Fig. 3.

Approaches to induce, detect, and isolate cells with specific aneuploidies. Non-transformed or transformed near-diploid cells with or without functional TP53 can acquire heterogeneous aneuploid karyotypes after transient or chronic induction of CIN by compounds that disrupt the chromosome segregation machinery. In addition, the mere knockout (KO) or knockdown (KD) of TP53 in hTERT-RPE1 cells or sequential mutation of APC, TP53, KRAS and SMAD4 (APKS) in colorectal organoids is sufficient to increase CIN. FACS-based single-cell sorting followed by WG DNA or RNA sequencing shortly after CIN induction permits assessment of karyotype heterogeneity in the initial aneuploidy landscape thereby revealing potential mis-segregation biases. At the same time, single cell culture after CIN induction can generate monoclonal lines harboring specific monosomies or trisomies. These can be subjected to bulk WG DNA or RNA sequencing to reveal their (altered) karyotypes. Finally, the initially heterogeneous and mosaic aneuploid population can be further cultured under standard conditions or under certain challenging conditions such as anti-cancer drugs. Aneuploidy patterns that eventually emerge can be detected by single-cell WG DNA or RNA sequencing. Of note, WG RNA sequencing, carried out either shortly after CIN induction or after prolonged culture, also allows for analyses of cellular responses to specific chromosomal gains and losses. i, inhibitor. This figure was partially created with Biorender