Mapping single cell spatial 3D genome landscape of localized and metastatic breast cancer sub-types
PaintScape™ enabled direct in situ visualization of 3D genome differences in single cells of different breast cancer (BC) cell lines
highlights
PaintScape direct 3D genome visualization identified novel ecDNA targets specific for localized (HCC 1954) and for metastatic (SKBR3) BC cells
PaintScape visualized ecDNA interacting elements in situ in single cells on specific chromosomes enriched with breakpoints
PaintScape identified cell sub-populations in SKBR3 with mesenchymal signatures
PaintScape revealed increased copy number of metastasis promoting factors ZFHX4 and HAS2-AS1 lncRNA
PaintScape revealed partial loss of regions neighboring CDH1 (an aberration known to be associated with reduced E-cadherin expression)
PaintScape visualized a deletion of an lncRNA target on Chr 19 (associated with poor prognosis in advanced breast cancer)
PaintScape identified cell sub-populations of a TNBC cell line (BT549) with inter-chromosomal rearrangement affecting the Wnt-β-catenin signaling pathway dysregulated in TNBC
