Funding opportunities

Development of nanoscale genomic methods for tracking of stem cell transplants.

Funding Type: 
Early Translational I
Grant Number: 
Funds requested: 
$5 384 661
Funding Recommendations: 
Not recommended
Grant approved: 
Public Abstract: 
There are millions of people in California who will benefit from the development of cell therapies for the treatment of diabetes, neurological disease, heart disease and other degenerative diseases. Because of their enormous developmental potential, pluripotent stem cells, which include embryonic stem cells and induced pluripotent cells, are considered to be a valuable source for the specific cell types required for cell therapies. A tremendous amount of effort has already been invested in developing stem cell-based therapies, and the first clinical tests of these therapies are expected to begin within a year. Under the regulations of the FDA, the first trials will be “Phase 1”, or safety trials, to determine whether the cells have any negative effects. Only after the safety of the cells has been assured can further tests be performed to determined whether the cells provide medical benefit. The FDA has major concerns about the use of pluripotent stem cell-based therapies, and will require considerable thoroughness in characterizing the cells before they are transplanted and in examining the first cell therapy patients for any signs of adverse effects. The agency is concerned that there is not enough known about how cells derived from pluripotent stem cells will behave after they have been transplanted- whether they will migrate away from the transplant site, continue to divide, be toxic to the patient, or become cancerous. There are currently no sensitive methods to trace transplanted cells, and this is a critical bottleneck that must be overcome to be able to satisfy the safety requirements. We propose to develop methods that can detect small numbers of transplanted cells within tissues, and determine whether they are behaving normally or are becoming toxic or cancerous. The new methods are based in cutting-edge genomic research that has already enabled breakthroughs in deciphering the human genome and in determining the genetic causes of disease. The technologies will be developed as a partnership between a leading corporation in the development of molecular analysis tools, a highly regarded academic human embryonic stem cell laboratory, and a prominent genome research center. By the time that the Phase I safety studies are underway, we plan to have the tools in place to detect and analyze the transplanted cells, to determine whether the cells are behaving normally or if they pose a risk to the health of the patients.
Statement of Benefit to California: 
Pluripotent stem cells hold the potential to revolutionize medicine and health care. Cell therapies may be the only viable treatment for devastating and presently incurable conditions such as diabetes, Parkinson's disease, spinal cord injuries, and many other diseases. California scientists have taken the first steps to clinical applications of pluripotent stem cells through their bold research to develop new ways to derive these cells and to differentiate them into cell types that can be used to replace damaged tissues. But there are tremendous challenges to overcome if cell therapy is to become a reality. Chief among these challenges is the need to be certain that the therapies are as safe as possible; the outcome of the first Phase I clinical safety trials will determine the future of this field of medicine. We propose to develop technologies to assess the outcome of the first clinical trials, by combining the skills of a leading corporation in the development of genomics and epigenomics analysis tools, a highly regarded academic human embryonic stem cell laboratory, and a prominent Genome Center. Our developments will help make cell therapy a standard medical practice, and will benefit California by significantly increasing the options available in the health care system, reducing the long-term health care costs to California, and attracting high-skill jobs and tax revenues.
Review Summary: 
The goal of this bottleneck proposal is to develop sensitive methods to determine location and phenotype of transplanted pluripotent-derived cells. The applicant proposes to develop a series of minimally invasive, nanoscale assays for detecting and phenotyping rare cells within tissue samples, particularly those that could be harmful. For the first aim, the applicants will apply several established genotyping strategies towards detecting and quantifying the presence of one particular cell type within a mixed population. Next, a panel of genomic analysis tools will be adapted for use at a very small scale (from 1-10 cells). For the third aim, the applicants propose to utilize a magnetic bead sorting device to develop a strategy for enrichment of rare cell types from blood or tissues based on cell surface markers. Finally, the tools and technologies developed in the previous aims will be used to profile a diverse collection of cell lines, tissues, and tumor samples. Data from these experiments will be combined with those from previous studies and used to develop a reference set that can be applied to future investigations. New bioinformatics tools will be developed and combined with existing ones in order to aid in the analysis and interpretation of this data. Reviewers agreed that the proposed effort addresses an important barrier to translation of stem cell therapies to the clinic. The ability to detect rare, potentially dangerous cells in a population before administering to a patient would do much to ameliorate the risk of potentially dangerous complications. Furthermore, the ability to perform detailed genomic analysis on small numbers of cells could enable minimally invasive methods to be devised for tracking cells after transplantation. Reviewers found the overall feasibility and practicality of this effort were limited, in part due to the paucity of experimental details that were provided for evaluation. For example, only one surface marker was mentioned as a candidate for rare cell enrichment experiments, and no alternatives were proposed in the event that this would prove to be inadequate. This oversight was particularly troublesome, as the preliminary data for this approach did not convincingly demonstrate or address the purity of the isolated cells. Moreover, reviewers criticized aim 4 for being open ended in scope, lacking in focus, and of ambiguous rationale. While the cell lines to be investigated were listed, reviewers were uncertain of the number and extent to which they would be individually characterized and how this information would ultimately be interpreted and applied diagnostically. One example of this uncertainty was discussed in light of the proposed monitoring of tissue samples after therapy. As stem cells would be expected to migrate, it was not clear how the detection of such cells in tissues would necessarily alter the course of a treatment, and no statistical approaches were offered that might allow such findings to be made meaningful. Furthermore, several reviewers felt that the proposed RNA experiments seemed rather speculative and were uncertain of the extent to which they would add value to this effort. Finally, they questioned whether the large diversity of cell phenotypes engendered by cancers and teratomas might ultimately pose a technical challenge to the molecular approach that is the backbone of this effort. The reviewers found the Principal Investigator and the research team to have the qualifications and experience to conduct the proposed research. They also found that the resources, environment and collaboration were fully supportive and adequate for the research proposal. In summary, the reviewers felt that this effort addressed an important roadblock to translation, but they were uncertain of the overall feasibility. While the research team and the environment were considered excellent, much of the proposed work was speculative, poorly justified, or suffered from a lack of focus. In general, the application lacked specific details and did not adequately provide alternatives for unanticipated difficulties, thereby complicating the reviewers’ assessment of its merits. Finally, while the proposed methodologies are likely to be useful, it was not clear from the applicants’ description how they would translate into clinical benefit.

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