Lan Kang

Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming.

DNA methylation and demethylation have been proposed to play an important role in somatic cell reprogramming. Here, we demonstrate that the DNA hydroxylase Tet1 facilitates pluripotent stem cell induction by promoting Oct4 demethylation and reactivation. Moreover, Tet1 (T) can replace Oct4 and initiate somatic cell reprogramming in conjunction with Sox2 (S), Klf4 (K), and c-Myc (M). We established an efficient TSKM secondary reprogramming system and used it to characterize the dynamic profiles of 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), and gene expression during reprogramming. Our analysis revealed that both 5mC and 5hmC modifications increased at an intermediate stage of the process, correlating with a transition in the transcriptional profile. We also found that 5hmC enrichment is involved in the demethylation and reactivation of genes and regulatory regions that are important for pluripotency. Our data indicate that changes in DNA methylation and hydroxymethylation play important roles in genome-wide epigenetic remodeling during reprogramming.

RCOR2 Is a Subunit of the LSD1 Complex That Regulates ESC Property and Substitutes for SOX2 in Reprogramming Somatic Cells to Pluripotency

Histone demethylase LSD1 can form complex with different Rcor family corepressors in different cell types. It remains unknown if cell‐specific Rcor proteins function specifically in distinct cell types. Here, we report that Rcor2 is predominantly expressed in ESCs and forms a complex with LSD1 and facilitates its nucleosomal demethylation activity. Knockdown of Rcor2 in ESCs inhibited ESC proliferation and severely impaired the pluripotency. Moreover, knockdown of Rcor2 greatly impaired the formation of induced pluripotent stem (iPS) cells. In contrast, ectopic expression of Rcor2 in somatic cells together with Oct4, Sox2, and Klf4 promoted the formation of iPS cells. Most interestingly, ectopic expression of Rcor2 in both mouse and human somatic cells effectively substituted the requirement for exogenous Sox2 expression in somatic cell reprogramming. STEM CELLS 2011;

Reprogramming of Trophoblast Stem Cells into Pluripotent Stem Cells by Oct4

ESCs and trophoblast stem (TS) cells are both derived from early embryos, yet these cells have distinct differentiation properties. ESCs can differentiate into all three germ layer cell types, whereas TS cells can only differentiate into placental cells. It has not been determined whether TS cells can be converted into ES‐like pluripotent stem (PS) cells. Here, we report that overexpression of a single transcription factor, Oct4, in TS cells is sufficient to reprogram TS cells into a pluripotent state. These Oct4‐induced PS (OiPS) cells have the epigenetic characteristics of ESCs, including X chromosome reactivation, elevated H3K27 me3 modifications, and hypomethylation of promoter regions in Oct4 and Nanog genes. Meanwhile, methylation of promoter region in the Elf5 gene occurred during reprogramming of TS cells. The gene expression profile of OiPS cells was very similar to ESCs. Moreover, OiPS cells can differentiate into the three germ layer cell types in vitro and in vivo. More importantly, chimeric mice with germline transmission could be efficiently produced from OiPS cells. Our results demonstrate that one single transcription factor, Oct4, could reprogram the nonembryonic TS cells into PS cells. STEM CELLS 2011;29:755–763

High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells

It remains controversial whether the abnormal epigenetic modifications accumulated in the induced pluripotent stem cells (iPSCs) can ultimately affect iPSC pluripotency. To probe this question, iPSC lines with the same genetic background and proviral integration sites were established, and the pluripotency state of each iPSC line was characterized using tetraploid (4N) complementation assay. Subsequently, gene expression and global epigenetic modifications of “4N-ON” and the corresponding “4N-OFF” iPSC lines were compared through deep sequencing analyses of mRNA expression, small RNA profile, histone modifications (H3K27me3, H3K4me3, and H3K4me2), and DNA methylation. We found that methylation of an imprinted gene, Zrsr1, was consistently disrupted in the iPSC lines with reduced pluripotency. Furthermore, the disrupted methylation could not be rescued by improving culture conditions or subcloning of iPSCs. Moreover, the relationship between hypomethylation of Zrsr1 and pluripotency state of iPSCs was further validated in independent iPSC lines derived from other reprogramming systems.

Mice Cloned from Induced Pluripotent Stem Cells (iPSCs)

Differentiated somatic cells of various species can be reprogrammed into induced pluripotent stem cells (iPSCs) by ectopically expressing a combination of several transcription factors that are highly enriched in embryonic stem cells (ESCs). The generation of iPSCs in large animals has raised the possibility of producing genetically modified large animals through the nuclear transplantation approach. However, it remains unknown whether iPSCs could be used for generating cloned animals through the nuclear transfer method. Here, we show the successful production of viable cloned mice from inducible iPSCs through the nuclear transfer approach, and the efficiency is similar to that of using ESCs derived via normal fertilization. Furthermore, the cloned mice are fertile and can produce second-generation offspring. These efforts strengthen the possibility of utilizing iPSCs to generate gene-modified large animals for pharmaceutical purposes in the future.

An Elaborate Regulation of Mammalian Target of Rapamycin Activity Is Required for Somatic Cell Reprogramming Induced by Defined Transcription Factors

The mammalian target of the rapamycin (mTOR) signaling pathway functions in many cellular processes, including cell growth, proliferation, differentiation, and survival. Recent advances have demonstrated that differentiated somatic cells can be directly reprogrammed into the pluripotent state by overexpression of several pluripotency transcription factors. However, whether the mTOR signaling pathway is involved in this somatic cell-reprogramming process remains unknown. Here, we provide evidence that an elaborate regulation of the mTOR activity is required for the successful reprogramming of somatic cells to pluripotency. The reprogramming of somatic cells collected from the Tsc2(-/-) embryo, in which the mTOR activity is hyperactivated, is entirely inhibited. By taking advantage of the secondary inducible pluripotent stem (iPS) system, we demonstrate that either elevating the mTOR activity by Tsc2 shRNA knockdown or using high concentrations of rapamycin to completely block the mTOR activity in cells derived from iPS mice greatly impairs somatic cell reprogramming. Secondary iPS induction efficiency can only be elevated by elaborately regulating the mTOR activity. Taken together, our data demonstrate that the precise regulation of the mTOR activity plays a critical role in the successful reprogramming of somatic cells to form iPS cells.

Viable mice produced from three-factor induced pluripotent stem (iPS) cells through tetraploid complementation.

Viable mice produced from three-factor induced pluripotent stem (iPS) cells through tetraploid complementation

Reprogramming of MLL-AF9 leukemia cells into pluripotent stem cells

The ‘Yamanaka factors’ (Oct4, Sox2, Klf4 and c-Myc) are able to generate induced pluripotent stem (iPS) cells from different cell types. However, to what degree primary malignant cells can be reprogrammed into a pluripotent state has not been vigorously assessed. We established an acute myeloid leukemia (AML) model by overexpressing the human mixed-lineage leukemia-AF9 (MLL-AF9) fusion gene in mouse hematopoietic cells that carry Yamanaka factors under the control of doxycycline (Dox). On addition of Dox to the culture, the transplantable leukemia cells were efficiently converted into iPS cells that could form teratomas and produce chimeras. Interestingly, most chimeric mice spontaneously developed the same type of AML. Moreover, both iPS reprogramming and leukemia reinitiation paths could descend from the same leukemia-initiating cell. RNA-seq analysis showed reversible global gene expression patterns between these interchangeable leukemia and iPS cells on activation or reactivation of MLL-AF9, suggesting a sufficient epigenetic force in driving the leukemogenic process. This study represents an important step for further defining the potential interplay between oncogenic molecules and reprogramming factors during MLL leukemogenesis. More importantly, our reprogramming approach may be expanded to characterize a range of hematopoietic malignancies in order to develop new strategies for clinical diagnosis and treatment.

Induced pluripotent stem cells (iPSCs)—a new era of reprogramming

Embryonic stem cells (ESCs) derived from the early embryos possess two important characteristics: self-renewal and pluripotency, which make ESCs ideal seed cells that could be potentially utilized for curing a number of degenerative and genetic diseases clinically. However, ethical concerns and immune rejection after cell transplantation limited the clinical application of ESCs. Fortunately, the recent advances in induced pluripotent stem cell (iPSC) research have clearly shown that differentiated somatic cells from various species could be reprogrammed into pluripotent state by ectopically expressing a combination of several transcription factors, which are highly enriched in ESCs. This ground-breaking achievement could circumvent most of the limitations that ESCs faced. However, it remains challenging if the iPS cell lines, especially the human iPSCs lines, available are fully pluripotent. Therefore, it is prerequisite to establish a molecular standard to distinguish the better quality iPSCs from the inferior ones.