Inactivation of RB1, CDKN2A, and TP53 have distinct effects on genomic stability at side‐by‐side comparison in karyotypically normal cells

Abstract

Chromosomal instability is a common feature in malignant tumors. Previous studies have indicated that inactivation of the classical tumor suppressor genes RB1, CDKN2A, and TP53 may contribute to chromosomal aberrations in cancer by disrupting different aspects of the cell cycle and DNA damage checkpoint machinery. We performed a side‐by‐side comparison of how inactivation of each of these genes affected chromosomal stability in vitro. Using CRISPR‐Cas9 technology, RB1, CDKN2A, and TP53 were independently knocked out in karyotypically normal immortalized cells, after which these cells were followed over time. Bulk RNA sequencing revealed a distinct phenotype with upregulation of pathways related to cell cycle control and proliferation in all three knockouts. Surprisingly, the RB1 and CDKN2A knocked out cell lines did not harbor more copy number aberrations than wild‐type cells, despite culturing for months. The TP53‐knocked out cells, in contrast, showed a massive amount of copy number alterations and saltatory evolution through whole genome duplication. This side‐by‐side comparison indicated that the effects on chromosomal stability from inactivation of RB1 and CDKN2A are negligible compared to inactivation of TP53, under the same conditions in a nonstressful environment, even though partly overlapping regulatory pathways are affected. Our data suggest that loss of RB1 and CDKN2A alone is not enough to trigger surviving detectable aneuploid clones while inactivation of TP53 on its own caused massive CIN leading to saltatory clonal evolution in vitro and clonal selection.

Disruption of the TP53 locus in osteosarcoma leads to TP53 promoter gene fusions and restoration of parts of the TP53 signalling pathway

“…Instead, the genomic footprint of TP53 promoter gene fusions mimics that of oncogene amplification through breakage–fusion–bridge cycles, found in, for example, low‐grade osteosarcoma with ring chromosomes and MDM2 amplification (Figure 2I). Thus, according to our model, transposition of the TP53 promoter is an early spark for genome‐wide rearrangements in osteosarcoma, including whole‐genome doubling [52–54]. Results from whole‐genome sequencing of multi‐sampled bulk and single‐cell tumour DNA supported this model.…”

A Review of the Repair of DNA Double Strand Breaks in the Development of Oral Cancer

“…Interestingly, mutant TP53 appears to be more important than inactive CDKN2A/p16 INK4A in inducing genetic instability [64]. Furthermore, current thinking suggests that mutant TP53 may play different roles at different stages of carcinogenesis.…”

CDKN2A promoter methylation enhances self-renewal of glioblastoma stem cells and confers resistance to carmustine

“…Genetic alterations affecting CDKN2A, such as homozygous deletions, point mutations, or promoter methylation, have been identified in various cancer types, including glioblastoma[ 12 ]. Loss of CDKN2A function has been associated with uncontrolled cell proliferation, decreased response to chemotherapy, and poor prognosis in glioblastoma patients[ 13 ].…”