Journal: Leukemia

Article Title: Identification and interrogation of the gene regulatory network of CEBPA -double mutant acute myeloid leukemia

doi: 10.1038/s41375-022-01744-5

Figure Lengend Snippet: A Contact matrix across chromosome 1 for healthy CD34 + blasts (top) and t(8;21) (middle) and CEBPA N/C (bottom) leukemic blasts at 10 Mb resolution. A UCSC genome browser track is shown below each matrix to highlight the DNAse I hypersensitive site pattern. B Overlap of DNase I-HS sites with interactions for t(8;21) and CEBPA N/C AML as compared to normal CD34+ cells.

Article Snippet: C/EBPA N/C -8 cells were cultured at the concentration of 1 × 10 6 cell/mL in StemSpanTM Serum-Free Expansion Medium II (SFEMII) plus 10% StemSpanTM CD34+ Expansion Supplement and 175 nM UM171 (STEMCELL Technologies).

Techniques:

Journal: Nature metabolism

Article Title: DNA methylation mediates HbA1c-associated complications development in Type 1 diabetes

doi: 10.1038/s42255-020-0231-8

Figure Lengend Snippet: a , Genomic location of the depicted region at/near TXNIP . b , Manhattan plots of association between mean-DCCT HbA1c and DNAme at the covered CpGs. Multiple linear regression models adjusting for covariates were applied to each CpG across all the samples (two-sided tests based on t-statistic, n=499). X-axis represents CpG location and Y-axis represents –log(p). Two HbA1c-assoc regions are highlighted with pink background. c , Heatmap showing the 15 chromatin states (top) and 18 states (bottom). Colors are shown in the legends ( panel j ). d , Ribbon plots representing the genomic interactions identified by IHEC PCHi-C data. Red represents the interactions involved in PIRs containing TXNIP 3’UTR. Blue represents interactions containing TXNIP promoter. Height of each ribbon represents the average CHiCAGO score (Y-axis) of the corresponding interaction across 5 major blood cells including monocytes, neutrophils, CD4 + T-cells, CD8 + T-cells and B-cells. e , Annotations of the RefSeq genes in the depicted region. f , Pearson correlation of DNAme at 33 CpGs in TXNIP and its 25kb flanking region. The associations of DNAme with mean-DCCT HbA1c at each CpG are obtained by the same linear regression model (n=499) indicated in panel b and shown as a Manhattan plot in the upper panel. HbA1c-assoc CpGs (FDR < 15%) are labeled in red font with the most significant cg19693031 underlined. Pair-wise correlations of DNAme of these CpGs were analyzed by Pearson correlation with coefficients shown as heatmap. Blue/red represents negative/positive correlation, respectively. The majority of the CpGs depict positive correlations including all 9 HbA1c-assoc CpGs (in red), while 5 CpGs (in blue) showed little to negative correlation with other CpGs. g , Ribbon plot representing the association of DNAme at cg19693031with expression of its nearby genes (including TXNIP ) in monocytes. Multiple linear regression models adjusting for covariates based were applied to DNAme at cg19693031and expression of each nearby gene within 500 bp distance (n=1202 monocytes) to identify DNAme-assoc genes with nominal p < 0.05 (two-sided tests based on t-statistic). Blue indicates negative association at FDR < 0.05, while grey indicates associations with p < 0.05. h , In-vitro DNA hypomethylation at 3 CpGs in the 3’UTR of TXNIP (including cg19693031) induced by high glucose (HG) treatment of human primary bone marrow CD34 + cells. DNAme was measured by amplicon-seq. i , Upregulation of TXNIP expression induced by HG treatment of human primary bone marrow CD34 + cells. Cells were cultured in medium (see ) containing 25mmol/L glucose (control), or same medium with the addition of 20mmol/L glucose (45mmol/L total) for 72 hours (HG treatment). RT-PCRs were performed in triplicate, and the data shown represent means of triplicates from one experiment. j , Color codes of chromatin states in the heatmaps for 15 and 18 chromatin states shown in panel c.

Article Snippet: Human primary bone marrow CD34 + cells (1M-101C, Lonza, Switzerland,) were cultured in growth medium (#09605, STEMCELL Technologies, MA), STEMSPAN II plus StemSpanTM CD34+ Expansion Supplement (#02691, STEMCELL Technologies, MA) containing 25mmol/L glucose (control), or same medium with the addition of 20mmol/L glucose for 72 hours (HG treatment).

Techniques: Labeling, Expressing, In Vitro, Amplification, Cell Culture, Control