Identifying sources of mutation in human induced pluripotent stem cells by whole genome sequencing

Identifying sources of mutation in human induced pluripotent stem cells by whole genome sequencing

Funding Type: 
Basic Biology III
Grant Number: 
RB3-02186
Award Value: 
$1,755,864
Stem Cell Use: 
iPS Cell
Status: 
Active
Public Abstract: 
Stem cell research offers new tools to help treat and cure diseases that affect diverse cells types in the body such as neurological diseases, heart disease and diabetes by producing human cells for transplantation or to enable drug discovery . Recent advances have allowed researchers to generate patient-matched cell types from the skin or other tissues of patients. These patient-matched cells are important because they are unlikely to cause immune rejection upon transplantation and they may help to model diseases caused by gene variations found only in rare individuals. Despite their promise, patient-matched cells differ from traditional stem cells in ways that may cause them to be less stable or increase their potential to cause tumors. This is because patient-matched cells are generated from tissues taken from adult patients using methods that dramatically alter the chromosomes of these cells. These factors could endow these reprogrammed cells with mutations that would not be present in cells derived from embryonic sources. To ensure the safety and clinical utility of reprogrammed cells, it is critical to establish methods to identify potentially oncogenic or detrimental mutations. This proposal is designed to identify the source and scope of mutations in reprogrammed pluripotent cell lines using cutting edge whole genome sequencing methods. Results of these studies will establish the relative safety of current methods to produce patient-matched reprogrammed cells and help to improve methods to speed the translation of these advances into therapies.
Statement of Benefit to California: 
California has become an epicenter of stem cell advancement in part due to the funding of innovative collaborative research by the CIRM. We have established new methods that will improve the safety and effectiveness of regenerative medicine in cases where cell therapies are generated by converting adult cells into other cell types, including pluripotent cells and differentiated cells such as neurons and heart cells. This will help to reduce the costs of ongoing research funded by CIRM and by other California entities. Results of these studies will help to accelerate the translational application of basic biomedical advances being achieved across the state.
Progress Report: 

Year 1

The goal of this study is to identify mutations in human iPSC lines and determine their likely origin. To accomplish this we previously used mouse models to develop and validate new methods to isolate iPSC lines from the same precursor donor cell and to perform comprehensive whole genome sequencing based mutation detection . In this grant period we have translated our iPSC tracing and lineage analysis methods to human iPSCs, established two methods to produce iPSCs using non integrating methods and improved our bioinformatic detection of mutations. We are now poised carry out the remainder of the proposed work within the timeframe allotted.

Year 2

The use of induced pluripotent stem cells (iPSCs) in research and translational medicine depends on our ability to identify iPSC cell lines that do not contain potentially dangerous mutations that can lead to cancer, degeneration or uncontrolled variability in cell survival or function. Such mutations may arise from numerous sources including somatic mutations that originated in patient donor cells during development or aging, and as a consequence of particular reprogramming methods. In order to identify the cause of mutations in iPSCs we have developed and successfully optimized a lineage tracing approach to identify clonally related sister iPSCs that we produce from fibroblasts and blood cells, which are the two most promising sources for patient specific iPSCs. This advance now allows us to perform whole genome sequencing on these iPSCs and determine the major source and type of mutation that arise under different commonly used conditions for iPSC generation. Results of genome sequencing of these iPSCs will inform future efforts to identify the best means to produce iPSCs for research and therapeutic applications.

© 2013 California Institute for Regenerative Medicine