Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes

Abstract

Although human induced pluripotent stem cells (hiPSCs) have enormous potential in regenerative medicine, their epigenetic variability suggests that some lines may not be suitable for human therapy. There are currently few benchmarks for assessing quality. Here we show that X-inactivation markers can be used to separate hiPSC lines into distinct epigenetic classes and that the classes are phenotypically distinct. Loss of XIST expression is strongly correlated with upregulation of X-linked oncogenes, accelerated growth rate in vitro, and poorer differentiation in vivo. Whereas differences in X-inactivation potential result in epigenetic variability of female hiPSC lines, male hiPSC lines generally resemble each other and do not overexpress the oncogenes. Neither physiological oxygen levels nor HDAC inhibitors offer advantages to culturing female hiPSC lines. We conclude that female hiPSCs may be epigenetically less stable in culture and caution that loss of XIST may result in qualitatively less desirable stem cell lines.

Figure 1. Partial X Reactivation and High-Frequency Class III Conversion in Female hiPSCs

(A) RNA FISH of IMR-90 and undifferentiated hiPS-10. XIST RNA, red; Cot-1 RNA, green; asterisk, XIST cloud; arrow, COT-1 hole. (B) RNA FISH for XIST and Cot-1, followed by X-paint DNA FISH. Arrows, Cot-1 holes; asterisk, XIST cloud; double arrowheads, X chromosomes. Shown is hiPS-1 p.6. (C) Immunostaining for H3K27me3 (red) followed by DNA FISH (green) for X chromosomes in differentiated (d16) hiPSCs. (D) Real-time PCR of XIST expression. Ct values were normalized to IMR-90 cells (set to 1) and GAPDH, and values represent averages of triplicates. Error bars indicate standard deviations (SD) of the mean. p values were calculated with one-tailed Student's t test assuming equal variance; *p = 0.04; **p = 0.004. See also Figure S4. (E) Summary of XIST RNA FISH. n, sample size. LO, 4% oxygen; HO, 20% oxygen. (F) Three classes of XXY hiPSCs (d0, p.4). Arrows, Cot-1 holes; asterisk, XIST cloud; double arrowheads, X chromosomes. See also Figure S5.

Figure 2. Class III Female hiPSCs Have Unique Global Gene Expression Patterns

(A) Pearson correlation coefficients between whole sets of gene expression levels (RMA normalization) in the ten female hiPSC samples. hiPS-2 p.9, hiPS-9 p.7, hiPS-10 p.24, hiPS-3 p.14, hiPS-12 p.23, hiPS-11 p.16: high O₂; hiPS-11 p.16: low O₂; hiPS-9 p.19 c.III; hiPS-12 p.30 c.III. (B and C) PCA of gene expression patterns in indicated samples. Plot of component loadings shows relations of each microarray sample (RMA normalization) in PC1 versus PC2 (B) and of PC2 versus PC3 (C). Class II to III conversion indicated by arrows. (D and E) Expression levels for genes downregulated (D) and upregulated (E) in class III samples. Shown are top genes with highest correlation (D) or anti-correlation (E) to XIST expression, among those that are differentially expressed in at least six out of eight class II versus class III lines. See also Figure S6.

Figure 3. Microarray Analyses of Male versus Female hiPSCs and hESCs

(A and B) PCA shown in two dimensions for ComBat-corrected (A) and uncorrected (B) samples. See Table S4 for list of samples, GEO numbers, PubMed ID, and abbreviations. Class III hiPSCs from this study (L3) in green; L3 LO, hiPS-2 c.III in low oxygen p.50; L3-6, hiPS-6C-1 c.III p. 28; L3-12, hiPS-12D-1 c.III p.28. Blue, male hiPSCs; pink, female hiPSCs; black, female hESCs. (C) Expression heatmaps normalized to hiPS-9 and hiPS-12 c.III average (expression set as 0). Shown are genes up- and downregulated in class III hiPSCs (Table 2). L3 (cIII), hiPS-9, hiPS-12 c.III; L3 (cIII) LO, hiPS-2 c.III; L3 (cIII) Dis., hiPS 6C-1, 12D-1 c.III. Averages shown for duplicate and triplicate samples. (D) XIST expression in indicated lines plotted against correlation of expression pattern across differentially expressed genes.

Figure 4. Comparative In Vitro Growth Rates and In Vivo Differentiation

(A) Growth profiles for indicated hiPSC lines in ambient oxygen. Doubling times calculated from line equations. One colony for each line was mechanically passaged and plated in ten replicate, MEF-coated wells. Cells were trypsinized and counted. Averages shown. Percentages of XIST⁺ nuclei at the end of the experiment shown. n, sample size; N.D., not determined. Two biological replicates performed; similar results; one shown. (B) Growth profiles for indicated lines in physiological oxygen. Three colonies for each line were plated in quadruplicate on MEF-coated plates, then processed as in (A). (C) Growth differences as a function of passage number at ambient or physiological oxygen. Average values shown. (D) Teratomas from matched class II-III sublines of hiPS-2 and hiPS-12. (E) Representative histologic sections of class II and III teratomas.