Status of KRAS in iPSCs Impacts upon Self-Renewal and Differentiation Propensity

Abstract

Oncogenic KRAS mutations in hematopoietic stem cells cause RAS-associated autoimmune lymphoproliferative syndrome-like disease (RALD). KRAS plays essential roles in stemness maintenance in some types of stem cells. However, its roles in pluripotent stem cells (PSCs) are poorly understood. Here, we investigated the roles of KRAS on stemness in the context of induced PSCs (iPSCs). We used KRAS mutant (G13C/WT) and wild-type isogenic (WT/WT) iPSCs from the same RALD patients, as well as wild-type (WT^ed/WT) and heterozygous knockout (Δ^ed/WT) iPSCs, both obtained by genome editing from the same G13C/WT clone. Compared with WT iPSCs, G13C/WT iPSCs displayed enforced retention of self-renewal and suppressed capacity for neuronal differentiation, while Δ^ed/WT iPSCs showed normalized cellular characteristics similar to those of isogenic WT^ed/WT cells. The KRAS-ERK pathway, but not the KRAS-PI3K pathway, was shown to govern these G13C/WT-specific phenotypes, indicating the strong impact of the KRAS-ERK signaling upon self-renewal and differentiation propensity in human iPSCs.

Keywords: KRAS; MAPK pathway; RAS-associated autoimmune lymphoproliferative syndrome-like disease; differentiation; iPSCs; self-renewal; stemness.

Graphical abstract

Figure 1

Establishment and Characterization of iPSC Clones Generated from Two RALD Patients (A) KRAS sequences of wild-type (WT/WT) and mutant (G13C/WT) iPSC lines derived from two RALD patients (cases no. 1 and no. 2). A position of mutation (G to T) is indicated by red letters. (B) Karyotypes of WT/WT and G13C/WT iPSC lines derived from case no. 2 (RALD patient). (C) Immunocytochemistry of iPSC markers (OCT4, NANOG, TRA-1-60, and SSEA4) in WT/WT and G13C/WT iPSC clones. Ho, Hoechst 33342. Scale bar, 100 μm. See also Tables S1 and S2.

Figure 2

Different Differentiation Propensity between WT/WT and G13C/WT iPSCs Generated from Two RALD Patients (A) Embryoid body formation of WT/WT and G13C/WT iPSC clones from case no. 2. Scale bar, 200 μm. (B) RNA-seq data showing gene expression levels of stemness and lineage markers from case no. 2 samples before and after 16-day in vitro differentiation. Undiff. and Diff., undifferentiated iPSCs and differentiated cells, respectively. (C) qRT-PCR analysis of 16-day in vitro differentiated cells from WT/WT and G13C/WT iPSC clones derived from case no. 2 (n = 3 independent experiments; mean ± SEM). (D) Immnunocytochemistry of βIII-Tubulin and MAP2 in 16-day in vitro differentiated cells from WT/WT and G13C/WT iPSC clones derived from case no. 2. Scale bar, 50 μm. See also Figures S1–S3.

Figure 3

Microarray Analysis of Isogenic WT/WT and G13C/WT KRAS Mutant iPSCs from a RALD Patient and Those Cultured without bFGF for 5 Days (A) Scatterplots with coefficients of correlation (R) for whole genes in WT/WT and G13C/WT iPSCs cultured with (w/) or without (w/o) bFGF for 5 days. Two clones per genotype were used: C2-1 and C2-2 for WT/WT; R2-1 and R2-2 for G13C/WT, derived from case no. 2. In this analysis, data of the same genotypes were averaged. Positions of POU5F1 (two probes), NANOG, and PAX6 (two probes) are indicated. The green lines indicate the diagonal and 2-fold changes between the two samples. (B) A heatmap with hierarchical clustering for stemness and lineage marker expression in the same samples as described above.

Figure 4

Enforced Retention of Self-Renewal of KRAS G13C/WT Mutant iPSCs in the Absence of bFGF, Revealed by Immunocytochemical Reactivity for Stemness Markers, Colony Formation, and Alkaline Phosphatase Staining (A) Immunocytochemistry of stemness markers (OCT4, NANOG, TRA-1-60, and SSEA-4) in WT/WT and G13C/WT iPSC clones from RALD patients cultured without bFGF for 5 days. Scale bar, 100 μm. (B and C) Quantitative imaging analysis for OCT4 in iPSC clones from RALD patients, cases no. 1 (B) and no. 2 (C), respectively (n = 8 independent experiments; mean ± SEM; ^∗∗∗p < 0.001; two-way ANOVA followed by Bonferroni's multiple comparison test). (D) Whole six-well (left) and magnified images (right) of alkaline phosphatase (ALP)-stained WT/WT (C2-1) and G13C/WT (R2-1) cells. Scale bar, 100 μm. (E) Quantification of ALP-positive (ALP⁺) colony number in (D) (n = 3 independent experiments; mean ± SEM; ^∗∗p < 0.01; ^∗∗∗p < 0.001; two-way ANOVA followed by Bonferroni's multiple comparison test). See also Figure S3; Table S4.

Figure 5

Biochemical Analysis on the ERK and AKT Pathways Activity in Enforced Retention of Self-Renewal of KRAS G13C/WT iPSCs (A) GST-RAF1 pull-down assays of RALD patient-derived iPSC (WT/WT and G13C/WT) clones from case no. 1 and no. 2 cultured with (w/) or without (w/o) bFGF for 3 days. (B) Densitometric analysis of western blotting results shown in (A). Each point indicates an individual clone's value (n = 4–6 independent clones; mean ± SEM; ^∗∗∗p < 0.001; Student's t test or Mann-Whitney test). (C) Western blot analysis of WT/WT and G13C/WT iPSC clones stimulated for the indicated time course after the removal of bFGF for 3 days. ERK and AKT were analyzed for their phosphorylation. β-Tubulin was used as an internal control. (D) Western blot analysis of WT/WT and G13C/WT clones cultured w/ or w/o bFGF for 2 days. Phosphorylation of ERK and AKT was analyzed as in (C). (E and F) Densitometric analysis of ERK (E) and AKT (F), respectively, in (D). Each point indicates an individual clone's value (n = 4–6 independent clones; mean ± SEM; ^∗∗∗p < 0.001; Student's t test or Mann-Whitney test). GST, glutathione S-transferase; RBD, Ras-binding domain. See also Figure S4.

Figure 6

Pharmacological Analysis on the Involvement of the RAF-MEK-ERK and PI3K-AKT Pathways in Enforced Retention of Self-Renewal of KRAS G13C/WT iPSCs (A and B) Effects of MEK inhibitors (PD184352 and U0126) on OCT4⁺ area (A) (n = 3 independent experiments; mean ± SEM) and phosphorylation of ERK and AKT (B), respectively, in G13C/WT iPSCs (clone R1-2). (C and D) Effects of RAF inhibitors (ZM336372 and AZ628) on OCT4⁺ area (C) (n = 3 independent experiments; mean ± SEM) and phosphorylation of ERK and AKT (D), respectively, in G13C/WT iPSCs (clone R1-2). (E) Representative fluorescent images of G13C/WT iPSCs (clone R1-2) treated with the compounds at indicated concentrations. Vehicle, 0.1% DMSO. Scale bar, 100 μm. See also Figure S5; Table S5.

Figure 7

Effects of a MEK Inhibitor on Suppressed Neuronal Differentiation in G13C/WT iPSCs (A) qRT-PCR analysis of a neuronal lineage marker (ASCL1) in 16-day differentiated cells from WT/WT (clones C1-1 and C2-1) and G13C/WT iPSCs (clones R1-2 and R2-1) treated with a MEK inhibitor (PD184352) at the concentrations of IC₂₀, IC₅₀, and IC₈₀ values as described in Table S5, or 0.1% DMSO (vehicle) (n = 3 independent experiments; mean ± SEM; ^∗p < 0.05; ^∗∗p < 0.01, ^∗∗∗p < 0.001; one-way ANOVA followed by Dunnett's test). (B) Immnunocytochemistry of βIII-Tubulin in 16-day differentiated cells from WT/WT and G13C/WT iPSCs treated with PD184352 as described above. Scale bar, 100 μm. PD, PD184352.