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Functional variability among human clones of induced pluripotent stem cells (hiPSCs) remains a limitation in assembling high-quality biorepositories. Beyond inter-person variability,the root cause of intra-person variability remains unknown. Mitochondria guide the required transition from oxidative to glycolytic metabolism in nuclear reprogramming. Moreover,mitochondria have their own genome (mitochondrial DNA [mtDNA]). Herein,we performed mtDNA next-generation sequencing (NGS) on 84 hiPSC clones derived from a cohort of 19 individuals,including mitochondrial and non-mitochondrial patients. The analysis of mtDNA variants showed that low levels of potentially pathogenic mutations in the original fibroblasts are revealed through nuclear reprogramming,generating mutant hiPSCs with a detrimental effect in their differentiated progeny. Specifically,hiPSC-derived cardiomyocytes with expanded mtDNA mutations non-related with any described human disease,showed impaired mitochondrial respiration,being a potential cause of intra-person hiPSC variability. We propose mtDNA NGS as a new selection criterion to ensure hiPSC quality for drug discovery and regenerative medicine. View Publication

Aberrant antioxidant activity and excessive deposition of extracellular matrix (ECM) are hallmarks of interstitial lung diseases (ILD). It is known that oxidative stress alters the ECM,but extracellular antioxidant defence mechanisms in ILD are incompletely understood. Here,we extracted abundance and detergent solubility of extracellular antioxidant enzymes from a proteomic dataset of bleomycin-induced lung fibrosis in mice and assessed regulation and distribution of glutathione peroxidase 3 (GPX3) in murine and human lung fibrosis. Superoxide dismutase 3 (Sod3),Gpx3,and Gpx activity were increased in mouse BALF during bleomycin-induced lung fibrosis. In lung tissue homogenates,Gpx3,but not Sod3,was upregulated and detergent solubility profiling indicated that Gpx3 associated with ECM proteins. Immunofluorescence analysis showed that Gpx3 was expressed by bronchial epithelial cells and interstitial fibroblasts and localized to the basement membrane and interstitial ECM in lung tissue. As to human ILD samples,BALF of some patients contained high levels of GPX3,and GPX3 was upregulated in lung homogenates from IPF patients. GPX3 expression in primary human bronchial epithelial cells and lung fibroblasts was downregulated by TNF-$$,but more variably regulated by TGF-$$1 and menadione. In conclusion,the antioxidant enzyme GPX3 localizes to lung ECM and is variably upregulated in ILD. View Publication

The vertebrate retina is a highly multilayered nervous tissue with a large diversity of cellular components. With the development of stem cell technologies,human retinas can be generated in three-dimensional (3-D) culture in vitro. However,understanding the factors modulating key productive processes and the way that they influence development are far from clear. Oxygen,as the most essential element participating in metabolism,is a critical factor regulating organic development. In this study,using 3-D culture of human stem cells,we examined the effect of intermittent high oxygen treatment (40% O2) on the formation and cellular behavior of neural retinas (NR) in the embryonic body (EB). The volume of EB and number of proliferating cells increased significantly under 40% O2 on day 38,50,and 62. Additionally,the ratio of PAX6+ cells within NR was significantly increased. The neural rosettes could only develop with correct apical-basal polarity under 40% O2. In addition,the generation,migration and maturation of retinal ganglion cells were enhanced under 40% O2. All of these results illustrated that 40% O2 strengthened the formation of NR in EB with characteristics similar to the in vivo state,suggesting that the hyperoxic state facilitated the retinal development in vitro. View Publication

While distinct stages of natural killer (NK) cell development have been defined,the molecular interactions that shape human NK cell maturation are poorly understood. Here we define intercellular interactions between developing NK cells and stromal cells which,through contact-dependent mechanisms,promote the generation of mature,functional human NK cells from CD34(+) precursors. We show that developing NK cells undergo unique,developmental stage-specific sustained and transient interactions with developmentally supportive stromal cells,and that the relative motility of NK cells increases as they move through development in vitro and ex vivo. These interactions include the formation of a synapse between developing NK cells and stromal cells,which we term the developmental synapse. Finally,we identify a role for CD56 in developmental synapse structure,NK cell motility and NK cell development. Thus,we define the developmental synapse leading to human NK cell functional maturation. View Publication

B cell aggregates in the central nervous system (CNS) have been associated with rapid disease progression in patients with multiple sclerosis (MS). Here we demonstrate a key role of carcinoembryogenic antigen-related cell adhesion molecule1 (CEACAM1) in B cell aggregate formation in MS patients and a B cell-dependent mouse model of MS. CEACAM1 expression was increased on peripheral blood B cells and CEACAM1(+) B cells were present in brain infiltrates of MS patients. Administration of the anti-CEACAM1 antibody T84.1 was efficient in blocking aggregation of B cells derived from MS patients. Along these lines,application of the monoclonal anti-CEACAM1 antibody mCC1 was able to inhibit CNS B cell aggregate formation and significantly attenuated established MS-like disease in mice in the absence of any adverse effects. CEACAM1 was co-expressed with the regulator molecule T cell immunoglobulin and mucin domain -3 (TIM-3) on B cells,a novel molecule that has recently been described to induce anergy in T cells. Interestingly,elevated coexpression on B cells coincided with an autoreactive T helper cell phenotype in MS patients. Overall,these data identify CEACAM1 as a clinically highly interesting target in MS pathogenesis and open new therapeutic avenues for the treatment of the disease. View Publication

Insights into the expression of pacemaker-speci�?c markers in human induced pluripotent stemcell (hiPSC)-derived cardiomyocyte subtypes can facilitate the enrichment and track differentia-tion and maturation of hiPSC-derived pacemaker-like cardiomyocytes. To date,no study hasdirectly assessed gene expression in each pacemaker-,atria-,and ventricular-like cardiomyocytesubtype derived from hiPSCs since currently the subtypes of these immature cardiomyocytescan only be identi�?ed by action potential pro�?les. Traditional acquisition of action potentialsusing patch-clamp recordings renders the cells unviable for subsequent analysis. We circum-vented these issues by acquiring the action potential pro�?le of a single cell optically followedby assessment of protein expression through immunostaining in that same cell. Our same-single-cell analysis for the �?rst time revealed expression of proposed pacemaker-speci�?cmarkers—hyperpolarization-activated cyclic nucleotide-modulated (HCN)4 channel and Islet(Isl)1—at the protein level in all three hiPSC-derived cardiomyocyte subtypes. HCN4 expressionwas found to be higher in pacemaker-like hiPSC-derived cardiomyocytes than atrial- andventricular-like subtypes but its downregulation over time in all subtypes diminished the differ-ences. Isl1 expression in pacemaker-like hiPSC-derived cardiomyocytes was initially not statisti-cally different than the contractile subtypes but did become statistically higher than ventricular-like cells with time. Our observations suggest that although HCN4 and Isl1 are differentiallyexpressed in hiPSC-derived pacemaker-like relative to ventricular-like cardiomyocytes,thesemarkers alone are insuf�?cient in identifying hiPSC-derived pacemaker-like cardiomyocytes. View Publication

In order to develop a novel method of visualizing possible Ca(2+) signaling during the early differentiation of hESCs into cardiomyocytes and avoid some of the inherent problems associated with using fluorescent reporters,we expressed the bioluminescent Ca(2+) reporter,apo-aequorin,in HES2 cells and then reconstituted active holo-aequorin by incubation with f-coelenterazine. The temporal nature of the Ca(2+) signals generated by the holo-f-aequorin-expressing HES2 cells during the earliest stages of differentiation into cardiomyocytes was then investigated. Our data show that no endogenous Ca(2+) transients (generated by release from intracellular stores) were detected in 1-12-day-old cardiospheres but transients were generated in cardiospheres following stimulation with KCl or CaCl2,indicating that holo-f-aequorin was functional in these cells. Furthermore,following the addition of exogenous ATP,an inositol trisphosphate receptor (IP3R) agonist,small Ca(2+) transients were generated from day 1 onward. That ATP was inducing Ca(2+) release from functional IP3Rs was demonstrated by treatment with 2-APB,a known IP3R antagonist. In contrast,following treatment with caffeine,a ryanodine receptor (RyR) agonist,a minimal Ca(2+) response was observed at day 8 of differentiation only. Thus,our data indicate that unlike RyRs,IP3Rs are present and continually functional at these early stages of cardiomyocyte differentiation. View Publication

Netrin-1 is a neuronal guidance cue that regulates cellular activation,migration,and cytoskeleton rearrangement in multiple cell types. It is a chemotropic protein that is expressed within tissues and elicits both attractive and repulsive migratory responses. Netrin-1 has recently been found to modulate the immune response via the inhibition of neutrophil and macrophage migration. However,the ability of Netrin-1 to interact with lymphocytes and its in-depth effects on leukocyte migration are poorly understood. In this study,we profiled the mRNA and protein expression of known Netrin-1 receptors on human CD4(+) T cells. Neogenin,uncoordinated-5 (UNC5)A,and UNC5B were expressed at low levels in unstimulated cells,but they increased following mitogen-dependent activation. By immunofluorescence,we observed a cytoplasmic staining pattern of neogenin and UNC5A/B that also increased following activation. Using a novel microfluidic assay,we found that Netrin-1 stimulated bidirectional migration and enhanced the size of migratory subpopulations of mitogen-activated CD4(+) T cells,but it had no demonstrable effects on the migration of purified CD4(+)CD25(+)CD127(dim) T regulatory cells. Furthermore,using a short hairpin RNA knockdown approach,we observed that the promigratory effects of Netrin-1 on T effectors is dependent on its interactions with neogenin. In the humanized SCID mouse,local injection of Netrin-1 into skin enhanced inflammation and the number of neogenin-expressing CD3(+) T cell infiltrates. Neogenin was also observed on CD3(+) T cell infiltrates within human cardiac allograft biopsies with evidence of rejection. Collectively,our findings demonstrate that Netrin-1/neogenin interactions augment CD4(+) T cell chemokinesis and promote cellular infiltration in association with acute inflammation in vivo. View Publication

Group 2 innate lymphoid cells (ILC2s) in the lung are stimulated by inhaled allergens. ILC2s do not directly recognize allergens but they are stimulated by cytokines including interleukin (IL)-33 released by damaged epithelium. In response to allergens,lung ILC2s produce T helper 2 cell type cytokines inducing T cell-independent allergic lung inflammation. Here we examined the fate of lung ILC2s upon allergen challenges. ILC2s proliferated and secreted cytokines upon initial stimulation with allergen or IL-33,and this phase was followed by a contraction phase as cytokine production ceased. Some ILC2s persisted long after the resolution of the inflammation as allergen-experienced ILC2s and responded to unrelated allergens more potently than naive ILC2s,mediating severe allergic inflammation. The allergen-experienced ILC2s exhibited a gene expression profile similar to that of memory T cells. The memory-like properties of allergen-experienced ILC2s may explain why asthma patients are often sensitized to multiple allergens. View Publication

Cancer-targeting alkylphosphocholine (APC) analogs are being clinically developed for diagnostic imaging,intraoperative visualization,and therapeutic applications. These APC analogs derived from chemically-synthesized phospholipid ethers were identified and optimized for cancer-targeting specificity using extensive structure-activity studies. While they strongly label human brain cancers associated with disrupted blood-brain barriers (BBB),APC permeability across intact BBB remains unknown. Three of our APC analogs,CLR1404 (PET radiotracer),CLR1501 (green fluorescence),and CLR1502 (near infrared fluorescence),were tested for permeability across a BBB model composed of human induced pluripotent stem cell-derived brain microvascular endothelial cells (iPSC-derived BMECs). This in vitro BBB system has reproducibly consistent high barrier integrity marked by high transendothelial electrical resistance (TEERtextgreater1500 Ω-cm(2)) and functional expression of drug efflux transporters. Our radioiodinated and fluorescent APC analogs demonstrated fairly low permeability across the iPSC-BMEC (35±5.7 (CLR1404),54±3.2 (CLR1501),and 26±4.9 (CLR1502) x10(-5) cm/min) compared with BBB-impermeable sucrose (13±2.5) and BBB-permeable diazepam (170±29). Only our fluorescent APC analogs (CLR1501,CLR1502) underwent BCRP and MRP polarized drug efflux transport in the brain-to-blood direction of the BBB model and this efflux can be specifically blocked with pharmacological inhibition. None of our tested APC analogs appeared to undergo substantial P-gp transport. Limited permeability of our APC analogs across an intact BBB into normal brain likely contributes to the high tumor to background ratios observed in initial human trials. Moreover,addition of fluorescent moieties to APCs resulted in greater BMEC efflux via MRP and BCRP,and may affect fluorescence-guided applications. Overall,the characterization of APC analog permeability across human BBB is significant for advancing future brain tumor-targeted applications of these agents. View Publication

Stem-cell differentiation to desired lineages requires navigating alternating developmental paths that often lead to unwanted cell types. Hence,comprehensive developmental roadmaps are crucial to channel stem-cell differentiation toward desired fates. To this end,here,we map bifurcating lineage choices leading from pluripotency to 12 human mesodermal lineages,including bone,muscle,and heart. We defined the extrinsic signals controlling each binary lineage decision,enabling us to logically block differentiation toward unwanted fates and rapidly steer pluripotent stem cells toward 80%???99% pure human mesodermal lineages at most branchpoints. This strategy enabled the generation of human bone and heart progenitors that could engraft in respective in??vivo models. Mapping stepwise chromatin and single-cell gene expression changes in mesoderm development uncovered somite segmentation,a previously unobservable human embryonic event transiently marked by HOPX expression. Collectively,this roadmap enables navigation of mesodermal development to produce transplantable human tissue progenitors and uncover developmental processes. Video Abstract View Publication

PAIRED (PRD)-like homeobox genes belong to a class of predicted transcription factor genes. Several of these PRD-like homeobox genes have been predicted in silico from genomic sequence but until recently had no evidence of transcript expression. We found recently that nine PRD-like homeobox genes,ARGFX,CPHX1,CPHX2,DPRX,DUXA,DUXB,NOBOX,TPRX1 and TPRX2,were expressed in human preimplantation embryos. In the current study we characterized these PRD-like homeobox genes in depth and studied their functions as transcription factors. We cloned multiple transcript variants from human embryos and showed that the expression of these genes is specific to embryos and pluripotent stem cells. Overexpression of the genes in human embryonic stem cells confirmed their roles as transcription factors as either activators (CPHX1,CPHX2,ARGFX) or repressors (DPRX,DUXA,TPRX2) with distinct targets that could be explained by the amino acid sequence in homeodomain. Some PRD-like homeodomain transcription factors had high concordance of target genes and showed enrichment for both developmentally important gene sets and a 36 bp DNA recognition motif implicated in Embryo Genome Activation (EGA). Our data implicate a role for these previously uncharacterized PRD-like homeodomain proteins in the regulation of human embryo genome activation and preimplantation embryo development. View Publication