New Single-Cell Multi-Omic Analysis Shines Light on Mechanisms of TP53-Mutant Myeloid Neoplasms

Take-aways

• TP53 is the most commonly mutated gene in human cancer and presence of “multi-hit” TP53 mutations is associated with lack of response to conventional treatments and poor outcome.
• Using TARGET-seq analysis, investigators identified convergent clonal evolution leading to complete loss of TP53 wild-type alleles upon disease transformation.
• Results indicated that TP53 missense mutation, loss of TP53 wild-type allele, and cytogenetic evolution are all required for leukemic stem cell expansion.

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In research presented as a plenary abstract at the 2021 American Society of Hematology Annual Meeting, researchers shared 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, according to lead author Alba Rodriguez-Meira, PhD-c, of MRC Weatherall Institute of Molecular Medicine at the University of Oxford in the United Kingdom.

As Ms. Rodriguez-Meira explained, TP53 is the most commonly mutated gene in human cancer, and the presence of “multi-hit” TP53 mutations is associated with lack of response to conventional treatments and poor outcomes. The team of researchers sought to better understand the biologic basis of TP53-mutant driven clonal evolution by studying this transformation process in a model of myeloproliferative neoplasms (MPNs). They noted that this model “represents an ideal tractable disease model to study this process, as progression to secondary acute myeloid leukemia frequently occurs through the acquisition of TP53 missense mutations,” the investigators noted.

To characterize tumor phylogenies, cellular hierarchies, and molecular features of TP53-driven transformation, Ms. Rodriguez-Meira and colleagues performed single-cell multi-omic TARGET-seq analysis of 22116 hematopoietic stem and progenitor cells (HPSCs) from 35 donors and 40 timepoint controls. Timepoints included MPN in chronic phase, pre-AML, and TP53-mutated secondary AML.

“We invariably 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 (n = 4/14) and JAK2-negative progression (n = 2/14),” Ms. Rodriguez-Meira said.

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.

The authors noted that these data indicate that TP53 missense mutation, loss of TP53 wild-type allele, and cytogenetic evolution are all required for leukemic stem cell expansion.

Next, Ms. Rodriguez-Meira and investigators performed integrated transcriptomic analysis of secondary AML samples. This analysis identified three major populations:

• a TP53-mutant cluster characterized by an erythroid signature (e.g., KLF1, GATA1, and GYPA)
• a leukemic stem cell TP53-mutant cluster
• a TP53-wild-type preleukemic cluster

The revelation of the TP53-mutant cluster was “an unexpected finding as no cases showed diagnostic features of erythroid leukemia,” the authors wrote.

Using the leukemic stem cell TP53-mutant cluster, the researchers then derived a 48-gene leukemic stem cell score. This score had prognostic impact in an independent AML cohort and was “predictive of outcome irrespective of TP53 status for both de novo and sAML, demonstrating its broader potential clinical utility.”

TARGET-seq also allowed the investigators to characterize rare TP53 wild-type preleukemic cells. These cells were almost exclusively identified in the immunophenotypic lineage hematopoietic stem cell compartment. Compared with hematopoietic stem cells from control donors or donors with MPN, the preleukemic cells from the secondary AML samples showed increased stemness, increased quiescence, aberrant inflammatory signaling, and differentiation defects. Researchers said that these findings indicate “cell-extrinsic suppression of residual TP53 wild-type hematopoiesis.”

Summarizing the findings, Ms. Rodriguez-Meira said that this comprehensive single-cell multi-omic analysis of the genetic, cellular, and molecular landscape of TP53-mediated transformation provides unique insights into the evolution of chronic MPNs toward aggressive acute leukemia. “We anticipate these findings will be of broader relevance to many other cancer types,” she said.

Disclosures: This research was supported by the Mead Group at the Haematopoietic Stem Cell Biology Laboratory at the University of Oxford Medical Sciences Division. Study authors report no relevant conflicts of interest.

Reference

Rodriguez-Meira A, Rahman H, Norfo R, et al. Single-cell multi-omics reveals the genetic, cellular and molecular landscape of TP53 mutated leukemic transformation in MPN. Abstract #3. Presented at the 2021 American Society of Hematology Annual Meeting, December 12, 2021.