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Genome-wide gene expression analyses during chondrogenic differentiation of hiPSC. A) Hierarchical clustering and representative heatmap of genome-wide gene expression at different stages during hiPSC differentiation to hiChondrocytes and comparison with undifferentiated hiPSC and adult chondrocytes. B) Top gene ontology terms significantly enriched at different stages during chondrogenic differentiation of hiPSCs. C) Gene expression for characteristic markers of mesodermal subtypes and posterior, mid-, anterior, and late PS observed at an early stage (d 4) during chondrogenic differentiation of hiPSCs. D–F) Expression of known Sox9-regulated genes including transcription factors, signaling molecules, and ECM proteins in the Sox9 low and Sox9 high populations induced during chondrogenic differentiation of hiPSCs. Data presented as means 6 SE for gene expression vs. hiPSCs (n = 2 biologic replicates). 

Genome-wide gene expression analyses during chondrogenic differentiation of hiPSC. A) Hierarchical clustering and representative heatmap of genome-wide gene expression at different stages during hiPSC differentiation to hiChondrocytes and comparison with undifferentiated hiPSC and adult chondrocytes. B) Top gene ontology terms significantly enriched at different stages during chondrogenic differentiation of hiPSCs. C) Gene expression for characteristic markers of mesodermal subtypes and posterior, mid-, anterior, and late PS observed at an early stage (d 4) during chondrogenic differentiation of hiPSCs. D–F) Expression of known Sox9-regulated genes including transcription factors, signaling molecules, and ECM proteins in the Sox9 low and Sox9 high populations induced during chondrogenic differentiation of hiPSCs. Data presented as means 6 SE for gene expression vs. hiPSCs (n = 2 biologic replicates). 

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Regeneration of human cartilage is inherently inefficient; an abundant autologous source, such as human induced pluripotent stem cells (hiPSCs), is therefore attractive for engineering cartilage. We report a growth factor-based protocol for differentiating hiPSCs into articular-like chondrocytes (hiChondrocytes) within 2 weeks, with an overall effi...

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... dye-binding assay with shark CS (Sigma-Aldrich) as the standard. GAG content of the acellular hydrogels was determined as a negative control and subtracted from the amount of GAG released by the encapsulated cells during the 4 wk of culture. . Clustering analysis performed on these combined gene lists enabled the generation of the heat map in Fig. 4. Network analysis of the genes that had a 1.5-fold or greater upregula- tion in expression at each stage of differentiation when com- pared to the hiPSCs (the hiPSCs were compared to adult chondrocytes) was performed using MetaCore. Raw microarray data was uploaded to the Gene Expression Omnibus [accession number: GSE62914; National ...
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... found to be highly ex- pressed, indicating that the differentiation was directed toward an articular chondrocyte fate rather than a growth plate chondrocyte. Moreover, hiChondrocytes maintained the coexpression of Sox9 and Col II upon multiple rounds of cell passaging after 14 d of differentiation as well as post- cryopreservation (Supplemental Fig. S4A). Taken together, these findings demonstrate that the reported differentiation method is efficient and ...
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... or type X collagen (Col10a1), showing a lack of both characteristic fibrocartilage and hypertrophic mark- ers. Quantification of the fluorescence intensity using Im- age J (National Institutes of Health, Bethesda, MD, USA) determined the staining intensity for type II collagen to be 20-fold higher than that of type I collagen (Supplemental Fig. ...
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... analysis for Sox9 at different times in the differentiation protocol during the stepwise growth-factor treatment for 14 d and quantified the Sox9 low and Sox9 high populations (Fig. 3A and Supple- mental Fig. S6B). The cells are exclusively Sox9 low at d 4 and 7 and were exclusively Sox9 high after passage 1. The repre- sentative Supplemental Fig. S6B demonstrates 3 batches (1, 3, and 4) from lentivirally generated hiPSCs and 2 batches (7 and 10) from retrovirally generated hiPSCs. Differentiation in all the batches is consistent with a 5-9% variation in the overall Sox9-expressing population at d 4, 9, and 14 that eventually gave rise to a very homogenous Sox9 high population after the first passage of cells. After ...
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... were similar to adult chondrocytes, but distinct from the intermediate differentiating pop- ulations and hiPSCs (Supplemental Fig. S8C). For the ini- tial analyses, we identified a subset of 270 genes, including the known critical markers for pluripotency, cartilage dif- ferentiation, and chondrocytes, as well as early mesoder- mal genes (Fig. 4A). Upon differentiation, gene expression of pluripotency markers, including SOX2, TET1, OCT4, NANOG, and SALL4, was immediately down-regulated, as observed clearly by d 4, concurrent with an increase in expression of mesodermal genes, including NOTCH1, HAND1, TBX20, TBX3, LEF1, NKX2.5, and ISL1, in the intermediate stages of ...
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... regulators to be enriched in hiPSCs, whereas cell-matrix interactors, cartilage development, and bone ossification and remodeling pathways were enriched in adult chondrocytes. For the intermediate stages, regu- lation of epithelial-to-mesenchymal transition, cell-matrix interactions, and BMP/TGFb signaling were the significant pathways identified (Fig. 4B). It has been an unresolved question whether the primitive streak (PS) mesodermal induction consists of a common mesenchymal progenitor or distinct progenitor cells destined for the downstream lineages. In a recent elegant study, investigators addressed this complex question and suggested the existence of multiple distinct progenitors, ...
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... further identifying the spatial and temporal patterns of genes that particularly charac- terize a prechondrogenic progenitor (31). To test whether our differentiation protocol leads to an enrichment of the newly described prechondrogenic me- sodermal progenitors, we sought to compare the gene expression of different mesodermal developmental genes (Fig. 4C). Indeed, we observed that, when compared to hiPSCs, the early mesodermal populations at d 4 of dif- ferentiation showed an enrichment for the genes associ- ated with posterior PS lateral plate mesoderm that later matures into the prechondrogenic mesoderm, whereas the genes associated with the anterior PS that develops into cardiac ...
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... as containing Sox9 interaction sites in a chondrogenic rat sarcoma cell line by chromatin immunoprecipitation, fol- lowed by global array (ChIP-chip) (33) in the Sox9 low mesodermal population and the Sox9 high chondrocytes. We divided the Sox9-regulated genes into 3 groups: tran- scription factors, signaling molecules, and ECM proteins ( Fig. 4D-F). In the group of transcription factors (Fig. 4D), expression of LEF1, which interacts with b-catenin under Wnt stimulation (32), was high in the Sox9 low population (d 4 and 9), whereas RUNX2, PRRX1 (34), and the tran- scriptional coactivator PGC-1a (35) expression was high in Sox9 high hiChondrocytes. In the signaling molecules ...
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... chondrogenic rat sarcoma cell line by chromatin immunoprecipitation, fol- lowed by global array (ChIP-chip) (33) in the Sox9 low mesodermal population and the Sox9 high chondrocytes. We divided the Sox9-regulated genes into 3 groups: tran- scription factors, signaling molecules, and ECM proteins ( Fig. 4D-F). In the group of transcription factors (Fig. 4D), expression of LEF1, which interacts with b-catenin under Wnt stimulation (32), was high in the Sox9 low population (d 4 and 9), whereas RUNX2, PRRX1 (34), and the tran- scriptional coactivator PGC-1a (35) expression was high in Sox9 high hiChondrocytes. In the signaling molecules group, BMP2, BMP4, and TGFb1 were highly expressed in ...
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... and the tran- scriptional coactivator PGC-1a (35) expression was high in Sox9 high hiChondrocytes. In the signaling molecules group, BMP2, BMP4, and TGFb1 were highly expressed in Sox9 low but were down-regulated in the Sox9 high hiChon- drocytes, whereas CD44, integrin, and epidermal growth factor receptor were highly expressed in those cells (Fig. 4E). We noted especially that the ECM proteins in the third group (Fig. 4F) exhibited the most significant in- crease in Sox9-regulated ECM genes, including COL3A1, BGN, COL11A1, DCN, ADAMTS5, COL2A1, ASPN, and OGN in Sox9 high hiChondrocytes. The ECM proteins encoded by these genes are critical for human articular cartilage ...
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... in Sox9 high hiChondrocytes. In the signaling molecules group, BMP2, BMP4, and TGFb1 were highly expressed in Sox9 low but were down-regulated in the Sox9 high hiChon- drocytes, whereas CD44, integrin, and epidermal growth factor receptor were highly expressed in those cells (Fig. 4E). We noted especially that the ECM proteins in the third group (Fig. 4F) exhibited the most significant in- crease in Sox9-regulated ECM genes, including COL3A1, BGN, COL11A1, DCN, ADAMTS5, COL2A1, ASPN, and OGN in Sox9 high hiChondrocytes. The ECM proteins encoded by these genes are critical for human articular cartilage ...
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... that had a persistent high expression of Sox9 (36). The hiChon- drocytes generated are stable and do not dedifferentiate upon cryopreservation, as in up to 3 passages of monolayer culture of hiChondrocytes in vitro, the process of freezing and thawing did not diminish the expression of the chondrogenic markers, Sox9 and Col2a1 (Supplemental Fig. S4A). In addition, the hiChondrocytes had a pro- liferative advantage over adult chondrocytes that could be beneficial for their expansion for research or therapeutic applications (Supplemental Fig. ...
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... EBs toward the mesoderm. Using our differentiation protocol, we have identified that the pos- terior PS markers, as was recently described to characterize a prechondrogenic mesodermal population (19), were markedly induced in the early populations during hiPSC differentiation (d 4), whereas the anterior PS/cardiac mesodermal markers were reduced (Fig. 4C). These results highlight that the combination of Wnt3A, Activin A, and the ROCK inhibitor Y27632 led to a preferential enrich- ment of prechondrogenic mesoderm at the onset of hiPSC differentiation in our ...
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... the cellular differentiation process is homogenous and that the maturation of Sox9 low to Sox9 high expression is a distinct step in chondrogenic differentiation. In addition, our study shows that Sox9 has a distinct set of binding targets when its levels are low and that it can especially activate these target genes (like LEF and BMP4, as in Fig. 4D, E) only at low levels. As expected, a different set of genes appeared to be activated when the levels were high (Fig. 4F), thereby providing new and interesting insights into the gene networks regulated by Sox9. In future studies, it will be interesting to illuminate the differences in the cofactors and binding targets when Sox9 ...
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... step in chondrogenic differentiation. In addition, our study shows that Sox9 has a distinct set of binding targets when its levels are low and that it can especially activate these target genes (like LEF and BMP4, as in Fig. 4D, E) only at low levels. As expected, a different set of genes appeared to be activated when the levels were high (Fig. 4F), thereby providing new and interesting insights into the gene networks regulated by Sox9. In future studies, it will be interesting to illuminate the differences in the cofactors and binding targets when Sox9 levels are low or high, to get detailed mechanistic information about Sox9 ...

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