POSTERS
AGBT 2026 | poster #106
In situ single cell spatial multiomic profiling of 3D genome organization in fresh frozen (FF) colorectal carcinoma tissue in spatially resolved tissue microenvironments
PaintScape™ enabled in situ direct visualization of the 3D genome in single cells of FF colorectal cancer tissue in spatially resolved tumor microenvironments
highlights
PaintScape™ enabled identification, characterization, and direct in situ visualization of single cell 3D genome features of different cell types in FF colorectal cancer tissue across different patients.
PaintScape™ revealed distinct structural genotypes between individual single cells in different cell sub-popluations (cancer vs normal cells) such as:
cancer-cell-type-specific ploidy variation of whole chromosomes and sub-chromosomal regions such as LOH of Chr14q and Chr4 in cancer cell sub-populations and
copy number variation (including amplification and deletions) and additional structural genome differences such as gain in Chr 8q, Chr 13q and Chr 20q in cancer cells
cancer cell sub-populations with Ioss in Chr 8p, Chr 14q, Chr 17p and Chr 20p
PaintScape unveiled differences in inter-chromosomal interactions, potential translocations, and simultaneous proximities of multi-loci interactions in situ in single cells from different patients
PaintScape revealed ecDNA copy number, nuclear locations, and in situ interactions in single cells of FF colon cancer tissue
Unique cancer cell sub-population having a fraction of amplified targets of Chr20q and Chr8q regions further from Chr20 or Chr8 territory, suggesting possible ecDNA nature of those amplified targets
PaintScape revealed cell-type-specific differences in 3D genome structure in situ in single cells in the tissue immune microenvironment
Identified and visualized unique 3D genome aberration of individual chromosomes in Pan-CK+ epithelial cells and CD45+CD163+ immune cells
Immune cells show relatively more compact 3D genome structure than cancerous epithelial cells
Cancer cells show sub-populations with unique sets of inter-chromosomal interactions that are absent in immune cells
PaintScape revealed multiomic correlations of cancer cell states between patients
Patient 2 with Chr8q gain shows much higher Ki-67 positivity rate for cancerous epithelial cell sub-populations compared to Patient 1 lacking Chr8q gain
Chr8q gain increases prevalence of key oncogene MYC which upregulates Ki-67 leading to higher proliferation and greater genome wide instability