Loss of an RNA tag can keep embryonic stem cells in suspended animation

October 24, 2014

The HSCI/MGH team (from left to right): Benoit Molinie, Alan Mullen, Kaveh Daneshvar, Chan Zhou, and Cosmas Giallourakis

Research reveals new strategy to control cellular identity and fate

A team of Boston and California laboratories presents compelling evidence that a specific chemical modification or “tag” on messenger RNA is a key player in determining the ability of embryonic stem cells to adopt different cellular identities. In the journal Cell Stem Cell, the researchers reveal that depleting or knocking out a key component of the machinery that places this chemical tag, known as m6A, on RNA significantly blocks embryonic stem cells from differentiating into more specialized cell types. Instead of marching toward a specific cell fate when prompted to, embryonic stem cells that have reduced ability to place m6A become stuck in a sort of ‘suspended animation,’ yet appear healthy.

“The scientific results represent a significant leap forward in identifying a critical new layer in both mouse and human control of stem cell flexibility,” said co-senior author Cosmas Giallourakis, MD, assistant professor of medicine at Harvard Medical School and a Harvard Stem Cell Institute (HSCI) affiliated faculty member at Massachusetts General Hospital. “Our collaborative work sets the conceptual rationale to develop tools for manipulating m6A levels globally or perhaps at the level of individual tags as a way to control cell identity and fate.”

The project involved a cross-country collaboration between Giallourakis and Alan Mullen, MD, PhD, at Massachusetts General Hospital and HSCI; the laboratory of co-senior author Yi Xing, PhD, at the University of California, Los Angeles (UCLA), who led the informatics analyses; along with the labs of Marius Wernig, PhD, and co-senior author Howard Chang, MD, PhD, at Stanford University who spearheaded the mouse work. Pedro Batista, PhD, Benoit Molinie, PhD, and Jinkai Wang, PhD, shared co-first authorship.

The study of naturally occurring chemical modifications on RNAs is part of an emerging field coined “epitranscriptomics.” The m6A tag (short for N6-methyladenosine) is found on thousands of messenger RNAs and hundreds of noncoding RNAs. The tags may help regulate RNA metabolism by marking them for destruction and have been implicated in the control of organism development.

Little was known however about the dynamics, conservation, and potential function(s) of m6A in human or mouse embryonic stem cells (ESCs) when the authors initiated the project. “Our analysis revealed a striking level of conservation of m6A patterns between mice and humans,” said Yi Xing of UCLA. “Suggesting that m6A has conserved functions in human and mouse embryonic stem cells.”

The investigators then found a strikingly conserved requirement for the presence of normal levels of m6A for differentiating ESCs into multiple cell types. Depletion of METTL3, which encodes the gene that places the m6A tag on RNAs in human ESCs, severely blocked cells from differentiating into the gut or neural precursors. While deletion of the mouse METTL3 gene also led to a severe block in the ability of ESCs to differentiate into neural and cardiac lineages. The authors propose a model whereby m6A modifications on RNA make the transition between cell states possible by instructing the cells to physically degrade those RNAs marked by m6A in ESCs, to allow the cells to move on and become another cell type. Yet, if the cells can no longer can tag RNA for destruction, the cells continues to think like its old self and cannot change.

“Although much remains to be learned, one immediately may envision that the development of small molecular inhibitors of the METTL3 enzyme may allow us to replace or supplement protocols in which millions of dollars are spent to keep stem cells in an undifferentiated state for biotechnology applications,” said Giallourakis.

“Furthermore the ability to block cellular differentiation will have important applications; such as potentially expanding patient stem cell populations in the clinic and then allowing differentiation—a sort of “catch and release” program,” he added. “Our work may also shed light on barriers to efficient induced pluripotent stem cell generation and the development of cancer.”

The research was supported by the Massachusetts General Hospital, California Institute for Regenerative Medicine, the National Institutes of Health, the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, the Damon Runyon Cancer Research Foundation, the Alfred P. Sloan Foundation, and the Howard Hughes Medical Institute.

Cited: Batista, PJ, Molinie, B, and Wang, J, et al. m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell. October 16, 2014. DOI: 10.1016/j.stem.2014.09.019