Genome Wide DNA Methylation and Transcriptome Analysis in HSC Aging

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2367-2367
Author(s):  
Mira Jeong ◽  
Deqiang Sun ◽  
Min Luo ◽  
Aysegul Ergen ◽  
Hongcang Gu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Differentially Expressed ◽  
Mouse Bone Marrow ◽  
Rna Seq ◽  
Differentiation Potential ◽  
Hematopoietic Stem ◽  
Exon Arrays ◽  
Age Related ◽  
Genome Wide

Abstract Abstract 2367 Hematopoietic stem cell (HSC) Aging is a complex process linked to number of changes in gene expression and functional decline of self-renewal and differentiation potential. While epigenetic changes have been implicated in HSC aging, little direct evidence has been generated. DNA methylation is one of the major underlying mechanisms associated with the regulation of gene expression, but changes in DNA methylation patterns with HSC aging have not been characterized. We hypothesize that revealing the genome-wide DNA methylation and transcriptome signatures will lead to a greater understanding of HSC aging. Here, we report the first genome-scale study of epigenomic dynamics during normal mouse HSC aging. We isolated SP-KSL-CD150+ HSC populations from 4, 12, 24 month-old mouse bone marrow and carried out genome-wide reduced representative bisulfite sequencing (RRBS) and identified aging-associated differentially methylated CpGs. Three biological samples were sequenced from each aging group and we obtained 30–40 million high-quality reads with over 30X total coverage on ∼1.1M CpG sites which gives us adequate statistical power to infer methylation ratios. Bisulfite conversion rate of non-CpG cytosines was >99%. We analyzed a variety of genomic features to find that CpG island promoters, gene bodies, 5'UTRs, and 3'UTRs generally were associated with hypermethylation in aging HSCs. Overall, out of 1,777 differentially methylated CpGs, 92.8% showed age-related hypermethylation and 7.2% showed age-related hypomethylation. Gene ontology analyses have revealed that differentially methylated CpGs were significantly enriched near genes associated with alternative splicing, DNA binding, RNA-binding, transcription regulation, Wnt signaling and pathways in cancer. Most interestingly, over 579 splice variants were detected as candidates for age-related hypermethylation (86%) and hypomethylation (14%) including Dnmt3a, Runx1, Pbx1 and Cdkn2a. To quantify differentially expressed RNA-transcripts across the entire transcriptome, we performed RNA-seq and analyzed exon arrays. The Spearman's correlation between two different methods was good (r=0.80). From exon arrays, we identified 586 genes that were down regulated and 363 gene were up regulated with aging (p<0.001). Most interestingly, overall expression of DNA methyl transferases Dnmt1, Dnmt3a, Dnmt3b were down regulated with aging. We also found that Dnmt3a2, the short isoform of Dnmt3a, which lacks the N-terminal region of Dnmt3a and represents the major isoform in ES cells, is more expressed in young HSC. For the RNA-seq analysis, we focused first on annotated transcripts derived from cloned mRNAs and we found 307 genes were down regulated and 1015 gene were up regulated with aging (p<0.05). Secondly, we sought to identify differentially expressed isoforms and also novel transcribed regions (antisense and novel genes). To characterize the genes showing differential regulation, we analyzed their functional associations and observed that the highest scoring annotation cluster was enriched in genes associated with translation, the immune network and hematopoietic cell lineage. We expect that the results of these experiments will reveal the global effect of DNA methylation on transcript stability and the translational state of target genes. Our findings will lend insight into the molecular mechanisms responsible for the pathologic changes associated with aging in HSCs. Disclosures: No relevant conflicts of interest to declare.

scholarly journals A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Sandra Steyaert ◽  
Jolien Diddens ◽  
Jeroen Galle ◽  
Ellen De Meester ◽  
Sarah De Keulenaer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zebra Finch ◽  
Model Organism ◽  
Rna Seq ◽  
Exon Arrays ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search ◽  
Upregulated Genes

Abstract Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two zebra finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in zebra finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.

scholarly journals Genome-wide DNA methylation and RNA-seq analyses identify genes and pathways associated with doxorubicin resistance in a canine diffuse large B-cell lymphoma cell line

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0250013
Author(s):  
Chia-Hsin Hsu ◽  
Hirotaka Tomiyasu ◽  
Chi-Hsun Liao ◽  
Chen-Si Lin
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Rna Seq ◽  
Doxorubicin Resistance ◽  
Large B Cell Lymphoma ◽  
Genome Wide ◽  
Large B Cell

Doxorubicin resistance is a major challenge in the successful treatment of canine diffuse large B-cell lymphoma (cDLBCL). In the present study, MethylCap-seq and RNA-seq were performed to characterize the genome-wide DNA methylation and differential gene expression patterns respectively in CLBL-1 8.0, a doxorubicin-resistant cDLBCL cell line, and in CLBL-1 as control, to investigate the underlying mechanisms of doxorubicin resistance in cDLBCL. A total of 20289 hypermethylated differentially methylated regions (DMRs) were detected. Among these, 1339 hypermethylated DMRs were in promoter regions, of which 24 genes showed an inverse correlation between methylation and gene expression. These 24 genes were involved in cell migration, according to gene ontology (GO) analysis. Also, 12855 hypermethylated DMRs were in gene-body regions. Among these, 353 genes showed a positive correlation between methylation and gene expression. Functional analysis of these 353 genes highlighted that TGF-β and lysosome-mediated signal pathways are significantly associated with the drug resistance of CLBL-1. The tumorigenic role of TGF-β signaling pathway in CLBL-1 8.0 was further validated by treating the cells with a TGF-β inhibitor(s) to show the increased chemo-sensitivity and intracellular doxorubicin accumulation, as well as decreased p-glycoprotein expression. In summary, the present study performed an integrative analysis of DNA methylation and gene expression in CLBL-1 8.0 and CLBL-1. The candidate genes and pathways identified in this study hold potential promise for overcoming doxorubicin resistance in cDLBCL.

Large Conserved Domains Of Low DNA Methylation Maintained By 5-Hydroxymethycytosine and Dnmt3a

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2406-2406
Author(s):  
Mira Jeong ◽  
Deqiang Sun ◽  
Min Luo ◽  
Yun Huang ◽  
Myunggon Ko ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Hox Genes ◽  
Conflicts Of Interest ◽  
P Value ◽  
Genomic Feature ◽  
Conserved Domains ◽  
Hematopoietic Stem ◽  
Genome Wide ◽  
The Impact

Abstract Identification of recurrent leukemia-associated mutations in genes encoding regulators of DNA methylation such as DNMT3A and TET2 have underscored the critical importance of DNA methylation in maintenance of normal physiology. To gain insight into how DNA methylation exerts the central role, we sought to determine the genome-wide pattern of DNA methylation in the normal precursors of leukemia cells: the hematopoietic stem cell (HSC), and investigate the factors that affect alterations in DNA methylation and gene expression. We performed whole genome bisulfite sequencing (WGBS) on purified murine HSCs achieving a total of 1,121M reads, resulting in a combined average of 40X coverage. Using Hidden Markov Model we identified 32,325 under-methylated regions (UMRs) with average proportion of methylation ≤ 10% and by inspecting the UMR size distribution, we discovered exceptionally large “methylation Canyons” which span highly conserved domains frequently containing transcription factors and are quite distinct from CpG islands and shores. Methylation Canyons are a distinct genomic feature that is stable, albeit with subtle differences, across cell-types and species. Canyon-associated genes showed a striking pattern of enrichment for genes involved in transcriptional regulation (318 genes, P=6.2 x 10-123), as well as genes containing a homeobox domain (111 genes, P=3.9 x 10-85). We compared Canyons with TF binding sites as identified from more than 150 ChIP-seq data sets across a variety of blood lineages (>10)19 and found that TF binding peaks for 10 HSC pluripotency TFs are significantly enriched in entirety of Canyons compared with their surrounding regions. Low DNA methylation is usually associated with active gene expression. However, half of Canyon genes associated with H3K27me3 showed low or no expression regardless of their H3K4me3 association while H3K4me3-only Canyon genes were highly expressed. Because DNMT3A is mutated in a high frequency of human leukemias24, we examined the impact of loss of Dnmt3a on Canyon size. Upon knockout of Dnmt3a, the edges of the Canyons are hotspots of differential methylation while regions inside of Canyon are relatively resistant. The methylation loss in Dnmt3a KO HSCs led Canyon edge erosion, Canyon size expansion and addition of 861 new Canyons for a total of 1787 Canyons. Canyons marked with H3K4me3 only were most likely to expand after Dnmt3a KO and the canyons marked only with H3K27me3 or with both marks were more likely to contract. This suggests Dnmt3a specifically is acting to restrain Canyon size where active histone marks (and active transcription) are already present. WGBS cannot distinguish between 5mC and 5hmC, so we determined the genome-wide distribution of 5hmC in WT and Dnmt3a KO HSCs using the cytosine-5-methylenesulphonate (CMS)-Seq method in which sodium bisulfate treatment convert 5hmC to CMS; CMS-containing DNA fragments are then immunoprecipitated using a CMS specific antiserum. Strikingly, 5hmC peaks were enriched specifically at the borders of Canyons. In particular, expanding Canyons, typically associated with highest H3K4me3 marking, were highly enriched at the edges for the 5hmC signal suggesting a model in which Tet proteins and Dnmt3a act concomitantly on Canyon borders opposing each other in alternately effacing and restoring methylation at the edges, particularly at sites of active chromatin marks. Using Oncomine data, we tested whether Canyon-associated genes were likely to be associated with hematologic malignancy development and found Canyon genes were highly enriched in seven signatures of genes over-expressed in Leukemia patients compared to normal bone marrow; in contrast, four sets of control genes were not similarly enriched. Further using TCGA data, we found that expressed canyon genes are significantly enriched for differentially expressed genes between patients with and without DNMT3A mutation (p value<0.05) Overall, 76 expressed canyon genes, including multiple HOX genes, are significantly changed in patients with DNMT3A mutation (p=0.0031). Methylation Canyons, the novel epigenetic landscape we describe may provide a mechanism for the regulation of hematopoiesis and may contribute to leukemia development. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Hormone Replacement Therapy Associated White Blood Cell DNA Methylation and Gene Expression are Associated With Within-Pair Differences of Body Adiposity and Bone Mass

2015 ◽  
Vol 18 (6) ◽  
pp. 647-661 ◽  
Author(s):  
Aileen Bahl ◽  
Eija Pöllänen ◽  
Khadeeja Ismail ◽  
Sarianna Sipilä ◽  
Tuija M. Mikkola ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Body Composition ◽  
Hormone Replacement Therapy ◽  
Bone Mass ◽  
Replacement Therapy ◽  
Hormone Replacement ◽  
Differentially Expressed ◽  
Body Adiposity ◽  
Genome Wide

The loss of estrogen during menopause causes changes in the female body, with wide-ranging effects on health. Estrogen-containing hormone replacement therapy (HRT) leads to a relief of typical menopausal symptoms, benefits bone and muscle health, and is associated with tissue-specific gene expression profiles. As gene expression is controlled by epigenetic factors (including DNA methylation), many of which are environmentally sensitive, it is plausible that at least part of the HRT-associated gene expression is due to changes in DNA methylation profile. We investigated genome-wide DNA methylation and gene expression patterns of white blood cells (WBCs) and their associations with body composition, including muscle and bone measures of monozygotic (MZ) female twin pairs discordant for HRT. We identified 7,855 nominally significant differentially methylated regions (DMRs) associated with 4,044 genes. Of the genes with DMRs, five (ACBA1, CCL5, FASLG, PPP2R2B, and UHRF1) were also differentially expressed. All have been previously associated with HRT or estrogenic regulation, but not with HRT-associated DNA methylation. All five genes were associated with bone mineral content (BMC), and ABCA1, FASLG, and UHRF1 were also associated with body adiposity. Our study is the first to show that HRT associates with genome-wide DNA methylation alterations in WBCs. Moreover, we show that five differentially expressed genes with DMRs associate with clinical measures, including body fat percentage, lean body mass, bone mass, and blood lipids. Our results indicate that at least part of the known beneficial HRT effects on body composition and bone mass may be regulated by DNA methylation associated alterations in gene expression in circulating WBCs.

scholarly journals Differential DNA Methylation and Gene Expression Between ALV-J-Positive and ALV-J-Negative Chickens

2021 ◽  
Vol 8 ◽  
Author(s):  
Yiming Yan ◽  
Huihua Zhang ◽  
Shuang Gao ◽  
Huanmin Zhang ◽  
Xinheng Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cancer Progression ◽  
Economic Losses ◽  
Effective Vaccine ◽  
Rna Seq ◽  
Genome Wide ◽  
Avian Leukosis Virus Subgroup ◽  
Genome Wide Gene Expression ◽  
Integration Analysis

Background: Avian leukosis virus subgroup J (ALV-J) is an oncogenic virus that causes serious economic losses in the poultry industry; unfortunately, there is no effective vaccine against ALV-J. DNA methylation plays a crucial role in several biological processes, and an increasing number of diseases have been proven to be related to alterations in DNA methylation. In this study, we screened ALV-J-positive and -negative chickens. Subsequently, we generated and provided the genome-wide gene expression and DNA methylation profiles by MeDIP-seq and RNA-seq of ALV-J-positive and -negative chicken samples; 8,304 differentially methylated regions (DMRs) were identified by MeDIP-seq analysis (p ≤ 0.005) and 515 differentially expressed genes were identified by RNA-seq analysis (p ≤ 0.05). As a result of an integration analysis, we screened six candidate genes to identify ALV-J-negative chickens that possessed differential methylation in the promoter region. Furthermore, TGFB2 played an important role in tumorigenesis and cancer progression, which suggested TGFB2 may be an indicator for identifying ALV-J infections.

scholarly journals Genome-wide age-related changes in DNA methylation and gene expression in human PBMCs

AGE ◽  
2014 ◽  
Vol 36 (3) ◽  
Author(s):  
Wilma T. Steegenga ◽  
Mark V. Boekschoten ◽  
Carolien Lute ◽  
Guido J. Hooiveld ◽  
Philip J. de Groot ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Human Pbmcs ◽  
Age Related ◽  
Genome Wide ◽  
Age Related Changes

scholarly journals The genome-wide impact of trisomy 21 on DNA methylation and its implications for hematopoiesis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ivo S. Muskens ◽  
Shaobo Li ◽  
Thomas Jackson ◽  
Natalina Elliot ◽  
Helen M. Hansen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Down Syndrome ◽  
Association Study ◽  
Fetal Liver ◽  
Differentially Methylated Regions ◽  
Hematopoietic Stem ◽  
Minimal Impact ◽  
Genome Wide ◽  
Study Results

AbstractDown syndrome is associated with genome-wide perturbation of gene expression, which may be mediated by epigenetic changes. We perform an epigenome-wide association study on neonatal bloodspots comparing 196 newborns with Down syndrome and 439 newborns without Down syndrome, adjusting for cell-type heterogeneity, which identifies 652 epigenome-wide significant CpGs (P < 7.67 × 10−8) and 1,052 differentially methylated regions. Differential methylation at promoter/enhancer regions correlates with gene expression changes in Down syndrome versus non-Down syndrome fetal liver hematopoietic stem/progenitor cells (P < 0.0001). The top two differentially methylated regions overlap RUNX1 and FLI1, both important regulators of megakaryopoiesis and hematopoietic development, with significant hypermethylation at promoter regions of these two genes. Excluding Down syndrome newborns harboring preleukemic GATA1 mutations (N = 30), identified by targeted sequencing, has minimal impact on the epigenome-wide association study results. Down syndrome has profound, genome-wide effects on DNA methylation in hematopoietic cells in early life, which may contribute to the high frequency of hematological problems, including leukemia, in children with Down syndrome.

scholarly journals Short-Term Effects on Gene-Expression and on DNA-Methylation at the Genome-Wide Level of the Iberian Ham Intake and Compared With Orange Intake: A Crossover Randomized Trial

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 937-937
Author(s):  
Dolores Corella ◽  
José Sorlí ◽  
Eva Asensio ◽  
Rocío Barragán ◽  
Olga Portolés ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Randomized Trial ◽  
Intervention Group ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
European Ancestry ◽  
Pathway Enrichment Analysis ◽  
Short Term ◽  
Genome Wide

Abstract Objectives Diet regulates gene expression and methylation profiles by several mechanisms. However, studies analyzing the simultaneous effect of specific foods on gene-expression and DNA methylation at the genome-wide level are very scarce. Therefore our aims were: To study the short-term transcriptomics and epigenomcis effects at the genome-wide level of the Iberian ham intake compared with orange intake in the same subjects. Methods We carried out a cross-over randomized trial (registered at ISRCTN17906849) in 33 healhty volunteers (aged 18–50 years and 50% females) of European ancestry. After 12h fasting, participants were randomly allocated to eat 67.5 g of Iberian ham (100% pure iberian breed and 100% acorn fed) or 500 g of peeled oranges (Citrus reticulata) depening on the intervention group. After a washout period, subjects were crossed over to the alternate treatment arm. Blood samples were taken at 0-h and at 4-h to isolate DNA and RNA from leukocytes. A random sample of 16 participants was selected for omics analyses (gene expression with the. GeneChip Human Gene 2.0 ST Array, and the EPIC-Illumina array (850K) for methylation). Eight arrays (2 times and 2 treatments per 2 omics) were obtained for each participant. Differences in gene expression and methylation (4 h vs baseline) were analyzed for Iberian ham, oranges and combined. Kyoto Encyclopedia of Genes and Genomes (KEGG) was used for pathway enrichment analysis. Results The top-ranked genes differentially expressed P &lt; 1 × 10–5) after Iberian ham intake (4 h vs baseline) were PKBP5 and PICALM. Pantothenate and CoA biosyntesis and the JAK-STAT singaling pathways were the most significantly enriched (P &lt; 5 × 10–7). After orange intake, the top-ranked differentially expressed genes (P &lt; 5 × 10–6) were: SMAP2 and RHEB, the pathways being (P &lt; 5 × 10–9): Cellular senescence and ABC transporters. We detected top-ranked methylated CpGs both for ham and oranges, resulting the Chemokine signaling pathway differentially methylated for oranges and in the Neurothrophine singaling pathway for Iberian ham intake. Comparative combined analysis revealed additional differences. Conclusions A short-term intake of Iberian ham or oranges results in differences in gene expression as well as in DNA-methylation. Funding Sources CIBEROBN-06/03/035, PROMETEO-17/2017 APOSTD/2019/136), P1–1B2013–54 and COGRUP/2016/06

scholarly journals Changes in DNA Methylation in Response to 6-Benzylaminopurine Affect Allele-Specific Gene Expression in Populus tomentosa

2020 ◽  
Author(s):  
Anran Xuan ◽  
Yuepeng Song ◽  
Chenhao Bu ◽  
Panfei Chen ◽  
Yousry A. El-Kassaby ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Patterns ◽  
Populus Tomentosa ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Snp Analysis ◽  
Specific Gene Expression ◽  
Genome Wide ◽  
Allele Specific

The cytokinins play important roles in plant growth and development by regulating gene expression at genome wide level. DNA methylation is responsive to the external environment, but whether DNA methylation changes in response to cytokinin treatment to regulate gene expression is still unclear. Here, we used bisulfite sequencing and RNA sequencing to examine genome-wide DNA methylation and gene expression patterns in poplar (Populus tomentosa) after treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 566 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 501 protein-coding genes, 262 long non-coding RNAs, and 15,793 24-nt small interfering RNAs were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa. Combined DNA methylation and gene expression analysis demonstrated that DNA methylation plays an important role in regulating allele-specific gene expression. To further investigate the relationship between these 6-BA-responsive genes and phenotypic variation, we performed SNP analysis of 507 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa and identified 206 SNPs that were significantly associated with growth and wood properties. Association analysis indicated that 53% of loci with allele-specific expression had primarily dominant effects on poplar traits. Our comprehensive analyses of P. tomentosa DNA methylation and the regulation of allele-specific gene expression suggest that DNA methylation is an important regulator of imbalanced expression between allelic loci.

Comprehensive Comparison Of Gene Expression, Genomic DNA Methylation, and In Vitro Hematopoietic Differentiation Among Many Human iPS and ES Cell Lines

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1187-1187
Author(s):  
Masatoshi Nishizawa ◽  
Kazuhisa Chonabayashi ◽  
Akiko Oishi ◽  
Ikue Takei ◽  
Misato Nishikawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cell Lines ◽  
Genomic Dna ◽  
Ips Cells ◽  
Hematopoietic Differentiation ◽  
Es Cell ◽  
Differentiation Potential ◽  
Genome Wide ◽  
Differentiation Efficiency

Abstract Objective Hematopoietic differentiation from human induced pluripotent stem (iPS)/embryonic stem (ES) cell attracts much attention due to its huge potential for regenerative medicine. As indicated by some earlier papers, there is large variation in differentiation potential among pluripotent stem cell (PSC) lines, and this is one of major concerns in clinical application of PSCs. If it becomes possible to predict which PSC line has high differentiation potential without real differentiation experiment, it would greatly contribute to clinical application of PSCs. Although some papers reported about presence of epigenetic memories of parental somatic cells in iPS cells, the amount of the influence on differentiation potential remains to be known. Furthermore, especially in studies using human PSCs, genetic difference among individual donors of iPS/ES cells seems to be large, thus the study using many PSC lines from many donors is warranted. To address these issues, we planned to collect data of many iPS/ES cell lines on genome-wide gene expression and genomic DNA methylation, and differentiation potentials of individual lines, and identify the factors which affected difference in differentiation potential among PSC lines. The final goal of this study is to create data base about gene expression and DNA methylation profile and differentiation potentials of many PSC lines. We believe that this dataset will allow us to predict differentiation potentials of individual PSC lines, and accelerate clinical application of PSC lines in hematology field. Method We utilized 39 iPS/ES lines (iPS 35 lines, ES 4 lines) in this study. The iPS cell lines were derived from dermal fibroblast (n = 16), cord blood (n = 3), peripheral blood (n = 10), keratinocyte (n = 3), and dental pulp cell (n = 3), and were generated by retrovirus vector (n = 9), episomal vector (n = 25), and sendai virus vector (n = 1). The iPS cells were derived from 15 donors, and the ES cells were derived from 4 donors. We assessed hematopoietic differentiation potential by investigating hematopoietic differentiation efficiency for the first 15 days from start of differentiation, and colony forming potential of hematopoietic precursor cells (CD34+CD38-CD43+lineage marker- population) generated from PSC lines using semi-solid methylcellulose based-media. In addition, we collected genome-wide mRNA expression and DNA methylation profile of PSC lines, parental lines of iPS cells, hematopoietic precursor cells generated from PSCs by using mRNA microarray, genomic methylation beads array, and next generation sequencers, and analyzed correlation of these data with differentiation potentials of individual PSC lines. Result We have found that there is large variation in hematopoietic differentiation efficiency and colony forming ability as reported previously. Genome-wide investigation of gene expression and genomic DNA methylation revealed that expression of some genes or some factors were significantly correlated with hematopoietic differentiation efficiency or colony forming ability of hematopoietic precursor cells. Importantly, the factors affecting differentiation efficiency for first 15 days and those affecting colony-forming ability were absolutely different. More importantly, by combining several factors discovered in this analysis, we can predict hematopoietic differentiation potential of individual iPS/ES cell lines regardless of what parental cell lines iPS cells are derived or whether it is an iPS cell or ES cell. Conclusion From genome-wide analysis of gene expression and genomic DNA methylation, and hematopoietic differentiation experiments, we discovered the factors that were associated with difference in differentiation potential among PSC lines. Now, we are focusing on investigating molecular mechanisms by which the discovered factors are responsible for the difference in hematopoietic differentiation potentials among PSC lines. We believe that our findings will contribute not only to clinical application of hematopoietic cells generated from human PSCs, but also to further understanding of human developmental hematopoiesis. Disclosures: No relevant conflicts of interest to declare.

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