Cell Cluster Sorting in Automated Differentiation of Patient-specific Induced Pluripotent Stem Cells Towards Blood Cells.

Induced pluripotent stem cells (iPS cells) represent a particularly versatile stem cell type for a large array of applications in biology and medicine. Taking full advantage of iPS cell technology requires high throughput and automated iPS cell culture and differentiation. We present an automated platform for efficient and robust iPS cell culture and differentiation into blood cells. We implemented cell cluster sorting for analysis and sorting of iPS cell clusters in order to establish clonal iPS cell lines with high reproducibility and efficacy. Patient-specific iPS cells were induced to differentiate towards hematopoietic cells via embryoid body (EB) formation. EB size impacts on iPS cell differentiation and we applied cell cluster sorting to obtain EB of defined size for efficient blood cell differentiation. In summary, implementing cell cluster sorting into the workflow of iPS cell cloning, growth and differentiation represent a valuable add-on for standard and automated iPS cell handling.

CRISPR/Cas9-engineered human ES cells harboring heterozygous and homozygous c-KIT knockout.

The receptor tyrosine kinase c-KIT (CD117) has a key role in hematopoiesis and is a marker for endothelial and cardiac progenitor cells. In vivo, deficiency of c-KIT is lethal and therefore using CRISPR/Cas9 editing we generated heterozygous and homozygous c-KIT knockout human embryonic stem cell (ES cell) lines. The c-KIT knockout left ES cell pluripotency unaffected as shown by immunofluorescence and trilineage differentiation potential. Heterozygous and homozygous c-KIT knockouts showed complete loss of exon 17, resulting in ablation of c-KIT protein from the cell surface. c-KIT knockout ES cells provide a valuable tool for further investigating c-KIT biology.

CRISPR/Cas9 editing in conditionally immortalized HoxB8 cells for studying gene regulation in mouse dendritic cells.

HoxB8 multipotent progenitors (MPP) are obtained by expression of the estrogen receptor hormone binding domain (ERHBD) HoxB8 fusion gene in mouse BM cells. HoxB8 MPP generate (i) the full complement of DC subsets (cDC1, cDC2, and pDC) in vitro and in vivo and (ii) allow CRISPR/Cas9-mediated gene editing, for example, generating homozygous deletions in cis-acting DNA elements at high precision, and (iii) efficient gene repression by dCas9-KRAB for studying gene regulation in DC differentiation.

The StemCellFactory: A Modular System Integration for Automated Generation and Expansion of Human Induced Pluripotent Stem Cells.

While human induced pluripotent stem cells (hiPSCs) provide novel prospects for disease-modeling, the high phenotypic variability seen across different lines demands usage of large hiPSC cohorts to decipher the impact of individual genetic variants. Thus, a much higher grade of parallelization, and throughput in the production of hiPSCs is needed, which can only be achieved by implementing automated solutions for cell reprogramming, and hiPSC expansion. Here, we describe the StemCellFactory, an automated, modular platform covering the entire process of hiPSC production, ranging from adult human fibroblast expansion, Sendai virus-based reprogramming to automated isolation, and parallel expansion of hiPSC clones. We have developed a feeder-free, Sendai virus-mediated reprogramming protocol suitable for cell culture processing via a robotic liquid handling unit that delivers footprint-free hiPSCs within 3 weeks with state-of-the-art efficiencies. Evolving hiPSC colonies are automatically detected, harvested, and clonally propagated in 24-well plates. In order to ensure high fidelity performance, we have implemented a high-speed microscope for in-process quality control, and image-based confluence measurements for automated dilution ratio calculation. This confluence-based splitting approach enables parallel, and individual expansion of hiPSCs in 24-well plates or scale-up in 6-well plates across at least 10 passages. Automatically expanded hiPSCs exhibit normal growth characteristics, and show sustained expression of the pluripotency associated stem cell marker TRA-1-60 over at least 5 weeks (10 passages). Our set-up enables automated, user-independent expansion of hiPSCs under fully defined conditions, and could be exploited to generate a large number of hiPSC lines for disease modeling, and drug screening at industrial scale, and quality.

Modelling IRF8 Deficient Human Hematopoiesis and Dendritic Cell Development with Engineered iPS Cells.

Human induced pluripotent stem (iPS) cells can differentiate into cells of all three germ layers, including hematopoietic stem cells and their progeny. Interferon regulatory factor 8 (IRF8) is a transcription factor, which acts in hematopoiesis as lineage determining factor for myeloid cells, including dendritic cells (DC). Autosomal recessive or dominant IRF8 mutations occurring in patients cause severe monocytic and DC immunodeficiency. To study IRF8 in human hematopoiesis we generated human IRF8-/- iPS cells and IRF8-/- embryonic stem (ES) cells using RNA guided CRISPR/Cas9n genome editing. Upon induction of hematopoietic differentiation, we demonstrate that IRF8 is dispensable for iPS cell and ES cell differentiation into hemogenic endothelium and for endothelial-to-hematopoietic transition, and thus development of hematopoietic progenitors. We differentiated iPS cell and ES cell derived progenitors into CD141+ cross-presenting cDC1 and CD1c+ classical cDC2 and CD303+ plasmacytoid DC (pDC). We found that IRF8 deficiency compromised cDC1 and pDC development, while cDC2 development was largely unaffected. Additionally, in an unrestricted differentiation regimen, IRF8-/- iPS cells and ES cells exhibited a clear bias toward granulocytes at the expense of monocytes. IRF8-/- DC showed reduced MHC class II expression and were impaired in cytokine responses, migration, and antigen presentation. Taken together, we engineered a human IRF8 knockout model that allows studying molecular mechanisms of human immunodeficiencies in vitro, including the pathophysiology of IRF8 deficient DC. Stem Cells 2017;35:898-908.

The polycomb protein Ezh2 impacts on induced pluripotent stem cell generation.

Reprogramming of somatic cells toward pluripotency involves extensive chromatin reorganization and changes in gene expression. Polycomb group (PcG) proteins are key regulators of chromatin structure, cell identity, and development. In this study, we investigated the impact of Ezh2, a core subunit of Polycomb repressive complex 2 (PRC2), on the generation of induced pluripotent stem (iPS) cells. We found that Ezh2 expression is induced during iPS cell generation and iPS cells contain high levels of Ezh2 mRNA and protein. Importantly, shRNA knockdown of Ezh2 during reprogramming severely impairs iPS cell generation. Mechanistically, Ezh2 acts during reprogramming at least in part through repressing the Ink4a/Arf locus, which represents a major roadblock for iPS cell generation. Interestingly, knockdown of Ezh2 in established pluripotent cells leaves pluripotency and self-renewal of embryonic stem cells and iPS cells unaffected. Altogether, our results demonstrate that Ezh2 is critical for efficient iPS cell generation, whereas it is dispensable for maintaining the reprogrammed iPS cell state.

To clone or not to clone? Induced pluripotent stem cells can be generated in bulk culture.

Induced pluripotent stem cells (iPSCs) are usually clonally derived. The selection of fully reprogrammed cells generally involves picking of individual colonies with morphology similar to embryonic stem cells (ESCs). Given that fully reprogrammed cells are highly proliferative and escape from cellular senescence, it is conceivable that they outgrow non-pluripotent and partially reprogrammed cells during culture expansion without the need of clonal selection. In this study, we have reprogrammed human dermal fibroblasts (HDFs) with episomal plasmid vectors. Colony frequency was higher and size was larger when using murine embryonic fibroblasts (MEFs) as stromal support instead of HDFs or human mesenchymal stromal cells (MSCs). We have then compared iPSCs which were either clonally derived by manual selection of a single colony, or derived from bulk-cultures of all initial colonies. After few passages their morphology, expression of pluripotency markers, and gene expression profiles did not reveal any significant differences. Furthermore, clonally-derived and bulk-cultured iPSCs revealed similar in vitro differentiation potential towards the three germ layers. Therefore, manual selection of individual colonies does not appear to be necessary for the generation of iPSCs - this is of relevance for standardization and automation of cell culture procedures.

Biological significance of DNA adducts: comparison of increments over background for various biomarkers of genotoxicity in L5178Y tk(+/-) mouse lymphoma cells treated with hydrogen peroxide and cumene hydroperoxide.

DNA is affected by background damage of the order of one lesion per one hundred thousand nucleotides, with depurination and oxidative damage accounting for a major part. This damage contributes to spontaneous mutation and cancer. DNA adducts can be measured with high sensitivity, with limits of detection lower than one adduct per one billion nucleotides. Minute exposures to an exogenous DNA-reactive agent may therefore result in measurable adduct formation, although, as an increment over total DNA damage, a small increment in mutation cannot be measured and would be considered negligible. Here, we investigated whether this discrepancy also holds for adducts that are present as background induced by oxidative stress. L5178Y tk(+/-) mouse lymphoma cells were incubated for 4h with hydrogen peroxide (0, 0.8, 4, 20, 100, 500muM) or cumene hydroperoxide (0, 0.37, 1.1, 3.3, 10muM). Five endpoints of genotoxicity were measured in parallel from aliquots of three replicates of large batches of cells: Two DNA adducts, 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) and 1,N(6)-etheno-2'-deoxyadenosine (varepsilondAdo) measured by LC-MS/MS, as well as strand breaks assessed with the comet assay and in vitro micronucleus test, and gene mutation as assessed using the thymidine kinase gene mutation assay. Background measures of 8-oxodGuo and varepsilondAdo were 500-1000 and 50-90 adducts per 10(9) nucleotides. Upon treatment, neither hydrogen peroxide nor cumene hydroperoxide significantly increased the DNA adduct levels above control. In contrast, dose-related increases above background were observed with both oxidants in the comet assay, the micronucleus test and the gene mutation assay. Differences in sensitivity of the assays were quantified by estimating the concentration of oxidant that resulted in a doubling of the background measure. We conclude that the increase in DNA breakage and mutation induced by hydrogen peroxide and cumene hydroperoxide observed in our in vitro experimental set-up was no direct consequence of the measured DNA adducts. In comparison with data obtained with the methylating agent methyl methanesulfonate we further conclude that the assumption of DNA adducts being oversensitive biomarkers is adduct-specific.

Lipid peroxidation-related 1,N2-propanodeoxyguanosine-DNA adducts induced by endogenously formed 4-hydroxy-2-nonenal in organs of female rats fed diets supplemented with sunflower, rapeseed, olive or coconut oil.

Animal and epidemiological studies confirm an impact of the fatty-acid composition in the diet on cancer development. We investigated the role of supplementation of the diet of female F344-rats with sunflower, rapeseed, olive or coconut oil on the formation of the promutagenic, exocyclic 1,N2-propanodeoxyguanosine adduct of the main lipid peroxidation product 4-hydroxy-2-nonenal in the mucosa of the glandular stomach, the small intestine, the colon, the whole kidney and the lung. This adduct is considered as the predominant DNA adduct arising from lipid peroxidation. The correlations between adduct levels and the different fatty acids were not uniform for all organs. No clear relationships between fatty acids and adduct levels were found in the colon. Significant positive correlations were observed between linoleic acid, total polyunsaturated fatty acids (PUFAs), vitamin E and DNA adduct levels in the small intestine and in the kidney. The results indicate an increasing effect on cancer risk in these organs as a result of high intake of linoleic acid. Inverse relationships between linoleic acid, PUFA and vitamin E intake and adduct levels were found in the glandular stomach and the lung. We could not confirm a chemopreventive effect of linolenic acid (C-18 omega-3 PUFA) on the formation of adducts in our animal study, as was shown in white blood cells of women in a previous study. A tendency towards a decrease in adduct levels was seen with monounsaturated fatty acids (MUFAs) in all organs except the lung. Saturated fatty acids showed a significant positive correlation with adduct levels in the mucosa of the glandular stomach and a significant inverse correlation in the small intestine. Saturated fatty acids are not considered to directly influence lipid peroxidation to a major extent.

DNA adducts as biomarkers for oxidative and genotoxic stress from pesticides in crop plants.

Plant studies have been carried out to identify the nature and extent of the formation of adducts with DNA bases when treated with pesticide formulations. DNA extracted from crop plants after treatment with pesticide formulations has yielded evidence of adduct formation. The extent of DNA modification has been established by (32)P postlabeling studies. The radiochromatograms from (32)P postlabeling of isolated plant DNA from grapes, bush beans, soybeans, pumpkins, and cucumbers show elevated adduct levels in treated vegetable plants as compared with untreated controls. A number of different adduct spots appear, likely indicating adduct formation with pesticide molecules or their metabolites. The DNA adducts from hexenal and 4-hydroxy-2-nonenal were clearly observed, indicating oxidative stress and lipid peroxidation in the plant.

Functional, biochemical, and pathological effects of repeated oral administration of ochratoxin A to rats.

Ochratoxin A (OTA), a mycotoxin produced by several fungi of Aspergillus and Penicillium species, may contaminate agricultural products, resulting in chronic human exposure. In rats, OTA is a potent nephrotoxin, and repeated administration of OTA for 2 years to rats in doses up to 0.21 mg/kg of body wt resulted in high incidences of renal tumors arising from the proximal tubular epithelial cells. The mechanism of tumor formation by OTA in the kidney is not well-defined, and controversial results regarding mode of action have been published. The aim of this study was to characterize dose-dependent changes induced by OTA by application of clinical chemistry, biochemical markers, and toxicokinetics for a better conclusion on modes of action. Administration of OTA (0, 0.25, 0.5, 1, and 2 mg/kg of body wt) to male F344 rats (n = 3 per group) by oral gavage for 2 weeks resulted in a dose-dependent increase in OTA plasma concentrations and concentrations of OTA in both liver and kidney. Although oxidative stress has been implicated in OTA carcinogenicity, treatment with OTA did not induce overt lipid peroxidation or an increase in 8-oxo-7,8-dihydro-2'deoxyguanosine (8-OH-dG) in kidney. In the kidney, OTA-induced pathology was present at all dose levels administered, with a clear increase in severity related to dose. Pathology was restricted to the outer stripe of the outer medulla and consisted of disorganization of the tubule arrangement, frequent apoptotic cells, and abnormally enlarged nuclei scattered through the S3 tubules. Consistent with the histopathology, a dose-dependent increase in the expression of proliferating cell nuclear antigen (PCNA), indicative of cell proliferation, was observed in kidneys, but not in livers of treated animals. The most prominent change in the composition of urine induced by OTA analyzed by 1H NMR and principal component analysis consisted of a major increase in the excretion of trimethylamine N-oxide. However, typical changes observed with other proximal tubular toxins such as increased excretion of glucose were not observed at any of the doses administered. Similarly, treatment with OTA had no clear effects on clinical chemical parameters indicative of nephrotoxicity, although urinary volume was increased at the higher-dose groups. Taken together, the uncommon changes induced by OTA suggest that a unique mechanism may be involved in OTA nephrotoxicity and carcinogenicity.

Ochratoxin A: lack of formation of covalent DNA adducts.

The mycotoxin ochratoxin A (OTA) is a potent nephrotoxin and renal carcinogen in rodents. However, the mechanism of OTA-induced tumor formation is unknown and conflicting results have been obtained regarding the potential of OTA to bind to DNA. OTA is poorly metabolized, and no reactive intermediates capable of interacting with DNA have been detected in vitro or in vivo. Recently, a hydroquinone/quinone redox couple and a carbon-bonded OTA-deoxyguanosine (OTA-dG) adduct formed by electrochemical oxidation and photoreaction of OTA have been reported and suggested to be involved in OTA carcinogenicity. This study was designed to characterize the role of DNA binding and to determine if formation of these derivatives occurs in vivo and in relevant activation systems in vitro using specific and sensitive methods. Horseradish peroxidase activation of OTA and its dechlorinated analogue ochratoxin B (OTB) yielded ochratoxin A-hydroquinone (OTHQ), but the postulated OTA-dG adduct was not detectable using LC-MS/MS. In support of this, no OTA-related DNA adducts were observed by 32P-postlabeling. In vivo, only traces of OTHQ were found in the urine of male F344 rats treated with high doses of OTA (2 mg/kg body wt) for 2 weeks, suggesting that this metabolite is not formed to a relevant extent. In agreement with the in vitro data, OTA-dG was not detected by LC-MS/MS in liver and kidney DNA extracted from treated animals. In addition, DNA binding of OTA and OTB was assessed in male rats given a single dose of 14C-OTA or 14C-OTB using accelerator mass spectrometry, a highly sensitive method for quantifying extremely low concentrations of radiocarbon. The 14C content in liver and kidney DNA from treated animals was not significantly different from controls, indicating that OTA does not form covalent DNA adducts in high yields. In summary, the results presented here demonstrate that DNA binding of OTA is not detectable with sensitive analytical methods and is unlikely to represent a mechanism for OTA-induced tumor formation.

Effect of enzyme-resistant starch on formation of 1,N(2)-propanodeoxyguanosine adducts of trans-4-hydroxy-2-nonenal and cell proliferation in the colonic mucosa of healthy volunteers.

The effect of enzyme-resistant starch (RS) on the development of colon cancer was reported to include both chemopreventive activity in humans and tumorigenic activity in animals. A study was performed to detect the influence of enzyme-RS on lipid peroxidation-induced DNA damage and cell proliferation. During two 4-week periods, 12 volunteers consumed a controlled diet in which starchy foods were enriched with a highly resistant amylomaize starch (Hylon VII) in the high-RS period and with an available corn starch in the low-RS period (second period). At the end of each test period, biopsy specimens of the rectosigmoidal mucosa were obtained from each subject and analyzed for trans-4-hydroxy-2-nonenal-1,N(2)-propanodeoxyguanosine-3'-monophosphate adducts using a (32)P postlabeling assay, and cell proliferation was determined by bromodeoxyuridine labeling. The trans-4-hydroxy-2-nonenal-1,N(2)-propanodeoxyguanosine-3'-monophosphate adduct level of DNA from colonic mucosa of eight evaluated volunteers was significantly higher in the high-RS period (mean adducts/10(7) nucleotides +/- SD, 3.83 +/- 0.60) than in the low-RS period (2.69 +/- 0.35; P < 0.05). There was no evidence for an increased cell proliferation in the upper crypt in the high-RS phase, compared with the low-RS phase. There are indications now that enzyme-RS induces oxidative stress that is not correlated with increased cell proliferation. If it is accepted that the formation of DNA adducts reflects oxidative stress, which in turn accelerates the process of carcinogenesis, then certain forms of RS may have a tumor-enhancing effect rather than a tumor-protective effect.