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RN1-00576-1: A novel system for understanding the effects of natural genetic variation and epigenetics of stem cells.
Recommendation: Not recommended for funding
Public Abstract (provided by applicant)
Understanding stem cell regulation holds the potential to treat many diseases. However, some experiments that would aid this understanding cannot be performed with humans due to ethics or practicality. One concern is whether the DNA marks (i.e. epigenetics) regulating stem cells and other genes are stable in cells grown in culture over long term. This is particularly important in that it is clear that cancers are also caused by stem cells. The effects of genetic variation on stem cells are also little known. Studies of house mouse stem cells have partly filled this gap. There are significant differences between house mouse stem and human stem cells. It is not clear whether these are simply species differences, or may partly reflect the artificial genetic make-up of laboratory mouse strains. For example, it is becoming clear that the complete inbreeding of the lab strains has affected their genome, and that the combination of genetic variants seen in these animals does not exist in nature. Further, these animals have been domesticated and selected for traits that do not exist in the wild (analogous to differences between poodles and wolves). Our system is unique in using animals with natural genetic variation. We use the most common Native American mammals, rodents of the genus Peromyscus. While these animals are commonly called deer or field mice, they are only distantly related to house mice and rats. One of many differences is that these animals live over twice as long as house mice. Captive strains derived from actual populations are available. Severe prenatal defects occur in hybrids between several of these populations are known. Many of these defects resemble human diseases. A common outcome is a growth with placental like tissues but no fetus. This is similar to a disease relatively common in California termed molar pregnancy. We have evidence that abnormal regulation of stem cells is involved in the hybrid defects. The research proposed here proposes to use these animals to study: 1. the stem cell basis of the hybrid defects, 2. the natural genetic variants that affect stem cells, 3. the stability of stem cell epigenetic marks of over long periods of time.
Statement of Benefit to California (provided by applicant)
Understanding of stem cell regulation has the potential to treat or prevent many diseases. These diseases are not limited to those requiring regenerative capacity, but include cancers and developmental defects. Human studies on some aspects of stem cell biology are unethical or impractical. Current animal models are highly genetically modified relative to their ancestors. Our proposal suggests a new system that may be used to understand the role of natural genetic variation on stem cell regulation, and the stability of cultured stem cells. The proposed system also utilizes native California wildlife. We therefore expect several types of benefit to the Citizens of California. First, our studies will likely suggest genetic variants and epigenetic profiles that will lead to improved human studies or therapies. Second, these animals may provide an alternative system for use bybiotech and pharmaceutical companies. Third, the research will provide graduate and undergraduate student research opportunities, and brings together several disparate areas of biological study. Finally, better understanding of native species, and the role of environment on epigenetics may ultimately benefit our care of the ecosystem.
Review
SYNOPSIS: This proposal explores the relationship between epigenetic specification of stem cell pluripotency and genetic imprinting. The Principal Investigator (PI) believes that embryonic stem (ES) cells from either the human or the mouse system have limitations that complicate the study of this phenomenon. Human ES cell systems suffer from ethical concerns and impracticality, and the mouse ES cells are not totipotent and do not represent any naturally occurring combination of alleles. Because of these shortcomings, the PI proposes to use two species of field mice. Crosses between these two species lead to parent-of-origin effects on development that are due to disruption of genomic imprinting. The PI will create ES cell lines from each of the two species of field mice as well as from interspecific hybrids and perform genetic and epigenetic analysis.
STRENGTHS AND WEAKNESSES OF THE RESEARCH PLAN: The model proposed in this application is interesting, however the level of enthusiasm of all three reviewers was low. The PI presents no support for the basic hypothesis that the observed defects in genomic imprinting also cause defects in the epigenetic regulation of stem cell regulatory genes. The background provided by the PI is limited to saying that because both imprinting and stem cell biology involve epigenetic changes, then both must be subject to regulation by the same gene. Furthermore, the assumption that the observed phenomena are due to epigenetics is also not supported by any data. A second problem is that even if stem cell regulatory genes are abnormally expressed in interspecies hybrids, there is no discussion as to how this would increase our understanding of stem cell biology. The PI is simply looking at genes already known to be important, and none of the experiments would provide any new information about their biological functions. The PI also aims to map the locus responsible for abnormal imprinting in interspecies mouse hybrids. Not enough information is provided to know whether this has any reasonable chance of success. Finally, there are no preliminary data provided on whether ES cell lines can be derived from these field mice or from the hybrids. If this cannot be achieved, the rest of the aim – and most of the entire project – cannot proceed. One reviewer also pointed out that the same type of studies as the ones proposed here can potentially be performed using monoparental (parthenogenetic or androgenetic) ES cells in laboratory mouse where all the reagents and know-how are available.
It is difficult to be enthusiastic about this project because instead of tackling emerging and high priority questions in the ES cell field, it adds an additional variable, in esoteric systems, not necessarily helpful for the understanding of ES cell fate specification in general, or for regenerative medicine in particular.
QUALIFICATIONS AND POTENTIAL OF THE PRINCIPAL INVESTIGATOR: The applicant is a talented investigator with many important contributions to his/her field, as shown by the list of publications. S/he received his/her PhD in the 1990s, and after postdoctoral work became an Assistant Professor at the applicant institution in 2001. S/he began the related work as a postdoc, publishing two interesting papers on imprinting. In the six years since starting his/her own lab, s/he has continued studies on genetic imprinting, and has published three senior author papers in genetics specialty journals. The PI has a grant from the NSF to support that work. The PI has limited experience with ES cell work; s/he is more familiar with the animal model.
INSTITUTIONAL COMMITMENT TO PRINCIPAL INVESTIGATOR: The applicant institution is well suited for these studies, encompassing all of the necessary resources and centers to successfully execute the proposed specific aims. The PI occupies adequate independent lab space. The institutional letter of support does not indicate that the school is providing any ongoing support to the PI.
DISCUSSION: During a brief discussion, it was reiterated that there is no precedent for the derivation of ES cell lines from the field mice, and no preliminary data are presented in the proposal to support the feasibility of such derivation. If not successful, many aims of this proposal cannot be pursued.
The following Working Group members had a conflict of interest with this application and were therefore recused from participating in review of, discussion of, and voting on the application:
- None