A major challenge in all human therapies, as paraphrased from Hippocrates, is “to do no harm” in treating patients. This proposal is designed to reduce or eliminate possible harms of stem cell therapies by improving their safety as well as effectiveness through the exploration of a new phenomenon observed in stem cell populations called “mosaic aneuploidy.” Mosaic refers to an assembly of similar yet distinct things, while aneuploidy refers to deviations from the normal number of chromosomes that should be present in a cell. Thus, a population of cells with different chromosomal compositions represents mosaic aneuploidy. We have found that stem cell populations in fact contain many different forms of aneuploidy. The repercussions of this mosaic aneuploidy are not known. Alterations in chromosome number have well-documented liabilities, as observed in Down Syndrome (where patients have 3 copies of chromosome 21 rather than the normal 2 copies), and many cancers where multiple chromosome copies are present. However, some forms of aneuploidy may in fact be advantageous. This proposal will determine functions for mosaic aneuploidies, and could lead to ways of eliminating “bad” stem cells while enriching for “good” ones, towards optimizing stem cell therapies in humans.
Statement of Benefit to California:
Health-related issues are major economic and societal challenges in the State of California. Stem cell science could provide new ways of treating major diseases that impact the state as well as its citizens, both directly through individuals, and indirectly through family members and friends. In addition to the development of new disease treatments, the infrastructure to develop this segment of the healthcare industry will benefit from studies supported by CIRM, towards bettering California and its citizens.
This proposal addresses the hypothesis that specific forms of mosaic aneuploidy (abnormal chromosome number) contribute to cell culture heterogeneity, which may impact the function and safety of human pluripotent stem cells (hPSCs). In the first specific aim, the applicant proposes to isolate subpopulations of hPSCs defined by their ploidy and/or DNA content. The second aim will involve determining the gene expression changes associated with the aneuploid state and identifying surrogate markers of these states. The third specific aim is focused on defining relationships between defined hPSC aneuploid states and cellular functions including survival, differentiation potential, and oncogenicity.
Reviewers believed that the proposal has potential for revealing novel properties of hPSC cultures and could provide new insights into stem cell heterogeneity. Reviewers recognized the innovative focus of the study but were divided about the potential importance of the research for the future therapeutic use of hPSCs. As various forms of aneuploidy are already well known to occur in hPSC cultures, it remains unclear how further documentation of this phenomenon would contribute to the stem cell field. Although the proposed investigation may supply correlative information defining the negative effects of specific aneuploid states in hPSC cultures, the proposal does not specifically address the mechanism of the formation of aneuploidy nor does it propose to develop methods to prevent the formation of such states.
Reviewers identified several substantial technical challenges and problems that raise doubts about the proposal’s feasibility. Although one reviewer was impressed by the preliminary data, another reviewer questioned the amount and quality of these preliminary results. Concerns were raised that sorted cell populations would likely contain mixtures of cells with different chromosomal abnormalities in the sorted populations, and this would confound analysis of specific gene expression changes that correlate with aneuploidy. The proposal to follow a few specific chromosomes via GFP tagging in some of the experiments was considered challenging and not well supported by preliminary data. In addition, one reviewer questioned whether the PI would be able to obtain adequate numbers of sorted cell subsets to perform definitive teratoma and oncogenesis assays and cautioned about the difficulties in correlating specific chromosomal abnormalities with the results of these assays. Finally, reviewers felt that approaches focused on identifying surrogate markers were inadequately developed and were concerned that the applicant had not sufficiently considered the contribution of cell culture artifacts.
The PI has solid credentials in the field of chromosomal abnormalities and an excellent publication record. The research environment is first class, and all of the cell lines needed in the proposed research would be available via a planned collaboration. The research team itself is well rounded, but one reviewer felt the proposal would benefit from a substantive collaboration with a human embryonic stem cell biologist.
In summary, the proposal targets a potential problem in the future therapeutic use of hPSCs by identifying and characterizing aneuploid cells. Despite its potential impact, the proposal suffers from some serious problems in its experimental design and feasibility and lacks a mechanistic focus.