Funding opportunities

Characterizing the ribosome code controlling gene expression and cell fate specification

Funding Type: 
Basic Biology V
Grant Number: 
Funds requested: 
$628 464
Funding Recommendations: 
Not recommended
Grant approved: 
Public Abstract: 
Understanding the basic mechanisms that control stem cell function and ability to differentiate into a myriad of more specialized cells such as a heart, muscle, or brain has tremendous potential to improve human health. A more complete understanding of this process will yield critical information for how a human develops from a single cell and also serious medical conditions such as cancer and birth defects that arise from perturbations in accurate cellular differentiation. For decades, it has long been known that turning specific genes “on” and “off” is critical for regulating cell division and differentiation. However, on the contrary, the dogma has been that key molecular machines in the cell such as the ribosome, which translates the human genome into functional effector molecules known as proteins, exerts only a passive, housekeeping function in this process. Central to this research proposal is our lab's paradigm-shifting discovery that not all ribosomes are the same and that they do not simply exert “rote-like” functions in the cell. On the contrary, our findings suggest that ribosomes may have more instructive and specialized functions in decoding the genome by regulating where and when certain protein products are expressed to direct specific cell fates. The goal of this proposal is to investigate how this previous unexplored and novel layer of control to how proteins are expressed guides molecular control of specific stem cell fates to instruct human development.
Statement of Benefit to California: 
This research proposal will be instrumental in opening a new direction in understanding the basic biology of stems cells and how critical decisions in cellular differentiation are guided by a newfound understanding of a key molecular machine in the cell, the ribosome. This work will have also important implications for a large group of human diseases collectively know as “ribosomopathies” including X-linked Dyskeratosis Congenita, cartilage-hair hypoplasia, Diamond-Blackfan anemia, Shwachman-Diamond syndrome, 5q- syndrome, Treacher Collins syndrome that are all caused by mutations in components of the ribosome. Ribosomopathies pose a real medical challenge, as the underlying molecular basis for these disorders is poorly understood and at present no targeted medical interventions have been developed. Defining at a more basic level the specificity and dynamics of ribosome activity, will prove to be invaluable for our understanding of how deregulations in this molecular machine underlie so many human pathologies. This research will also delineate a new layer in control of gene expression during human development and will lead to the creation of new technologies and methods of examining the most downstream and final steps in expression of gene products that are critical for stem cell biology.
Review Summary: 
Ribosomes are the molecular machines that translate mRNA into protein; this is generally viewed as a universal process occurring similarly in all cell types. This Exploratory Concepts Award proposal is based on studies in mouse embryos and mouse embryonic stem cells (ESC) in the applicant’s laboratory providing evidence that ribosomes may control where and when certain protein products are expressed, thus directing specific cell fates. The investigator proposes to characterize ribosome composition in human (h)ESC and differentiated derivatives, and to profile the mRNAs associated with cell type-specific ribosomes to test the hypothesis that diverse ribosomes control gene expression at the protein translation level. Novelty and Transformative Potential - Reviewers noted that the hypothesis is somewhat innovative and that the proposed research could reveal some new molecular mechanisms that guide development. Feasibility and Experimental Design - Overall, the proposal was viewed as an open-ended profiling project with unclear outcomes. - The applicant aims to determine the functional significance of ribosome heterogeneity. However, definitive experiments that would establish a causative role of ribosomes in cell fate specification are not included in the proposed studies. - Reviewers pointed out that Aim 2 depends on the successful outcome of Aim 1, but felt that based on preliminary data Aim 1 is likely to yield the necessary data. Principal Investigator (PI) and Research Team - The PI and PI’s laboratory have relevant molecular biology expertise including experience with ribosomes, but do not have experience with human pluripotent stem cells (hPSC). - Letters of support are provided from colleagues with hPSC experience, but these individuals are not included in the budget information; thus their commitment to the project is questionable. Responsiveness to the RFA - The research is not tightly related to stem cell biology; reviewers noted that stem cells are not necessary to test the hypothesis and that non-human models may be better suited to pursue the goals of this research. Therefore, responsiveness to the RFA is weak.

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