New design tool 'IRENE' increases efficiency of cell conversions

Scientists have developed a new, more efficient method for converting one type of human cell into another type of human cell for use in disease modeling, cell transplants, and gene therapies.

The computer-guided design tool – known as IRENE, for Integrative Gene REgulatory NEtwork – was created by an international team of researchers to help identify which genes confer cellular identify and need to be manipulated for efficient conversion.

The new design tool integrates many kinds of cellular data to recreate a specific gene regulatory network for the cell type (e.g. immune cells or skin cells). Once the gene regulatory model is built, different simulations of gene manipulation can be run. The simulation that transforms the initial cell to look most similar to the target cell type can then be tried experimentally. A transposon-based system called "piggyBac" is being used to do the experimental part.

Current methods of cell type conversion that will most successfully convert to another type are unreliable technologies. Researchers typically over-express certain genes to obtain the desired type, but this method has proven inefficient. 

The research group set out to find a way to optimize the conversion process. 

The researchers demonstrated their technique on three types of cells used for medical applications: human mammary epithelial cells for replacement after surgery, melanocytes to replace damaged skin cells and natural killer cells used after chemotherapy for leukemia.

They successfully increased the efficiency up to nine-fold for two currently used conversion protocols for natural killer cells and melanocytes. The researchers also increased the efficiency for producing mammary epithelial cells from gene-corrected, patient-derived, induced pluripotent stem cells.

The work appears in the March 12 journal Nature Communications.

As advanced cell transplant therapies and gene therapies become more widely used for disease treatment, the low efficiency of producing appropriate cells presents a "major obstacle," the researchers state.

Author George M. Church told Current Science Daily that the current "low efficiency can mean contamination with unwanted starting material or side-products, and slow and/or costly clean-up." 

Church is at The Wyss Institute for Biologically Inspired Engineering and the Department of Genetics at Harvard Medical School in Boston.

IRENE "systematically integrates gene expression, histone modification, chromatin accessibility," and other genetic data to reconstruct the gene regulatory network for a particular cell type. 

With this information, IRENE computes conversion simulations that identify which genes, when over-expressed, would maximize cellular identity parameters to that of the target cells.

"IRENE helps us prioritize genetic 'factors' which regulate the state of the cells (the kind of cells, e.g. immune cells or skin cells which make pigment)," Church said.

The new computer-guided design tool also makes use of a transposon-based genomic integration system, piggyBAC™ to further increase efficiency. 

"We find that the "piggyBac transposase" method overcomes limitations of viral vector gene delivery--100,000 base pairs rather than 4,700 base pair payloads and much higher copy number (expression of the payload)," Church said.