In Vivo Genome Editing as a Therapeutic Approach.

Genome editing has been well established as a genome engineering tool that enables researchers to establish causal linkages between genetic mutation and biological phenotypes, providing further understanding of the genetic manifestation of many debilitating diseases. More recently, the paradigm of genome editing technologies has evolved to include the correction of mutations that cause diseases via the use of nucleases such as zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs), and more recently, Cas9 nuclease. With the aim of reversing disease phenotypes, which arise from somatic gene mutations, current research focuses on the clinical translatability of correcting human genetic diseases in vivo, to provide long-term therapeutic benefits and potentially circumvent the limitations of in vivo cell replacement therapy. In this review, in addition to providing an overview of the various genome editing techniques available, we have also summarized several in vivo genome engineering strategies that have successfully demonstrated disease correction via in vivo genome editing. The various benefits and challenges faced in applying in vivo genome editing in humans will also be discussed.

Differential effect of solar light in increasing the toxicity of silver and titanium dioxide nanoparticles to a fish cell line and zebrafish embryos.

The increasing use of silver (Ag) and titanium dioxide (TiO2) nanoparticles (NPs) in consumer products and their inevitable seepage into the environment prompted us to investigate their potential toxicity to a fish cell line (BF-2) and zebrafish embryos under dark and Simulated Solar Light (SSL) exposure conditions. Using high throughput screening (HTS) platforms, we showed that the oxidative stress-dependent cytotoxicity and embryonic toxicity of NPs were significantly increased upon exposure to SSL. While, the toxicity of TiO2 NPs under SSL exposure could be explained by hydroxyl radical generation, the enhanced toxicity of Ag NPs under SSL exposure was due to surface oxidation and physicochemical modification of Ag NPs and shedding of Ag+, leading to an increased bioavailability of silver. Our observations that solar light could induce physicochemical transformation of TiO2 and Ag NPs and enhance their toxic potential emphasizes the need for conducting future toxicity studies under environmentally relevant exposure conditions to guide decision making on the safe handling of NPs.

Characterizing arrhythmia using machine learning analysis of Ca2+ cycling in human cardiomyocytes.

Accurate modeling of the heart electrophysiology to predict arrhythmia susceptibility remains a challenge. Current electrophysiological analyses are hypothesis-driven models drawing conclusions from changes in a small subset of electrophysiological parameters because of the difficulty of handling and understanding large datasets. Thus, we develop a framework to train machine learning classifiers to distinguish between healthy and arrhythmic cardiomyocytes using their calcium cycling properties. By training machine learning classifiers on a generated dataset containing a total of 3,003 healthy derived cardiomyocytes and their various arrhythmic states, the multi-class models achieved >90% accuracy in predicting arrhythmia presence and type. We also demonstrate that a binary classifier trained to distinguish cardiotoxic arrhythmia from healthy electrophysiology could determine the key biological changes associated with that specific arrhythmia. Therefore, machine learning algorithms can be used to characterize underlying arrhythmic patterns in samples to improve in vitro preclinical models and complement current in vivo systems.

Robust generation of human-chambered cardiac organoids from pluripotent stem cells for improved modelling of cardiovascular diseases.

BACKGROUND: Tissue organoids generated from human pluripotent stem cells are valuable tools for disease modelling and to understand developmental processes. While recent progress in human cardiac organoids revealed the ability of these stem cell-derived organoids to self-organize and intrinsically formed chamber-like structure containing a central cavity, it remained unclear the processes involved that enabled such chamber formation. METHODS: Chambered cardiac organoids (CCOs) differentiated from human embryonic stem cells (H7) were generated by modulation of Wnt/ß-catenin signalling under fully defined conditions, and several growth factors essential for cardiac progenitor expansion. Transcriptomic profiling of day 8, day 14 and day 21 CCOs was performed by quantitative PCR and single-cell RNA sequencing. Endothelin-1 (EDN1) known to induce oxidative stress in cardiomyocytes was used to induce cardiac hypertrophy in CCOs in vitro. Functional characterization of cardiomyocyte contractile machinery was performed by immunofluorescence staining and analysis of brightfield and fluorescent video recordings. Quantitative PCR values between groups were compared using two-tailed Student's t tests. Cardiac organoid parameters comparison between groups was performed using two-tailed Mann-Whitney U test when sample size is small; otherwise, Welch's t test was used. Comparison of calcium kinetics parameters derived from the fluorescent data was performed using two-tailed Student's t tests. RESULTS: Importantly, we demonstrated that a threshold number of cardiac progenitor was essential to line the circumference of the inner cavity to ensure proper formation of a chamber within the organoid. Single-cell RNA sequencing revealed improved maturation over a time course, as evidenced from increased mRNA expression of cardiomyocyte maturation genes, ion channel genes and a metabolic shift from glycolysis to fatty acid ß-oxidation. Functionally, CCOs recapitulated clinical cardiac hypertrophy by exhibiting thickened chamber walls, reduced fractional shortening, and increased myofibrillar disarray upon treatment with EDN1. Furthermore, electrophysiological assessment of calcium transients displayed tachyarrhythmic phenotype observed as a consequence of rapid depolarization occurring prior to a complete repolarization. CONCLUSIONS: Our findings shed novel insights into the role of progenitors in CCO formation and pave the way for the robust generation of cardiac organoids, as a platform for future applications in disease modelling and drug screening in vitro.

Pbx1 is essential for growth of zebrafish swim bladder.

pbx1, a TALE (three-amino acid loop extension) homeodomain transcription factor, is involved in a diverse range of developmental processes. We examined the expression of pbx1 during zebrafish development by in situ hybridization. pbx1 transcripts could be detected in the central nervous system and pharyngeal arches from 24 hpf onwards. In the swim bladder anlage, pbx1 was detected as early as 28 hpf, making it the earliest known marker for this organ. Morpholino-mediated gene knockdown of pbx1 revealed that the swim bladder failed to inflate, with eventual lethality occurring by 8 dpf. The knockdown of pbx1 did not perturb the expression of prdc and foxA3, with both early swim bladder markers appearing normally at 36 and 48 hpf, respectively. However, the expression of anxa5 was completely abolished by pbx1 knockdown at 60 hpf suggesting that pbx1 may be required during the late stage of swim bladder development.

Arterial and venous vessels are required for modulating developmental relocalization and laterality of the interrenal tissue in zebrafish.

During zebrafish embryogenesis, the endothelium signals to emergent bilateral interrenal primordia to converge toward the midline, yet the merged interrenal tissue has been found to be situated lateral to the midline. We show in this study that bilateral interrenal tissue clusters fused at the central midline, before relocating laterally to be juxtaposed between the dorsal aorta and the posterior cardinal vein. In ets1b morphants where the midtrunk vasculature failed to assemble, various degrees of interrenal fusion defects were displayed, and the interrenal laterality was lost. As either arterial or venous endothelium was specifically reduced, the interrenal tissue was defective in its relocalization and laterality, yet remained closely associated with the malformed vasculature. Our results showed evidence to support that assembly of the axial artery and vein, and its resulting vascular topology at the midtrunk, is required for patterning relocalization and laterality of the interrenal tissue after the initial medial fusion.

Insights to Heart Development and Cardiac Disease Models Using Pluripotent Stem Cell Derived 3D Organoids.

Medical research in the recent years has achieved significant progress due to the increasing prominence of organoid technology. Various developed tissue organoids bridge the limitations of conventional 2D cell culture and animal models by recapitulating in vivo cellular complexity. Current 3D cardiac organoid cultures have shown their utility in modelling key developmental hallmarks of heart organogenesis, but the complexity of the organ demands a more versatile model that can investigate more fundamental parameters, such as structure, organization and compartmentalization of a functioning heart. This review will cover the prominence of cardiac organoids in recent research, unpack current in vitro 3D models of the developing heart and look into the prospect of developing physiologically appropriate cardiac organoids with translational applicability. In addition, we discuss some of the limitations of existing cardiac organoid models in modelling embryonic development of the heart and manifestation of cardiac diseases.

Multi-species single-cell transcriptomic analysis of ocular compartment regulons.

The retina is a widely profiled tissue in multiple species by single-cell RNA sequencing studies. However, integrative research of the retina across species is lacking. Here, we construct the first single-cell atlas of the human and porcine ocular compartments and study inter-species differences in the retina. In addition to that, we identify putative adult stem cells present in the iris tissue. We also create a disease map of genes involved in eye disorders across compartments of the eye. Furthermore, we probe the regulons of different cell populations, which include transcription factors and receptor-ligand interactions and reveal unique directional signalling between ocular cell types. In addition, we study conservation of regulons across vertebrates and zebrafish to identify common core factors. Here, we show perturbation of KLF7 gene expression during retinal ganglion cells differentiation and conclude that it plays a significant role in the maturation of retinal ganglion cells.

Upregulation of the JAK-STAT pathway promotes maturation of human embryonic stem cell-derived cardiomyocytes.

The immature characteristics and metabolic phenotypes of human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) restrict their applications for disease modeling, drug discovery, and cell-based therapy. Leveraging on the metabolic shifts from glycolysis to fatty acid oxidation as CMs mature, a human hexokinase1-GFP metabolic reporter cell line (H7 HK1-GFP) was generated to facilitate the isolation of fetal or more matured hPSC-CMs. RNA sequencing of fetal versus more matured CMs uncovered a potential role of interferon-signaling pathway in regulating CM maturation. Indeed, IFN-γ-treated CMs resulted in an upregulation of the JAK-STAT pathway, which was found to be associated with increased expression of CM maturation genes, shift from MYH6 to MYH7 expression, and improved sarcomeric structure. Functionally, IFN-γ-treated CMs exhibited a more matured electrophysiological profile, such as increased calcium dynamics and action potential upstroke velocity, demonstrated through calcium imaging and MEA. Expectedly, the functional improvements were nullified with a JAK-STAT inhibitor, ruxolitinib.

Re-entering the pluripotent state from blood lineage: promises and pitfalls of blood reprogramming.

Blood reprogramming, in which induced pluripotent stem cells (iPSCs) are derived from haematopoietic lineages, has rapidly advanced over the past decade. Since the first report using human blood, haematopoietic cell types from various sources, such as the peripheral bone marrow and cord blood, have been successfully reprogrammed. The volume of blood required has also decreased, from around tens of millilitres to a single finger-prick drop. Besides, while early studies were limited to reprogramming methods relying on viral integration, nonintegrating reprogramming systems for blood lineages have been subsequently established. Together, these improvements have made feasible the future clinical applications of blood-derived iPSCs. Here, we review the progress in blood reprogramming from various perspectives, including the starting materials and subsequent reprogramming strategies. We also discuss the downstream applications of blood-derived iPSCs, highlighting their clinical value in terms of disease modelling and therapeutic development.

Prox1 is a novel coregulator of Ff1b and is involved in the embryonic development of the zebra fish interrenal primordium.

Steroidogenic factor 1 (SF-1) plays an essential role in adrenal development, although the exact molecular mechanisms are unclear. Our previous work established that Ff1b is the zebra fish homologue of SF-1 and that its disruption by antisense morpholinos leads to a complete ablation of the interrenal organ. In this study, results of biochemical analyses suggest that Ff1b and other Ff1 members interact with Prox1, a homeodomain protein. Fine mapping using site-directed mutants showed that this interaction requires an intact Ff1b heptad 9 and AF2, as well as Prox1 NR Box I. In vivo, this physical interaction led to the inhibition of Ff1-mediated transactivation of pLuc3XFRE, indicating that Prox1 acts to repress the transcriptional activity of Ff1b. In situ hybridization demonstrates that prox1 colocalizes with ff1a and ff1b in the liver and interrenal primordia, respectively. Embryos microinjected with prox1 morpholino displayed a consistent partial reduction of 3 eta-Hsd activity in the interrenal organ, while ff1b morpholino led to a disappearance of prox1. Based on these results, we propose that during the course of interrenal organogenesis, Prox1 functions as a tissue-specific coregulator of Ff1b and that the subsequent inhibition of Ff1b activity, after its initial roles in the specification of interrenal primordium, is critical for the maturation of the interrenal organ.

Human feeders support prolonged undifferentiated growth of human inner cell masses and embryonic stem cells.

Previous reports have demonstrated the growth of undifferentiated human embryonic stem (HES) cells on mouse embryonic fibroblast (MEF) feeders and on laminin- or Matrigel-coated plastic surfaces supplemented with MEF-conditioned medium. These xenosupport systems run the risk of cross-transfer of animal pathogens from the animal feeder, matrix, or conditioned medium to the HES cells, thus compromising later clinical application. Here we show that human fetal and adult fibroblast feeders support prolonged undifferentiated HES cell growth of existing cell lines and are superior to cell-free matrices (collagen I, human extracellular matrix, Matrigel, and laminin) supplemented with human or MEF feeder-conditioned medium. Additionally, we report the derivation and establishment of a new HES cell line in completely animal-free conditions. Like HES cells cultured on MEF feeders, the HES cells grown on human feeders had normal karyotypes, tested positive for alkaline phosphatase activity, expressed Oct-4 and cell surface markers including SSEA-3, SSEA-4, Tra 1-60, and GCTM-2, formed teratomas in severely combined immunodeficient (SCID) mice, and retained all key morphological characteristics. Human feeder#150;supported HES cells should provide a safer alternative to existing HES cell lines in therapeutic applications.

Gene duplication, gene loss and evolution of expression domains in the vertebrate nuclear receptor NR5A (Ftz-F1) family.

Fushi tarazu factor 1 (Ftz-F1, NR5A) is a zinc-finger transcription factor that belongs to the nuclear receptor superfamily and regulates genes that are involved in sterol and steroid metabolism in gonads, adrenals, liver and other tissues. To understand the evolutionary origins and developmental genetic relationships of the Ftz-F1 genes, we have cloned four homologous Ftz-f1 genes in zebrafish, called ff1a, ff1b, ff1c and ff1d. These four genes have different temporal and spatial expression patterns during development, indicating that they have distinct mechanisms of genetic regulation. Among them, the ff1a expression pattern is similar to mammalian Nr5a2, while the ff1b pattern is similar to that of mammalian Nr5a1. Genetic mapping experiments show that these four ff1 genes are located on chromosome segments conserved between the zebrafish and human genomes, indicating a common ancestral origin. Phylogenetic and conserved synteny analysis show that ff1a is the orthologue of NR5A2, and that ff1b and ff1d genes are co-orthologues of NR5A1 that arose by a gene-duplication event, probably a whole-genome duplication, in the ray-fin lineage, and each gene is located next to an NR6A1 co-orthologue as in humans, showing that the tandem duplication occurred before the divergence of human and zebrafish lineages. ff1c does not have a mammalian counterpart. Thus we have characterized the phylogenetic relationships, expression patterns and chromosomal locations of these Ftz-F1 genes, and have demonstrated their identities as NR5A genes in relation to the orthologous genes in other species.

Dioxonaphthoimidazoliums are Potent and Selective Rogue Stem Cell Clearing Agents with SOX2-Suppressing Properties.

Pluripotent stem cells are uniquely positioned for regenerative medicine, but their clinical potential can only be realized if their tumorigenic tendencies are decoupled from their pluripotent properties. Deploying small molecules to remove remnant undifferentiated pluripotent cells, which would otherwise transform into teratomas and teratomacarcinomas, offers several advantages over non-pharmacological methods. Dioxonapthoimidazolium YM155, a survivin suppressant, induced selective and potent cell death of undifferentiated stem cells. Herein, the structural requirements for stemotoxicity were investigated and found to be closely aligned with those essential for cytotoxicity in malignant cells. There was a critical reliance on the quinone and imidazolium moieties but a lesser dependence on ring substituents, which served mainly to fine-tune activity. Several potent analogues were identified which, like YM155, suppressed survivin and decreased SOX2 in stem cells. The decrease in SOX2 would cause an imbalance in pluripotent factors that could potentially prompt cells to differentiate and hence decrease the risk of aberrant teratoma formation. As phosphorylation of the NF-κB p50 subunit was also suppressed, the crosstalk between phospho-p50, SOX2, and survivin could implicate a causal role for NF-κB signaling in mediating the stem cell clearing properties of dioxonaphthoimidazoliums.

Cloning and tissue expression of 6-pyruvoyl tetrahydropterin synthase and xanthine dehydrogenase from Poecilia reticulata.

Guppy is a popular ornamental fish owing to its diverse body and fin coloration. More than 40 established color varieties have been selectively bred. The complementary DNAs for 2 enzymes that are involved in the de novo synthesis of pteridines and purines, which are important for the production of color pigments, were cloned from the caudal fin. Two cDNA isoforms for 6-pyruvoyl tetrahydropterin synthase (PTPS), with an open reading frame of 130 and 147 amino acids, respectively, were cloned from the Red Tail variety. The deduced amino acid sequence of the longer isoform shows an overall identity of about 65% to the mammalian PTPS sequences. The cDNA for xanthine dehydrogenase (XDH) was cloned from the Yellow Tail variety, and consists of an open reading frame of 1331 amino acids. Although it shows a higher overall identity to bovine aldehyde oxidase (AO; 54%) than to chicken XDH (51%), it has a NAD-binding domain that is specific to XDHs. Northern blot analysis indicated that both PTPS and XDH messenger RNAs were highly expressed in the liver, but absent in the muscle. In the caudal fins, guppy varieties with a higher proportion of xanthophores and erythrophores showed higher expression of PTPS, while XDH mRNA levels were too low to indicate obvious differential expression among the color guppy varieties. The results implied that high expression of PTPS is correlated with the biosynthesis of pteridines in the erythrophores and xanthophores, while the association between the putative guppy XDH with specific chromatophores is less clear.

Genetic diversity within and among feral populations and domesticated strains of the guppy (Poecilia reticulata) in Singapore.

Genetic variability within and among feral populations and cultured strains of the guppy (Poecilia reticulata) was investigated by random amplification of polymorphic DNA (RAPD) fingerprinting. Feral guppies were collected from 6 isolated populations (BT, Bukit Timah; NS, Nee Soon; TS, Tuas; MF, Mount Faber; KR, Kranji; LI, laboratory-inbred feral line), while the Tuxedo and Green Variegated strains were sampled from 2 guppy farms in Singapore. Pairwise genetic distances analyzed by unweighted pair-group method with arithmetic means revealed distinct clustering of guppy individuals into their respective populations and strains. Percentage polymorphic loci ranged from 54.96% (TS) to 68.70% (KR), while average heterozygosity ranged from 0.220 (GV) to 0.271 (KR). In contrast, TS guppies had the highest (0.850) intrapopulation genetic similarity (S), whereas KR had the lowest (0.781). Among populations and strains, S ranged from 0.703 (between GV and LI) to 0.809 (between NS and MB). The GV strain S was closer to TX (0.784) than to the feral guppies. Bootstrapped genetic distance trees depicted 3 major nodes comprising BT-TS, NS-MF, and TX-GV. Principal coordinate analysis also differentiated the 6 feral populations from the 2 cultured strains.

Genetic linkage maps of the guppy ( Poecilia reticulata): assignment of RAPD markers to multipoint linkage groups.

Genetic linkage maps of the guppy ( Poecilia reticulata) were constructed from independent crosses between the Tuxedo strain and a feral line (Wildtype). Segregation patterns of random amplified polymorphic DNA (RAPD) markers and phenotypic markers were investigated in F(2) offspring of Tuxedo male symbol male symbol x Wildtype female symbol female symbol and Wildtype male symbol male symbol x Tuxedo female symbol female symbol crosses. Among the 300 and 276 RAPD markers scored for the respective crosses, linkages were identified for 230 and 212, respectively. The Tuxedo male symbol male symbol x Wildtype female symbol female symbol and Wildtype male symbol male symbol x Tuxedo female symbol female symbol maps spanned 2100 Kosambi centiMorgans (cM(K)) and 1900 cM(K), respectively, in 28 linkage groups. Average marker resolution was 10 cM(K). Genome length was estimated at 4410 cM(K) and 4060 cM(K) for the respective crosses, with an average physical distance of 166 kbp/cM(K). Several RAPD markers were closely linked to or mapped onto the loci for the sex-determining region (SdR), and the sex-linked black caudal-peduncle ( Bcp) and red tail ( Rdt) genes. These primary linkage maps are the initial step toward the construction of a composite high-density map to facilitate map-based cloning and marker-assisted selection of quantitative trait loci that are essential for the development of comprehensive breeding programs for the guppy.

A new class of pluripotent stem cell cytotoxic small molecules.

A major concern in Pluripotent Stem Cell (PSC)-derived cell replacement therapy is the risk of teratoma formation from contaminating undifferentiated cells. Removal of undifferentiated cells from differentiated cultures is an essential step before PSC-based cell therapies can be safely deployed in a clinical setting. We report a group of novel small molecules that are cytotoxic to PSCs. Our data indicates that these molecules are specific and potent in their activity allowing rapid eradication of undifferentiated cells. Experiments utilizing mixed PSC and primary human neuronal and cardiomyocyte cultures demonstrate that up to a 6-fold enrichment for specialized cells can be obtained without adversely affecting cell viability and function. Several structural variants were synthesized to identify key functional groups and to improve specificity and efficacy. Comparative microarray analysis and ensuing RNA knockdown studies revealed involvement of the PERK/ATF4/DDIT3 ER stress pathway. Surprisingly, cell death following ER stress induction was associated with a concomitant decrease in endogenous ROS levels in PSCs. Undifferentiated cells treated with these molecules preceding transplantation fail to form teratomas in SCID mice. Furthermore, these molecules remain non-toxic and non-teratogenic to zebrafish embryos suggesting that they may be safely used in vivo.

Derivation and long-term culture of an embryonic stem cell-like line from zebrafish blastomeres under feeder-free condition.

Existing zebrafish embryonic stem (ES) cell lines are derived and maintained using feeder layers. We describe here the derivation and long-term culture of an ES cell-like line derived from zebrafish blastomeres without the use of feeder cells. This line, designated as ZES1, has been maintained for more than 800 days in defined Dulbecco's modified Eagle's medium supplemented with fetal bovine serum, zebrafish embryo extract, trout serum, and human basic fibroblast growth factor. ZES1 cells possessed a morphology typical of ES cells, being round or polygonal in shape with a large nucleus and sparse cytoplasm and were mostly diploid. The cells formed individual colonies consisting of tightly packed cells that stained positively for alkaline phosphatase. ZES1 cells also formed embryoid bodies when transferred onto uncoated wells. The pluripotent nature of ZES1 cells was confirmed when they could be induced to differentiate in vitro into several cell types, through low- or high-density culture conditions. Treatment with retinoic acid also induced the differentiation of ZES1 cells into primarily neuronal cells. Using immunostaining and real-time polymerase chain reaction, we showed that Sox2, a known pluripotent marker in mammalian ES cells, was also present in ZES1 cells. Chimera experiments revealed that fluorescent-labeled ZES1 cells microinjected into zebrafish blastulas participated in the formation of all three germ layers. Using GFP-labeled ZES1 cells, chimera germline transmission was also demonstrated at the F1 generation. In conclusion, ZES1 cells possess both in vitro and in vivo pluripotency characteristics, indicating that nonmammalian ES cells can be readily derived and maintained for a long term under feeder-free culture conditions.

Human Wharton's jelly stem cells have unique transcriptome profiles compared to human embryonic stem cells and other mesenchymal stem cells.

The human umbilical cord that originates from the embryo is an extra-embryonic membrane and the Wharton's jelly within it is a rich source of stem cells (hWJSCs). It is not definitely known whether these cells behave as human embryonic stem cells (hESCs), human mesenchymal stem cells (hMSC) or both. They have the unique properties of high proliferation rates, wide multipotency, hypoimmunogenicity, do not induce teratomas and have anticancer properties. These advantages are important considerations for their use in cell based therapies and treatment of cancers. In a search for properties that confer these advantages we compared a detailed transcriptome profiling of hWJSCs using DNA microarrays with that of a panel of known hESCs, hMSCs and stromal cells. hWJSCs expressed low levels of the pluripotent embryonic stem cell markers including POUF1, NANOG, SOX2 and LIN28, thus explaining why they do not produce teratomas. Several cytokines were significantly upregulated in hWJSCs including IL12A which is associated with the induction of apoptosis, thus explaining their anticancer properties. When GO Biological Process analysis was compared between the various stem cell types, hWJSCs showed an increased expression of genes associated with the immune system, chemotaxis and cell death. The ability to modulate immune responses makes hWJSCs an important compatible stem cell source for transplantation therapy in allogeneic settings without immunorejection. The data in the present study which is the first detailed report on hWJSC transcriptomes provide a foundation for future functional studies where the exact mechanisms of these unique properties of hWJSCs can be confirmed.