GRADUATE SCHOOL OF BIOMEDICAL SCIENCES BIOCHEMISTRY & MOLECULAR PHARMACOLOGY PhD THESIS DEFENSE CHAO‐SHUN YANG

Mentor: Tariq M. Rana, PhD

WEDNESDAY, FEBRUARY 26, 2014 AT 1:00 PM S2‐307C Molecular Landscape of Induced

Induced pluripotent stem cells (iPSCs) provide alternative means to obtain ES‐like cells without destroying embryos by introducing four reprogramming factors (Oct4, , , c‐) into somatic cells. However, the molecular basis of reprogramming is largely unknown. To address that, we employed several tools, such as microRNA, small molecules, and genome‐wide RNAi screen, to investigate the regulatory mechanisms during reprogramming.

First we show that depleting miR‐21 and miR‐29a enhances reprogramming efficiency in MEFs, through regulating and ERK1/2 pathways. By combining computational chemical biology with genomics analysis, we discovered that depleting MEF‐specific encoding catalytic or regulatory (WISP1, PRRX1, HMGA2, NFIX, PRKG2, COX2, TGFβ3) greatly increased reprogramming efficiency. NSAID Nabumetone could replace Sox2 or c‐Myc, and the anti‐ cancer drug OHTM could replace Sox2 during reprogramming.

Finally, we integrated genome‐wide RNAi screen with transcriptome analysis to dissect reprogramming mechanisms. We found that extensive interactions of embryonic stem cell core circuitry regulators are established in mature iPS cells. Remarkably, genes with non‐differential change play important roles to the transitions of reprogramming. Functional validation showed that genes (Dmbx1, Gsc, Med21, Hnf4g, Mef2c, Psmd9, Tfdp1, Nfe2, Foxn3, Erf, Cdkn2aip, Msx3, Ssbp3, Dbx1, Hoxd4, Lzts1, Arx, Hoxd12, Gtf2i, Nkx6‐2, Ankrd22, Hoxc10) act as essential or barrier roles to reprogramming. We also confirmed several genes required for maintaining ESC identities, including Srsf2, Hcfc1, Ruvbl2, Asb4, Dmbx1, Gbx2, Gsc, Hnf4g, Klf5, L3mbtl2, Med21, Mef2c, Nobox, Pcgf6, Phox2a, Tcf15, and Trim28. Altogether, our work further advanced the field by identifying several new key modulations with various approaches.

Mentor(s) Dissertation Exam Committee Tariq M. Rana PhD Charles Sagerstrom, PhD (Chair) Zuoshang Xu, PhD Kendall Knight, PhD Jamie Rivera, PhD Bing Ren, PhD