In Vivo Human Somitogenesis Guides Somite Development from hPSCs

Abstract

Somites form during embryonic development and give rise to unique cell and tissue types, such as skeletal muscles and bones and cartilage of the vertebrae. Using somitogenesis-stage human embryos, we performed transcriptomic profiling of human presomitic mesoderm as well as nascent and developed somites. In addition to conserved pathways such as WNT-β-catenin, we also identified BMP and transforming growth factor β (TGF-β) signaling as major regulators unique to human somitogenesis. This information enabled us to develop an efficient protocol to derive somite cells in vitro from human pluripotent stem cells (hPSCs). Importantly, the in-vitro-differentiating cells progressively expressed markers of the distinct developmental stages that are known to occur during in vivo somitogenesis. Furthermore, when subjected to lineage-specific differentiation conditions, the hPSC-derived somite cells were multipotent in generating somite derivatives, including skeletal myocytes, osteocytes, and chondrocytes. This work improves our understanding of human somitogenesis and may enhance our ability to treat diseases affecting somite derivatives.

Keywords: chondrogenesis; development; differentiation; human pluripotent stem cells; osteogenesis; skeletal myogenesis; somite.

Figure 1. Transcriptomic profiling of somitogenesis stage human embryos identifies differentially regulated pathways among PSM, SM and SM Dev

(A) Illustration of human PSM, SM and SM Dev dissection. FLB and HLB: fore- and hind-limb bud. (B) PCA of PSM, SM and SM Dev replicates. (C) Volcano plot of PSM and SM gene expression profiles with selected PSM and SM markers highlighted in blue and black, respectively. (D) Heatmap showing RNA-seq expression of selected components of the differentially regulated signaling pathways between PSM and SM that were evaluated in this study. (E) Heatmap showing RNA-seq expression of selected components of the WNT signaling pathway that are differentially regulated between SM and SM Dev. See also Figure S1 and Tables S1–S3.

Figure 2. Transient activation of canonical WNT/β-catenin signaling progressively specifies hPSCs to the PS and pPSM fate

(A) Schematic of differentiation procedure in (B–F). Expression of the PS (B) and pPSM (C) markers by qRT-PCR shown as average ± SEM (n = 5). *, p<0.05, **, p<0.01, and ***, p<0.001 to the corresponding vehicle-treated (no treatment or NT) controls. Data were shown as relative expression to GAPDH levels. (D) Representative IF staining of TBX6 (top) and quantification of TBX6⁺ cells (bottom) shown as average ± SEM (n = 3). **, p<0.01 to Undiff (undifferentiated/day 0 samples). Scale bar: 100 µm. (E) Representative flow plots of PDGFRα and KDR (bottom) and quantification of PDGFRα⁺KDR⁻ cell population (top) shown as average ± SEM (n = 3). **, p<0.01 to Undiff. (F) Representative flow plots of CDX2 and quantification of CDX2⁺ cell population shown as average ± SEM (n = 4). See also Figures S2 and S5, and Table S4.

Figure 3. BMP inhibition drives pPSM cells to a somite fate

(A) Schematic of differentiation procedure in (B–D). Expression of the aPSM/somite (B) as well as Scl, neural crest and neural tube (C) markers by qRT-PCR shown as average ± SEM (n = 6). *, p<0.05, **, p<0.01, and ***, p<0.001 to the corresponding NT controls. Data were shown as relative expression to GAPDH levels. (D) Representative IF staining of TCF15 and PAX3 of cells treated by LDN (left) or NT (right) (n = 5). Scale bar: 100 µm. See also Figure S3.

Figure 4. Inhibition of TGFβ signaling synergizes with BMP inhibition to increase somite specification efficiency

(A) Schematic of differentiation procedure. LSB: LDN+SB. Expression of the aPSM/somite (B) and neural tube (C) markers by qRT-PCR shown as average ± SEM (n = 5). GAPDH was used as the housekeeping gene and fold changes (FC) were compared to LDN only-treated samples (which were set to 1.0). *, p<0.05 and **, p<0.01 to LDN only. (D) Representative flow plots of PAX3 and quantification of PAX3⁺ population shown as average ± SEM (n = 7). *, p<0.05 to NT and #, p<0.05 to LDN only. (E) Representative Western blots of PAX3 protein expression (n = 2). Numbers under each treatment condition indicate intensity of PAX3 normalized to GAPDH. (F) Representative flow charts of FOXC2 and quantification of FOXC2⁺ population shown as average ± SEM (n = 3). (G and H) Expression of select PSM (G) and somite (H) markers from dissected mouse tail paraxial mesoderm and differentiating H9 cells. Mouse microarray data were obtained from GEO database (series#: GSE39613) and shown as average ± SEM (n = 3 biological replicates). Increasing part number represents posterior (tail bud; Part 1) to anterior (nascent somites; Part 7). Human data were obtained from cells pre-treated with 2 days of CHIR (labeled as Hour 0) followed by another 2 days of LSB (Hour 6–48) and analyzed by qRT-PCR shown as average ± SD of technical triplicates from a representative experiment (n = 3). Mouse data were absolute expression value from microarray, and human data were relative expression to GAPDH levels. See also Figures S4 and S5.

Figure 5. hPSC-derived somite cells can undergo skeletal myogenesis

(A) Schematic of differentiation procedure in (B–D). (B) Expression of the DM and Scl markers by qRT-PCR shown as average ± SEM (n = 10). *, p<0.05, **, p<0.01 and ***, p<0.001. Data were shown as relative expression to GAPDH levels. (C) Expression of the myogenic markers by qRT-PCR shown as average ± SEM (n = 3). *, p<0.05 to d0 and #, p<0.05 to d6. Data were shown as relative expression to GAPDH levels. (D) Representative IF staining of the indicated myogenic markers at day 27 of differentiation (n = 3). DAPI is shown in blue in merged images. Scale bar: 200 µm. (E) Schematic of split, expansion (SkGM2+FGF2) and fusion (N2) of cells pre-differentiated as in (A). (F) Left: Representative IF staining of the indicated myogenic markers at the end of the culture (n = 2). A portion of PAX7⁺ cells (arrowhead) lie next to the MyHC⁺ myotubes containing multiple MYOD⁺ nuclei (arrow). Scale bar: 100 µm. Right: Quantification of nuclei within the MyHC⁺ myotubes, as well as those that were outside myotubes and either PAX7 and MYOD single or double positive. Total myogenic percentage was calculated as the sum of all the above populations. See also Figure S6.

Figure 6. hPSC-derived somite cells are osteogenic and chondrogenic

(A) Schematic of differentiation procedure in (B–I). (B) Expression of the Scl and DM markers by qRT-PCR shown as average ± SEM (n = 9). *, p<0.05 and ***, p<0.001. Data were shown as relative expression to GAPDH levels. (C) Expression of the osteogenic markers by qRT-PCR shown as average ± SEM (n = 4). *, p<0.05, **, p<0.01 and ***, p<0.001 compared to d0; #, p<0.05, ##, p<0.01 and ###, p<0.001 compared to d6. Data were shown as relative expression to GAPDH levels. (D) Alizarin Red S staining showing representative images of whole wells (left) and higher magnification (5X objective; right) (n = 6). (E) Representative confocal images of RUNX2 staining and quantification of RUNX2⁺ population shown as average ± SEM (n = 2). RUNX2 is shown in red and DAPI in blue. Scale bar: 50 µm. (F) Expression of the chondrogenic markers by qRT-PCR shown as average ± SEM (n = 3). *, p<0.05 and ***, p<0.001 compared to d0; #, p<0.05 and ###, p<0.001 compared to d6. Data were shown as relative expression to GAPDH levels. (G) Alcian Blue staining showing representative images of whole pellets (10X objective; left) and central areas under higher magnification (32X objective; right) (n = 3). (H) IHC of Collagen II showing representative images of whole pellets (10X objective; left) and lower-left areas under higher magnification (40X objective; right) (n = 2). (I) Representative images of chondrogenic pellets sectioned and stained with SOX9 and quantification of SOX9⁺ population shown as average ± SEM (n = 2; total of 4 pellets each time point). Insets showing lower magnification images capturing larger areas of the pellets. SOX9 is shown in green and DAPI in blue. Scale bar: 100 µm (insets 200 µm).