Mouse Cell Types Research Articles

A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting.

Proteomics and other protein-based analysis methods such as Western blotting all face the challenge of discriminating changes in the levels of proteins of interest from inadvertent changes in the amount loaded for analysis. Mass-spectrometry-based proteomics can now estimate the relative and absolute amounts of thousands of proteins across diverse biological systems. We reasoned that this new technology could prove useful for selection of very stably expressed proteins that could serve as better loading controls than those traditionally employed. Large-scale proteomic analyses of SDS lysates of cultured cells and tissues revealed deglycase DJ-1 as the protein with the lowest variability in abundance among different cell types in human, mouse, and amphibian cells. The protein constitutes 0.069 ± 0.017% of total cellular protein and occurs at a specific concentration of 34.6 ± 8.7 pmol/mg of total protein. Since DJ-1 is ubiquitous and therefore easily detectable with several peptides, it can be helpful in normalization of proteomic data sets. In addition, DJ-1 appears to be an advantageous loading control for Western blot that is superior to those used commonly used, allowing comparisons between tissues and cells originating from evolutionarily distant vertebrate species. Notably, this is not possible by the detection and quantitation of housekeeping proteins, which are often used in the Western blot technique. The approach introduced here can be applied to select the most appropriate loading controls for MS-based proteomics or Western blotting in any biological system.

Localization of PPAR isotypes in the adult mouse and human brain.

Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that act as ligand-activated transcription factors. PPAR agonists have well-documented anti-inflammatory and neuroprotective roles in the central nervous system. Recent evidence suggests that PPAR agonists are attractive therapeutic agents for treating neurodegenerative diseases as well as addiction. However, the distribution of PPAR mRNA and protein in brain regions associated with these conditions (i.e. prefrontal cortex, nucleus accumbens, amygdala, ventral tegmental area) is not well defined. Moreover, the cell type specificity of PPARs in mouse and human brain tissue has yet to be investigated. We utilized quantitative PCR and double immunofluorescence microscopy to determine that both PPAR mRNA and protein are expressed ubiquitously throughout the adult mouse brain. We found that PPARs have unique cell type specificities that are consistent between species. PPARα was the only isotype to colocalize with all cell types in both adult mouse and adult human brain tissue. Overall, we observed a strong neuronal signature, which raises the possibility that PPAR agonists may be targeting neurons rather than glia to produce neuroprotection. Our results fill critical gaps in PPAR distribution and define novel cell type specificity profiles in the adult mouse and human brain.

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT.

Retinal Organoids from Pluripotent Stem Cells Efficiently Recapitulate Retinogenesis.

SummaryThe plasticity of pluripotent stem cells provides new possibilities for studying development, degeneration, and regeneration. Protocols for the differentiation of retinal organoids from embryonic stem cells have been developed, which either recapitulate complete eyecup morphogenesis or maximize photoreceptor genesis. Here, we have developed a protocol for the efficient generation of large, 3D-stratified retinal organoids that does not require evagination of optic-vesicle-like structures, which so far limited the organoid yield. Analysis of gene expression in individual organoids, cell birthdating, and interorganoid variation indicate efficient, reproducible, and temporally regulated retinogenesis. Comparative analysis of a transgenic reporter for PAX6, a master regulator of retinogenesis, shows expression in similar cell types in mouse in vivo, and in mouse and human retinal organoids. Early or late Notch signaling inhibition forces cell differentiation, generating organoids enriched with cone or rod photoreceptors, respectively, demonstrating the power of our improved organoid system for future research in stem cell biology and regenerative medicine.

Practical Analysis of Genome Contact Interaction Experiments.

The three dimensional (3D) architecture of chromosomes is not random but instead tightly organized due to chromatin folding and chromatin interactions between genomically distant loci. By bringing genomically distant functional elements such as enhancers and promoters into close proximity, these interactions play a key role in regulating gene expression. Some of these interactions are dynamic, that is, they differ between cell types, conditions and can be induced by specific stimuli or differentiation events. Other interactions are more structural and stable, that is they are constitutionally present across several cell types. Genome contact interactions can occur via recruitment and physical interaction between chromatin-binding proteins and correlate with epigenetic marks such as histone modifications. Absence of a contact can occur due to presence of insulators, that is, chromatin-bound complexes that physically separate genomic loci. Understanding which contacts occur or do not occur in a given cell type is important since it can help explain how genes are regulated and which functional elements are involved in such regulation. The analysis of genome contact interactions has been greatly facilitated by the relatively recent development of chromosome conformation capture (3C). In an even more recent development, 3C was combined with next generation sequencing and led to Hi-C, a technique that in theory queries all possible pairwise interactions both within the same chromosome (intra) and between chromosomes (inter). Hi-C has now been used to study genome contact interactions in several human and mouse cell types as well as in animal models such as Drosophila and yeast. While it is fair to say that Hi-C has revolutionized the study of chromatin interactions, the computational analysis of Hi-C data is extremely challenging due to the presence of biases, artifacts, random polymer ligation and the huge number of potential pairwise interactions. In this chapter, we outline a strategy for analysis of genome contact experiments based on Hi-C using R and Bioconductor.

Mapping the effects of drugs on the immune system.

Understanding how drugs affect the immune system has consequences for treating disease and minimizing unwanted side effects. Here we present an integrative computational approach for predicting interactions between drugs and immune cells in a system-wide manner. The approach matches gene sets between transcriptional signatures to determine their similarity. We apply the method to model the interactions between 1,309 drugs and 221 immune cell types and predict 69,995 known and novel interactions. The resulting immune-cell pharmacology map is used to predict how 5 drugs influence 4 immune cell types in humans and mice. To validate the predictions, we analyzed patient records and examined cell population changes from in vivo experiments. Our method offers a tool for screening thousands of interactions to identify relationships between drugs and the immune system.

Specific Tandem 3'UTR Patterns and Gene Expression Profiles in Mouse Thy1+ Germline Stem Cells.

A recently developed strategy of sequencing alternative polyadenylation (APA) sites (SAPAS) with second-generation sequencing technology can be used to explore complete genome-wide patterns of tandem APA sites and global gene expression profiles. spermatogonial stem cells (SSCs) maintain long-term reproductive abilities in male mammals. The detailed mechanisms by which SSCs self-renew and generate mature spermatozoa are not clear. To understand the specific alternative polyadenylation pattern and global gene expression profile of male germline stem cells (GSCs, mainly referred to SSCs here), we isolated and purified mouse Thy1+ cells from testis by magnetic-activated cell sorting (MACS) and then used the SAPAS method for analysis, using pluripotent embryonic stem cells (ESCs) and differentiated mouse embryonic fibroblast cells (MEFs) as controls. As a result, we obtained 99,944 poly(A) sites, approximately 40% of which were newly detected in our experiments. These poly(A) sites originated from three mouse cell types and covered 17,499 genes, including 831 long non-coding RNA (lncRNA) genes. We observed that GSCs tend to have shorter 3'UTR lengths while MEFs tend towards longer 3'UTR lengths. We also identified 1337 genes that were highly expressed in GSCs, and these genes were highly consistent with the functional characteristics of GSCs. Our detailed bioinformatics analysis identified APA site-switching events at 3'UTRs and many new specifically expressed genes in GSCs, which we experimentally confirmed. Furthermore, qRT-PCR was performed to validate several events of the 334 genes with distal-to-proximal poly(A) switch in GSCs. Consistently APA reporter assay confirmed the total 3'UTR shortening in GSCs compared to MEFs. We also analyzed the cis elements around the proximal poly(A) site preferentially used in GSCs and found C-rich elements may contribute to this regulation. Overall, our results identified the expression level and polyadenylation site profiles and these data provide new insights into the processes potentially involved in the GSC life cycle and spermatogenesis.

Role of Sortilin in Models of Autoimmune Neuroinflammation.

The proneurotrophin receptor sortilin is a protein with dual functions, being involved in intracellular protein transport, as well as cellular signal transduction. The relevance of the receptor for various neuronal disorders, such as dementia, seizures, and brain injury, is well established. In contrast, little is known about the role of sortilin in immune cells and inflammatory diseases. The aim of our study was to elucidate the distribution of sortilin in different immune cell types in mice and humans and to analyze its function in autoimmune CNS inflammation. Sortilin was expressed most profoundly in murine and human macrophages and dendritic cells and to a much lesser extent in B and T cells. In dendritic cells, sortilin had an impact on Ag processing. Accordingly, sortilin was highly expressed by infiltrated perivascular myeloid cells, mainly in vessel cuffs, in the CNS of patients suffering from multiple sclerosis, the most common inflammatory autoimmune disease of the CNS. Yet, sortilin gene-targeted mice (Sort1(-/-)) and chimeras deficient in sortilin in the immune system were as susceptible as wild-type littermates to T cell-dependent experimental autoimmune encephalomyelitis. Considering our results and recent data from other investigators, we conclude that the proneurotrophin receptor sortilin plays a role in innate, rather than in adaptive, immune processes and, thus, not in autoimmune neuroinflammation.

Enhanceosome transcription factors preferentially dimerize with high mobility group proteins.

BackgroundThe enhanceosome is an enhancer located upstream of the human interferon β gene, bound by transcription factor (TF) complex of extremely rigid structure. Within these rigid constraints, even a slight change of distances between transcription factor binding sites (TFBS) results in loss of functionality of the enhanceosome. We hypothesized that smaller subunits of the enhanceosome may entail TF complex formation in other regulatory regions.ResultsIn order to verify this hypothesis we systematically searched for dimerization preferences of the TFs that have TFBS in the enhanceosome. For this we utilized our recently developed tool, TACO. We performed this computational experiment in a cell-type–specific manner by utilizing cell-type–specific DNase-seq data for 105 human cell types. We also used 20 TRANSFAC motifs comprising not only the usual TFs constituting the enhanceosome but also the architectural proteins of High Mobility Group I(Y) (HMG I). A similar experiment used 42 DNase-seq data sets for mouse cell types. We found 137 statistically significant dimer predictions in the human genome, and 37 predictions in the mouse genome, that matched the positioning on the enhanceosome with ±2 bp tolerance. To characterize these predicted TF dimers, we performed functional analysis (Gene Ontology enrichment) for sets of genes which were in the neighbourhood of predicted dimer instances. A notable feature of these instances is that (1) most of them are located in introns of genes, (2) they are enriched in regulatory states, and (3) those instances that are located near transcription start sites are enriched for inclusion in computationally predicted enhancers. We also investigated similarity of dimer predictions between human and mouse.ConclusionsIt follows from our experiments that, except for homodimer formed by IRF proteins, the rest of the dimers were formed exclusively between one of the transcriptional activators (ATF-2/c-Jun and IRF) and a HMG I protein. NF- κB did not participate in forming dimers with other proteins. Dimers predicted in mouse were fully contained in those predicted in human, with exactly the same spacing and orientation. Intriguingly, in most of the cases the enhanceosome motifs have 1 bp wider spacing than the corresponding dimers predicted genome-wide, which is likely caused by the overall 3D structure constraints of the enhanceosome-bound complex.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0258-3) contains supplementary material, which is available to authorized users.

Burkholderia pseudomallei induces IL-23 production in primary human monocytes.

Burkholderia pseudomallei, a gram-negative intracellular bacterium, is a causative agent of melioidosis. The bacterium has been shown to induce the innate immune response, particularly pro-inflammatory cytokine production in several of both mouse and human cell types. In the present study, we investigate host immune response in B. pseudomallei-infected primary human monocytes. We discover that wild-type B. pseudomallei is able to survive and multiply inside the primary human monocytes. In contrast, B. pseudomallei LPS mutant, a less virulent strain, is susceptible to host killing during bacterial infection. Moreover, microarray result showed that wild-type B. pseudomallei but not B. pseudomallei LPS mutant is able to activate gene expression of IL-23 as demonstrated by the up-regulation of p19 and p40 subunit expression. Consistent with gene expression analysis, the secretion of IL-23 analyzed by ELISA also showed that wild-type B. pseudomallei induces a significantly higher level of IL-23 secretion than that of B. pseudomallei LPS mutant. These results implied that IL-23 may be an important cytokine for the innate immune response during B. pseudomallei infection. The regulation of IL-23 production may drive the different host innate immune responses between patients and may relate to the severity of melioidosis.

DbMAE: the database of autosomal monoallelic expression.

Recently, data on ‘random’ autosomal monoallelic expression has become available for the entire genome in multiple human and mouse tissues and cell types, creating a need for better access and dissemination. The database of autosomal monoallelic expression (dbMAE; https://mae.hms.harvard.edu) incorporates data from multiple recent reports of genome-wide analyses. These include transcriptome-wide analyses of allelic imbalance in clonal cell populations based on sequence polymorphisms, as well as indirect identification, based on a specific chromatin signature present in MAE gene bodies. Currently, dbMAE contains transcriptome-wide chromatin identification calls for 8 human and 21 mouse tissues, and describes over 16 000 murine and ∼700 human cases of directly measured biased expression, compiled from allele-specific RNA-seq and genotyping array data. All data are manually curated. To ensure cross-publication uniformity, we performed re-analysis of transcriptome-wide RNA-seq data using the same pipeline. Data are accessed through an interface that allows for basic and advanced searches; all source references, including raw data, are clearly described and hyperlinked. This ensures the utility of the resource as an initial screening tool for those interested in investigating the role of monoallelic expression in their specific genes and tissues of interest.

Targeting Batf2 for infectious diseases and cancer.

The family members Batf, Batf2 and Batf3 belong to a class of transcription factors containing basic leucine zipper domains that regulate various immunological functions and control the development and differentiation of immune cells. Functional studies by others demonstrated a predominant role for Batf in controlling Th2 cell functions and lineage development of T lymphocytes as well as a critical role of Batf, Batf2 and Batf3 in CD8α+dendritic cell development. Moreover, Batf family member expression was measured in a vast collection of mouse and human cell types by cap analysis gene expression (CAGE), a recent developed sequencing technology, showing reasonable expression spectrum in immune cells consistent with previously published expression profiles. Batf and Batf3 were highly expressed in lymphocytes and the earlier moderately expressed in myeloid lineages. Batf2 was predominantly expressed in monocytes/macrophages. Functional studies in mice demonstrated that Batf2 has a central role in macrophage activation by regulating inflammatory responses during lipopolysaccharides stimulation and mycobacterial infection. Hence, Batf2 could be used as a biomarker and a potential host directed drug target in tuberculosis. Moreover, Batf2 act as a tumor suppressor gene and augmenting Batf2 in malignant cells might be an encouraging therapeutic treatment against cancer.

Tracing Dynamic Changes of DNA Methylation at Single-Cell Resolution

Mammalian DNA methylation plays an essential role in development. To date, only snapshots of different mouse and human cell types have been generated, providing a static view on DNA methylation. To enable monitoring of methylation status as it changes over time, we establish a reporter of genomic methylation (RGM) that relies on a minimal imprinted gene promoter driving a fluorescent protein. We show that insertion of RGM proximal to promoter-associated CpG islands reports the gain or loss of DNA methylation. We further utilized RGM to report endogenous methylation dynamics of non-coding regulatory elements, such as the pluripotency-specific super enhancers of Sox2 and miR290. Loci-specific DNA methylation changes and their correlation with transcription were visualized during cell-state transition following differentiation of mouse embryonic stem cells and during reprogramming of somatic cells to pluripotency. RGM will allow the investigation of dynamic methylation changes during development and disease at single-cell resolution.

Abstract 2211: A comparative analysis of the cis-regulatory landscape between human and mouse

Abstract As the premier model organism in biomedical research, the laboratory mouse shares the vast majority of protein-coding genes with humans, but significant differences exist between the two mammals, posing considerable challenges in the study and modeling of human diseases. The mouse ENCODE consortium applied the same high throughput approaches as the human ENCODE studies and produced more than1000 coordinated datasets in over 100 mouse cell types and tissues and greatly expanded the annotation of the mouse genome. By comparative analysis with the human genome, we found that although the majority of gene expression and cis-regulatory elements are conserved between the two species, a large degree of gene regulatory elements appear to be species-specific and these species-specific elements are enriched for genes involved in immune system and metabolic process, suggesting that different gene pathways evolve at distinct rates. Moreover, we found that species-specific elements are also enriched for repetitive DNA elements such LTR and SINE, which we hypothesize to be responsible generating the species-specific elements. Finally, we developed a novel computational method to study the functional conservation between two species without requiring perfectly matched cell lines or tissues. The result confirms that cis-elements with different evolutionary rates are associated distinct biological pathways and reveals the complex driving forces in the evolution of cis-regulatory landscape in mammals. Note: This abstract was not presented at the meeting. Citation Format: Feng Yue, Yin Shen, Zhen Ye, Bing Ren. A comparative analysis of the cis-regulatory landscape between human and mouse. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2211. doi:10.1158/1538-7445.AM2015-2211

Rescue of corpus callosum agenesis in two ciliary mutants by the short repressor isoform of Gli3

Agenesis of the Corpus callosum (AgCC) is a frequent brain disorder found in over 50 human congenital syndromes including ciliopathies. Here, we report a severe AgCC in Ftm/Rpgrip1l knock-out mice, which provide a valuable model for Meckel-Gruber syndrome. Ftm encodes a protein of the ciliary transition zone, which is essential for ciliogenesis in some, but not all cell types in mice, including neuroepithelial cells in the developing forebrain. We show that AgCC in Ftm-/- fetuses results from a mislocalization of guidepost cells in the dorsomedial telencephalon and not from a reduction of callosal neurons in the cortex. This abnormal distribution of the guideposts primarily results from patterning defects in the medial telencephalon, which relies on Gli3 processing defects. These patterning defects, mispositioning of dorsomedial guideposts and AgCC can all be rescued by reintroducing Gli3R in Ftm-/- embryos, provided by the Gli3D699 allele, which produces only the short repressor isoform of Gli3. This rescue of AgCC of Ftm-/- mutants by one allele of Gli3D699 confirms and completes our knowledge on the pre-eminent role of Gli3 in CC formation. Furthermore, Gli3D699 also rescue AgCC in Rfx3-/- mutant, another ciliary mutant deficient for a transcription factor controlling several ciliary genes. Rescuing the CC formation in two independent ciliary mutants by a single molecule, namely Gli3R, highlight the crucial role of primary cilia in maintaining the proper level of Gli3R required for CC morphogenesis. These data demonstrate that Gli3 processing is the major outcome of primary cilia function in CC formation.

The role of primary cilia in corpus callosum formation is mediated by production of the Gli3 repressor.

Agenesis of the corpus callosum (AgCC) is a frequent brain disorder found in over 80 human congenital syndromes including ciliopathies. Here, we report a severe AgCC in Ftm/Rpgrip1l knockout mouse, which provides a valuable model for Meckel-Grüber syndrome. Rpgrip1l encodes a protein of the ciliary transition zone, which is essential for ciliogenesis in several cell types in mouse including neuroepithelial cells in the developing forebrain. We show that AgCC in Rpgrip1l(-/-) mouse is associated with a disturbed location of guidepost cells in the dorsomedial telencephalon. This mislocalization results from early patterning defects and abnormal cortico-septal boundary (CSB) formation in the medial telencephalon. We demonstrate that all these defects primarily result from altered GLI3 processing. Indeed, AgCC, together with patterning defects and mispositioning of guidepost cells, is rescued by overexpressing in Rpgrip1l(-/-) embryos, the short repressor form of the GLI3 transcription factor (GLI3R), provided by the Gli3(Δ699) allele. Furthermore, Gli3(Δ699) also rescues AgCC in Rfx3(-/-) embryos deficient for the ciliogenic RFX3 transcription factor that regulates the expression of several ciliary genes. These data demonstrate that GLI3 processing is a major outcome of primary cilia function in dorsal telencephalon morphogenesis. Rescuing CC formation in two independent ciliary mutants by GLI3(Δ699) highlights the crucial role of primary cilia in maintaining the proper level of GLI3R required for morphogenesis of the CC.

An excitatory amacrine cell detects object motion and provides feature-selective input to ganglion cells in the mouse retina.

Retinal circuits detect salient features of the visual world and report them to the brain through spike trains of retinal ganglion cells. The most abundant ganglion cell type in mice, the so-called W3 ganglion cell, selectively responds to movements of small objects. Where and how object motion sensitivity arises in the retina is incompletely understood. In this study, we use 2-photon-guided patch-clamp recordings to characterize responses of vesicular glutamate transporter 3 (VGluT3)-expressing amacrine cells (ACs) to a broad set of visual stimuli. We find that these ACs are object motion sensitive and analyze the synaptic mechanisms underlying this computation. Anatomical circuit reconstructions suggest that VGluT3-expressing ACs form glutamatergic synapses with W3 ganglion cells, and targeted recordings show that the tuning of W3 ganglion cells' excitatory input matches that of VGluT3-expressing ACs' responses. Synaptic excitation of W3 ganglion cells is diminished, and responses to object motion are suppressed in mice lacking VGluT3. Object motion, thus, is first detected by VGluT3-expressing ACs, which provide feature-selective excitatory input to W3 ganglion cells.DOI: http://dx.doi.org/10.7554/eLife.08025.001

Recellularization of decellularized lung scaffolds is enhanced by dynamic suspension culture.

Strategies are needed to improve repopulation of decellularized lung scaffolds with stromal and functional epithelial cells. We demonstrate that decellularized mouse lungs recellularized in a dynamic low fluid shear suspension bioreactor, termed the rotating wall vessel (RWV), contained more cells with decreased apoptosis, increased proliferation and enhanced levels of total RNA compared to static recellularization conditions. These results were observed with two relevant mouse cell types: bone marrow-derived mesenchymal stromal (stem) cells (MSCs) and alveolar type II cells (C10). In addition, MSCs cultured in decellularized lungs under static but not bioreactor conditions formed multilayered aggregates. Gene expression and immunohistochemical analyses suggested differentiation of MSCs into collagen I-producing fibroblast-like cells in the bioreactor, indicating enhanced potential for remodeling of the decellularized scaffold matrix. In conclusion, dynamic suspension culture is promising for enhancing repopulation of decellularized lungs, and could contribute to remodeling the extracellular matrix of the scaffolds with subsequent effects on differentiation and functionality of inoculated cells.

300. AAV Vector-Mediated In Vivo Reprogramming of Various Cell Types in Adult Mice

The 2006/7 discovery that somatic cells of different tissue origins can be converted into induced pluripotent stem cells (iPSC) by mere introduction of a cocktail of “reprogramming” factors, such as Oct4, Klf4, Sox2 and c-Myc (OKSM), has revolutionized the field of regenerative medicine. A major part of this success story is due to the fact that delivery of the OKSM combination (or variants thereof) to cultured target cells can be accomplished using virtually any of the existing non-viral or viral gene transfer systems. Here, we specifically engineered Adeno-associated viral (AAV) vectors for OKSM delivery, based on their superior safety profile and their typical persistence as episomal DNA that is lost during cell division, which we considered beneficial for reprogramming. A third advantage is that AAV vectors can be pseudotyped with natural or synthetic viral capsids exhibiting high specificities and efficiencies in a given cell. Indeed, we reproducibly found that OKSM expression from four AAV vectors – each encoding a single factor under the strong and ubiquitous SFFV promoter, and pseudotyped with the potent chimeric AAV-DJ capsid – resulted in reprogramming of murine embryonic fibroblasts. Notably, the up to 0.2% reprogramming efficiency obtained with our AAV vectors is comparable to the best lentiviral system. Curiously, and defying our original prediction, we observed by PCR that the AAV vector DNA persisted in the reprogrammed cells even after extended cultivation for up to 21 passages. Using a combination of LAM-PCR and SureSelect technologies, we were then able to identify a variety of OKSM vector integration sites in the mouse genome, including a previously reported hot spot for AAV vector insertion. We speculate that the unusual high frequency of genomic AAV integration in iPSC is either related to mutational inactivation of genes that inhibit reprogramming, or merely a by-product of the relaxation of the chromatin structure triggered by OKSM expression. Based on the robust ex vivo efficiency, we next asked whether our OKSM vectors could also mediate reprogramming in vivo, and therefore applied different doses of AAV8-pseudotyped variants to adult mice via tail vein injection. Strikingly, four to eight weeks later, we found various small and large teratomas in their livers that we identified through histological analysis and isolation of residual iPSC. Moreover, by week eight, one mouse showed signs of extra-hepatic reprogramming in the pancreas and the thoracic cavity, congruent with the in vivo tropism of AAV serotype 8. These features make our novel AAV vector-mediated in vivo reprogramming strategy comparable to our previously published OKSM-transgenic mice (Nature 2013, 502:340-5), with the added benefits that AAV vectors can be applied in any mouse strain or other animals, and can be re-targeted to specific tissues, which opens up entirely novel avenues for stem cell research.

Extrahepatic sources of factor VIII potentially contribute to the coagulation cascade correcting the bleeding phenotype of mice with hemophilia A.

A large fraction of factor VIII in blood originates from liver sinusoidal endothelial cells although extrahepatic sources also contribute to plasma factor VIII levels. Identification of cell-types other than endothelial cells with the capacity to synthesize and release factor VIII will be helpful for therapeutic approaches in hemophilia A. Recent cell therapy and bone marrow transplantation studies indicated that Küpffer cells, monocytes and mesenchymal stromal cells could synthesize factor VIII in sufficient amount to ameliorate the bleeding phenotype in hemophilic mice. To further establish the role of blood cells in expressing factor VIII, we studied various types of mouse and human hematopoietic cells. We identified factor VIII in cells isolated from peripheral and cord blood, as well as bone marrow. Co-staining for cell type-specific markers verified that factor VIII was expressed in monocytes, macrophages and megakaryocytes. We additionally verified that factor VIII was expressed in liver sinusoidal endothelial cells and endothelial cells elsewhere, e.g., in the spleen, lungs and kidneys. Factor VIII was well expressed in sinusoidal endothelial cells and Küpffer cells isolated from human liver, whereas by comparison isolated human hepatocytes expressed factor VIII at very low levels. After transplantation of CD34(+) human cord blood cells into NOD/SCIDγNull-hemophilia A mice, fluorescence activated cell sorting of peripheral blood showed >40% donor cells engrafted in the majority of mice. In these animals, plasma factor VIII activity 12 weeks after cell transplantation was up to 5% and nine of 12 mice survived after a tail clip-assay. In conclusion, hematopoietic cells, in addition to endothelial cells, express and secrete factor VIII: this information should offer further opportunities for understanding mechanisms of factor VIII synthesis and replenishment.