Applications and technical challenges of fluorescence in situ hybridization in stem cell research

Stem cell research, maintenance, and manipulations have advanced significantly in recent years, and we now witness successful clinical applications of stem therapies. However, challenges in regard to karyotypic stability and the ploidy status of stem cell lines have been addressed only marginally. Our approach to develop technology to address these highly relevant issues is based on fluorescence in situ hybridization (FISH) using nonisotopically labeled DNA probes. As a single cell analysis technique, FISH is expected to be applicable to a variety of cells and tissues including interphase and metaphase cell preparations as well as tissue sections and biopsy material. Over the last decade, our laboratories generated a large number of probes and probe sets for the molecular cytogenetic analyses of stem cells derived from different species. These probes and the introduction of spectral imaging bring us close to be able to perform a comprehensive karyotype analysis of single interphase cell nuclei. It should furthermore be possible to couple cytogenetic investigations of the cellular genotype with analysis of gene expression. This report summarizes our technical achievements relevant to stem cell research and outlines plans for future research and developments.