PaintScape™ enables tissue based unique multiomic protocol for direct in situ visualization of single cell spatial 3D genome organization of fresh frozen glioblastoma cells in tumor microenvironments
The PaintScape™ multiomic tissue protocol enabled direct, in situ visualization of genome organization in fresh frozen (FF) human glioblastoma tissue — revealing differences in the structural genome of individual cells in the tumor microenvironment and in hypoxic vs normoxic regions of tissue
highlights
PaintScape enabled first-of-its-kind identification, characterization, and direct in situ visualization of single cell spatial 3D genome structure of various tissue microenvironments in 30-µm fresh frozen (FF) glioblastoma (GBM) tissue. The multiomic jebFISH protocols for tissue samples enabled identification of specific cell types or tissue regions for further direct visualization and analysis of 3D genome organization.
The power of the single-cell nature of the data allows for unprecedented filtering, analysis, and comparison of genomic landscapes or specific chromosomal aberrations in specific single cells as well as specific subpopulations of cells.
Distinct structural genotypes and genome conformations revealed by jebFISH on the PaintScape System:
For example, the anonical GBM genomic features including Chr10 loss and subpopulations
Distinct structural genotypes and genome conformation differences in hypoxic vs normoxic tissue regions:
CNVs in GBM and hypoxia related genes and 3D genome differences (Chr10 further from other chromosomes in hypoxic)
Chr7 3N cells: CNVs in GBM and hypoxia related genes and 3D genome differences (Chr7 and Chr10 differential interactions)
PaintScape revealed high levels of MET amplification forming ecDNA with neighboring genes CAPZA2 and ST7 in hypoxic and normoxic regions
