Single-Cell Multi-Omic Analysis Provides Insights into TP53-Mediated Evolution of Malignancies

As a plenary abstract at the 2021 ASH Annual Meeting, Alba Rodriguez-Meira, PhD-c, of MRC Weatherall Institute of Molecular Medicine at the University of Oxford in the United Kingdom, described a new single-cell multi-omic analysis of the genetic, cellular, and molecular landscape of TP53-driven transformation. The tool can provide unique insights into the evolution of chronic hematologic malignancies towards an aggressive acute leukemia.

TP53 is the most commonly mutated gene in human cancer. Presence of “multi-hit” TP53 mutations is associated with lack of response to conventional treatments and poor outcomes, the authors explained.

To better understand the biologic basis of TP53-mutant driven clonal evolution, Ms. Rodriguez-Meira and colleagues studied this process in a model of myeloproliferative neoplasm (MPN). This model is ideal as progression to secondary acute myeloid leukemia (AML) frequently occurs through the acquisition of TP53 missense mutations, they noted.

Next, to characterize tumor phylogenies, cellular hierarchies, and molecular features of TP53-driven transformatiom Ms. Rodriguez-Meira and colleagues performed single-cell multi-omic TARGET-seq analysis of 22,116 hematopoietic stem and progenitor cells (HPSCs) from 35 donors and 40 timepoint controls. They identified convergent clonal evolution leading to complete loss of TP53 wild-type alleles upon transformation, including parallel evolution of separate TP53 multi-hit subclones in the same patient and JAK2-negative progression.

All patients had complex clonal evolution driven by chromosomal abnormalities. In addition, TP53 multi-hit HSPCs without chromosomal abnormalities were rarely observed, according to Ms. Rodriguez-Meira. Subclones with recurrent abnormalities such as monosomy 7 showed upregulation of RAS-associated transcription and preferentially expanded in xenograft models.

These data indicated that TP53 missense mutation, loss of TP53 wild-type allele, and cytogenetic evolution are all required for leukemic stem cell expansion.

Further, the researchers performed integrated transcriptomic analysis of secondary AML samples. This revealed three major populations:

  • a TP53-mutant cluster characterized by an erythroid signature
  • a leukemic stem cell TP53-mutant cluster
  • a TP53-wild-type preleukemic cluster

Ms. Rodriguez-Meira said that the TP53-mutant cluster characterized by an erythroid signature was an unexpected finding given that there were no cases that showed diagnostic features of erythroid leukemia.

The researchers then derived a 48-gene leukemic stem cell score from the leukemic stem cell cluster. This score had prognostic impact in an independent AML cohort (hazard ratio = 3.13). Ms. Rodriguez-Meira said that the score was predictive of outcome irrespective of TP53 status for both de novo and secondary AML, “demonstrating its broader potential clinical utility.”

TARGET-seq also allowed the researchers to characterize rare TP53 wild-type preleukemic cells, which were found almost exclusively in the immunophenotypic lineage (CD34+CD38-CD90+CD45RA-) HSC compartment. These preleukemic cells from the secondary AML samples showed increased stemness, increased quiescence, aberrant inflammatory signaling, and differentiation defects compared with HSCs from control donors or donors with MPN. Ms. Rodriguez-Meira said these findings indicate “cell-extrinsic suppression of residual TP53 wild-type hematopoiesis”.

Finally, longitudinal analysis of TP53-heterozygous mutant HSPCs at different stags of evolution showed that aberrant inflammatory signaling in the genetic ancestors of TP53 multi-hit leukemia stem cell, but not the presence of TP53 mutants alone, was predictive of subsequent transformation.