion and presynaptic functional paralysis of targeted circuits by high-frequency local stimulation. Compared to hPSC-derived neurons generated solely by small molecule treatment, forward-programmed excitatory and inhibitory neurons enable the composition of highly confectionized networks. In silico simulation of induced biological network responses can be directly used to devise and validate mechanistic hypotheses underlying the recorded network dynamics. The present study demonstrates the prospect of the iPSC technology for conducting personalized in vitro studies of human neuronal networks and their responses to electric stimuli. It also illustrates how the combined use of biological and in silico neuronal networks can support the development of mechanistic hypotheses underlying network responses to specific stimuli. • Functional iPSC-derived neuronal networks with defined E/I ratios. • In silico modeling of biological human neuronal network dynamics. • Synaptic vesicle pool depletion as cause of local circuit paralysis. [ABSTRACT FROM AUTHOR]

Zika virus (ZIKV) is a mosquito-borne virus, which can cause brain abnormalities in newborns, including microcephaly. MicroRNAs (miRNAs) are small non-coding RNAs, which post- transcriptionally regulate gene expression. They are involved in various processes including neurological development and host responses to viral infection, but their potential role in ZIKV pathogenesis remains poorly understood. MiRNAs can be incorporated into extracellular vesicles (EVs) and mediate cell-to-cell communication. While it is well known that in viral infections EVs carrying miRNAs can play a crucial role in disease pathogenesis, ZIKV effects on EV-delivered miRNAs and their contribution to ZIKV pathogenesis have not been elucidated. In the present study, we profiled intracellular and EV-derived miRNAs by next generation sequencing and analyzed the host mRNA transcriptome of neural stem cells during infection with ZIKV Uganda and French Polynesia strains. We identified numerous miRNAs, including miR-4792, which were dysregulated at the intracellular level and had altered levels in EVs during ZIKV infection. Integrated analyses of differentially expressed genes and miRNAs showed that ZIKV infection had an impact on processes associated with neurodevelopment and oxidative stress. Our results provide insights into the roles of intracellular and EV-associated host miRNAs in ZIKV pathogenesis. [ABSTRACT FROM AUTHOR]

The incidence of Alzheimer's disease is increasing with the aging population, and it has become one of the main health concerns of modern society. The dissection of the underlying pathogenic mechanisms and the development of effective therapies remain extremely challenging, also because available animal and cell culture models do not fully recapitulate the whole spectrum of pathological changes. The advent of human pluripotent stem cells and cell reprogramming has provided new prospects for tackling these challenges in a human and even patient-specific setting. Yet, experimental modeling of non-cell autonomous and extracellular disease-related alterations has remained largely inaccessible. These limitations are about to be overcome by advances in the development of 3D cell culture systems including organoids, neurospheroids and matrix-embedded 3D cultures, which have been shown to recapitulate extracellular pathologies such as plaque formation in vitro. Recent xenograft studies have even taken human stem cell-based disease modeling to an in vivo scenario where grafted neurons are probed in a disease background in the context of a rodent brain. Here, we review the latest developments in this emerging field along with their advantages, challenges, and future prospects. • IPS cells provide prospects for modeling AD in patient backgrounds • Genome editing increases the fidelity of stem cell-based disease models • Organoids and 3D matrix cultures provide access to extracellular pathologies • Xenografts offer a gateway to in vivo disease modeling using human cells [ABSTRACT FROM AUTHOR]