Jonathan received his B.Sc. in Biology with 1st Class honours from the National University of Singapore (NUS) (2003). He did Ph.D. research (2003-2007) in the laboratory of Dr Ng Huck-Hui at the Genome Institute of Singapore where he elucidated the link between the genetic and epigenetic regulation mechanisms controlling embryonic stem cells (ESCs). He completed his Postdoctoral fellowship (2008-2011) with Dr George Q. Daley at the Children’s Hospital Boston, Harvard Medical School. Jonathan’s work has shown that terminally differentiated human blood cells can be epigenetically reprogrammed to pluripotent stem cells. Jonathan is currently a Principal Investigator at the Institute of Molecular and Cell Biology (IMCB), and an Assistant Professor with the Department of Biological Sciences, NUS. His laboratory is interested in dissecting the regulatory mechanisms regulating cell fate changes, and developing novel tools in deriving reprogrammed and differentiated cell types. Jonathan’s papers have been cited over 4500 times. He is a recipient of the Singapore Youth award (2010), A*STAR Investigatorship research award (2011) and the inaugural MIT TR35 (Asia Pacific) @Singapore award (2012). He sits on the executive committee of the Stem Cell Society Singapore (2011-) and is an elected Fellow of the World Technology Network (2012-)

Pluripotency
Pluripotent stem cells display a remarkable capacity to form differentiated cell types in laboratory cultures. The ability to derive multiple lineages from ESCs opens exciting new opportunities for its use as unlimited source of cells for the treatment of degenerative diseases such as diabetes and Parkinson’s disease. The unique properties of pluripotent cells are controlled by genetic and epigenetic factors. We had sought to identify, characterize and understand the role of transcription regulators and chromatin-modifying enzymes in regulating gene expression programs in pluripotent embryonic stem cells. We have detailed the regulatory relationships between the master regulators of ESCs, Oct4, Sox2 and Nanog (Loh et al. 2006; Chew et al. 2005). This has enhanced our understanding of the transcriptional regulatory network and how they orchestrate early cell fate decisions and establish the transcriptional landscape essential for self-renewal and pluripotency. Furthermore we have uncovered novel transcription factors such as Esrrb and Rif1 which regulate self-renewal, pluripotency and differentiation of ES cells (Figure 1) (Loh et al. 2006).

Figure 1:(A) Transcription circuitry regulating stem cell pluripotency. (B) Knockdown of Esrrb or Rif1 led to differentiation of ES cells. Cells were stained for alkaline phosphatase (pink), which is a characteristic of non-differentiated cells. (Adapted from Boyer et al 2005; Loh et al. 2006; Loh et al. 2011)

Epigenetic
We have elucidated the novel link between transcriptional circuitry and epigenetic regulation of ESCs chromatin. We showed that Oct4 controls the expression of genes which encode for histone H3 lysine 9 histone demethylases (Jmjd1a and Jmjd2c) that are important for maintaining the ESCs state through their regulation of the H3K9me status at the promoters of pluripotency genes such as Tcl1  and Nanog (Loh et al. 2007, Loh et al. 2008).

Figure 2: Transcription Network modulation. Transcription factors and epigenetic factors interact to modulate the ESC regulatory network. Several ESC-specific epigenetic factors are regulated by the core ESC transcription factors. For example, Oct4 activates the expression of histone demethylases, Jmjd1a and Jmjd2c, which in turn modify global chromatin H3K9 methylation and regulate the expression of Tcl1 and Nanog (Loh et al. 2007) (Adapted from Ng et al. 2008).

Cell fate reversal
Recent studies have shown that the epigenome of differentiated cells are remarkably plastic. Cellular reprogramming or lineage conversions can be effected simply through the introduction of defined set of transcription factors. The ability to generate autologous, patient-specific stem cells offers unprecedented potential for disease research, drug screening, and regenerative medicine. We have uncovered novel ways of establishing iPS cells from cell types that are more accessible and requiring lesser manipulations. Blood derived iPS cells are molecularly and functionally indistinguishable from ESCs. Reprogramming from blood cells has several advantages, these include: 1) large amount of blood cells can be obtained from donors; this help to shorten the time required for reprogramming experiment. Approximately three weeks of culture would be required for conventional skin cell sample as oppose to 1-2 day for blood samples. 2) Efficient and easy way of obtaining blood samples from donor without the need for invasive surgical skin biopsies. 3) Safer source of cells as compared to skin cells which are constantly exposed to the UV radiation and may harbor undesirable mutations. Reprogramming of blood cells is therefore an important step towards the development of more efficient ways of generating patient-specific pluripotent stem cells (Loh et al. 2009; Loh et al. 2010).

Figure 3: (A) Images of human peripheral blood (PB) CD34+ cells and T cells (Left), the PB34 iPSC and T-iPSC colonies (Right). SV T-iPSC colonies were generated using sendai RNA viruses. (B)  Epigenetic reprogramming of the NANOG promoters revealed by Bisulfite genomic sequencing. Each horizontal row of circles represents an individual sequencing reaction for a given amplicon. Open and filled circles represent unmethylated and methylated CpGs dinucleotides, respectively. Percentage of methylation is indicated for each cell line. (Unpublished data and adapted from Loh et al. 2010).

Our current research focuses on understanding the molecular mechanisms underpinning the process of cellular reprogramming and cell fate decision. Ongoing projects include: 1) Understanding the function of DNA and Histone modifiers in cell fate changes and 2) Epigenetic Reprogramming/Transdifferentiation using defined factors expression. Ultimately we want to harness these molecular switches to derive high-quality stem cells or differentiated cell types that can potentially be used for therapeutic applications.