The development of cancer after p53 inactivation is determined by a series of genomic changes that occur in four steps. The loss of heterozygosity of TP53 (the gene encoding p53 in humans, named Trp53 in mice) is followed by an accumulation of deletions, genome doubling, and the emergence of gains and amplifications.

In a study published in the August 17, 2022, issue of Nature, researchers have further observed that these four phases of genomic evolution are associated with specific histological stages before and after the malignant condition developed.

Although p53 plays a role in genome stability, it is unclear how TP53 heterozygosity arises and how cancer develops. Now, scientists have seen that after the loss of p53 (the so-called guardian of the genome), deletions trigger a series of homogeneous events.

"While previous work clearly shows that the genomes of p53 mutant cancers are chaotic, we were surprised to see that they evolved through an ordered and reproducible pattern," study director Scott Lowe, chair of the Cancer Biology & Genetics Program in the Memorial Sloan Kettering Cancer Center and investigator of the Howard Hughes Medical Institute, told BioWorld Science.

"We show that loss of p53 is not sufficient to produce malignant features, but that subsequent evolution of the genome is required. The study demonstrates that p53's role as 'guardian' keeps this type of evolution in check during sporadic tumorigenesis," Lowe said. His team's findings could be used to develop new strategies for the treatment of TP53 mutant tumors, types of cancer that are particularly aggressive and refractory to therapy. "Our study implies that, if the evolution of tumors sustaining p53 mutations harbors rules, there may eventually be strategies to exploit them," Lowe remarked.

The researchers used a pancreatic ductal adenocarcinoma (PDAC) mouse model to identify p53 heterozygosity loss before cancer develops. To study stage-specific genetic perturbations, they developed PDAC cell models from multiallelic embryonic stem cells and they applied single-cell sequencing and in situ genotyping techniques.

PDAC is a lethal disease in which mutations in other oncogenes such as KRAS, mutations that inactivate CDKN2A, or on the effector of the TGF-beta SMAD4 pathway also occur. The loss of TP53 is associated with the invasive progression of PDAC.

Most studies on human tumors focus on the bulk tumor after it has formed. Tissues are obtained after diagnosis. However, their availability from PDAC patients is limited, so until now, although p53 was thought to function as a barrier to tumorigenesis very early, it was not possible to obtain a time sequence from p53 inactivation to malignancy progression.

Scientists have observed how tumors evolve from benign to malignant at the resolution of a single cell. "Our new model allowed us to visualize and capture incipient cancer cells before and after they inactivated p53 and characterize them throughout all stages of cancer, giving us a level of granularity that was previously lacking".

Tracking p53 for future cancer approaches

Research on p53, encoded by TP53, one of the most studied tumor suppressor genes, started in the late 1970s. This wide family of proteins, which blocks cell cycle progression and promotes apoptosis when there is DNA damage, is also crucial for genome stability and DNA repair, senescence, the preservation of telomere length, or the maintenance of stem cells.

Four decades after its description in 1979, different laboratories around the world keep studying p53 functions and its relationship with cancer. The mutation of the TP53 gene is present in half of all human tumors, including breast, lung, skin, colon, liver, bladder or prostate cancers.

However, there are still significant keys to unveil around this versatile transcription factor that also plays distinct roles at a post-transcriptional or post-translational level. "Despite our extensive efforts, we still do not fully understand which biological process p53 controls that blocks cancer growth, or the role of tissue context in output. We also do not understand the signals that engage p53 to suppress cancer to begin with," Lowe said.

Researchers may answer these questions with the development of new technologies, as it is happening already after single-cell sequencing maps or the expansion of new animal models. Lowe's expectations do not point to a single answer. "Precisely how p53 works will depend on organ site and organism physiology."

Although there are no immediate therapeutic benefits, Lowe's findings for p53 have opened the door to the development of new strategies for the treatment of TP53 mutant tumors. Some of them could be directed to the deletion processes after p53 mutation.

"One speculative suggestion is based on our observations that chromosomal deletions are the first event after p53 mutation, and as such are homogenous in the tumor. Targeting the vulnerabilities produced by deletions might be less prone to resistance and so might therefore lead to durable responses," Lowe explained.

The model that Lowe's team developed could be suited to study some of these questions. "We are using it to help understand what goes wrong as cells cross the benign to malignant transition. We hope that this might help identify better ways to detect early cancer or even develop strategies to prevent it. But these are long-term plans," he said. "Our work suggests interesting forces at play when cancer evolves that can be studied in the future."