By Neha MathurNov 11 2022Reviewed by Danielle Ellis, B.Sc. In a recent study published in Nature, researchers developed a genetic clone mapping workflow centered around base-specific in situ sequencing technology to derive quantitative maps of multiple genetic clones of cancer cells.
BaSISS workflow The BaSISS targeted subclones identified by a WGS-derived phylogenetic tree. BaSISS mutation-specific padlock probes first hybridized to complementary DNA of mutant and wild-type alleles of clone-defining somatic variants in situ. All completely targeted-complementary padlock probes ligated and formed closed circles.
Across three samples from P1, P1-oestrogen receptor 1, P1-ER2, and P1-D1, WGS experiments identified mutation clusters linked to six phylogenetic tree branches. BaSISS padlock probes targeted 51 alleles on each phylogenetic tree branch. The team identified a subclone by a patient identifier and the color of the corresponding phylogenetic tree node.
DCIS is known to be genetically heterogeneous but how DCIS clones organize and grow through the wider duct system remains incomprehensible. So the team examined three DCIS samples from P1 that spanned a tissue surface area of 224 mm2. Finally, the team performed spatial gene expression analysis using targeted in situ sequencing .
Consistent with bulk WGS data, BaSISS detected two to four subclones per PBC. The quantitative examination revealed that individual subclones formed spatial patterns related to the histological progression of cancer states. For instance, in P1-ER2, a region of hyperplasia was genetically unrelated to cancer, as confirmed by LCM–WGS. In each PBC, the genetic and histological progression models were largely stable.
P1-orange epithelial cells exhibited higher expression of the cell-cycle regulatory oncogenes cyclin D1 and cyclin B1 and the oncogene zinc finger protein 3 , which have been linked to adverse clinical outcomes. Overall, architectural and nuclear appearances and gene expression profiles were remarkably lineage-specific, and their different patterns could also be visualized spatially.