Fig. 1: rs6048205-G affected pancreatic progenitor cell differentiation. | Nature Communications

Fig. 1: rs6048205-G affected pancreatic progenitor cell differentiation.

From: A noncoding variant confers pancreatic differentiation defect and contributes to diabetes susceptibility by recruiting RXRA

Fig. 1

a Schematic diagram of the SNP rs6048205 location. Locus of rs6048205 was shown in red. b Schematic of pancreatic differentiation protocol from human PSCs. Differentiation stages and key markers are shown. hPSCs, human pluripotent stem cells; DE, definitive endoderm; PP1, pancreatic progenitors 1 marked by PDX1; PP2, pancreatic progenitors 2 marked by PDX1 and NKX6-1; β-like cells, insulin-producing β-like cells. c Time-course mRNA levels of key stage-specific markers detected by RT-qPCR (n = 3 independent experiments). d Statistical analysis of PDX1-positive pancreatic progenitor cells in PP1 detected by flow cytometry in Supplementary Fig. 2d (n = 3 independent experiments). e mRNA levels of PP1 markers (PDX1 and NKX6-1) quantified by RT-qPCR. Gene expression levels were normalized to GAPDH and then further normalized to the A/A group (n = 4 independent experiments). f, g Representative immunofluorescence images (f) of PP2 cells stained by PDX1 (red) and NKX6-1 (green) and quantitative analysis for the percentage of cells expressing each marker (g) (n = 6 images in A/A, n = 7 in A/G and n = 10 in G/G). Nuclei were counterstained with DAPI (blue). Scale bar, 100 µm. h mRNA levels of PP2 markers (PDX1, NKX6-1 and PTF1A) detected by RT-qPCR. Gene expression levels were normalized to GAPDH and then further normalized to the A/A group (n = 3 independent experiments). i, j Flow cytometric analysis of PDX1- and NKX6-1-positive cells in PP2 stage (i) and quantitative analysis (j) (n = 3 independent experiments). k Scatterplot showing differentially expressed genes (DEGs) identified by RNA-seq of G group and A group in PP2 stage (n = 2 independent samples). Up-regulated and downregulated genes in the allele G group were shown in red and blue, respectively. l GO analysis of the up- and downregulated genes in the risk allele G group compared to the A group. Data are presented as the mean ± SD. Statistical significance was determined using the unpaired, two-tailed t-test in (d, e, g, f, j) (ns not significant), one-sided hypergeometric test with multiple comparison adjustments was used in (l). Source data are provided as a Source Data file.

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