NCE (Year 4)

Stem cells have the unique ability to switch from a proliferative cell state in which they reproduce themselves to a differentiated cell state that allows them to carry out the functions of fully mature cells. The stem cell field has made considerable effort to address the underlying mechanisms behind this switch. Most effort has been focused on a class of proteins that determine whether our genetic material—DNA—generates a copy of itself in the form of messenger RNA (mRNA), a process called transcription. While this transcription factor-centric view of stem cells explains some aspects of stem cells, it is not sufficient to explain all of their behavior. In our grant, we proposed to test the role of another mechanism—called selective mRNA decay—that we hypothesized influences the stem vs. differentiation switch. In particular, we proposed to study nonsense-mediated RNA decay (NMD), a highly conserved RNA decay pathway that degrades specific kinds of mRNAs. One of our goals was to identify the specific mRNAs targeted for decay by NMD in human embryonic stem (ES) cells. During the final progress period, we completed this analysis, leading to a list of high-confidence NMD target mRNAs in hES cells. We found that many of these mRNAs encode proteins previously known to be important for differentiation and development. This supported the possibility that NMD acts in hES cells just as it does in mouse ES cells – to maintain them in the “stem cell state” by degrading mRNAs encoding proteins that drive differentiation. We found that another class of mRNAs degraded by NMD in hES cells is those encoding signaling proteins. This raises the possibility that NMD also acts to influence differentiation through known signaling pathways, including the FGF, WNT, TGF-beta, and BMP pathways. Another goal of our project was to determine whether NMD directly influences hES differentiation. During the last progress period we obtained additional evidence that this is the case. In brief, we found that NMD is differentially regulated during mesoderm and endoderm differentiation and that this regulation is both necessary and sufficient for human ES cells to differentiate into these two primary germ layers. As further support, we found that induced pluripotent cells (iPSCs) from patients with mutations in a key NMD gene, UPF3B, have a tendency to spontaneously differentiate into endoderm. Patients with mutations in UPF3B also often suffer from schizophrenia, autism, and/or attention-deficit/hyperactivity disorder. Thus, the study of NMD may provide insight into a wide spectrum of cognitive and psychological disorders.