Cell-intrinsic, heritable clonal fitness is characterized by increased transcriptional heterogeneity.

  • Major Finding: Cell-intrinsic, heritable clonal fitness is characterized by increased transcriptional heterogeneity.

  • Concept: Heterogeneous transcriptional states with high Slpi and low B2m expression govern clonal fitness.

  • Impact: This work reveals nongenetic intratumoral heterogeneity that influences malignant clonal fitness.

Most human cancers display a high degree of intratumoral heterogeneity, complicating the development of therapies that fully eradicate malignant cells. Despite considerable advances in our understanding of genetic heterogeneity, nongenetic intratumoral heterogeneity has not been well characterized. To investigate how nongenetic heterogeneity influences clonal fitness, Fennell, Vassiliadis, and colleagues developed a single-cell profiling and lineage tracing method, utilizing an expressed barcode system, to assess clonal fate and corresponding gene expression profile in a time-resolved manner. Applying this in models of acute myeloid leukemia (AML), mouse hematopoietic stem and progenitor cells (HSPC) were transformed with the MLL–AF9 fusion oncogene and barcoded, before transplantation into mice. Following disease development, bone marrow and spleen samples were sequenced and revealed that identical clones functioned as dominant leukemia-initiating clones across multiple mice, implying cell-intrinsic mechanisms of clonal fitness. When secondary oncogenic mutations, KrasG12D or FltITD, were introduced into MLL–AF9-expressing leukemia cells and resulting distinct genotypes were pooled and transplanted into mice to mimic competition within human tumors, several dominant clones showed fitness specifically in the context of competition. These clones displayed high expression of the secretory leukocyte peptidase inhibitor gene Slpi and downregulation of antigen processing and presentation pathways. High Slpi and decreased B2m expression were hallmarks of dominant disease clones that developed in different immune contexts and from different tissue microenvironments, with Slpi knockout impairing clonal fitness and increasing survival in vivo. Notably, heterogeneous transcriptional states that were enriched in dominant, cancer-initiating clones preexisted prior to transplantation, and lineage tracing experiments revealed that the nongenetic clonal fitness conferred by these transcriptional states was heritable over the course of tumor progression. Classified as high, medium, or low clonal output, leukemia stem cells from the bone marrow actively adapted in response to intensive chemotherapy via different transcriptional routes depending on intrinsic clonal output. In summary, this work demonstrates nongenetic, cell-intrinsic properties of clonal dominance that govern fitness in tumor development in AML.

Fennell KA, Vassiliadis D, Lam EYN, Martelotto LG, Balic JJ, Hollizeck S, et al. Non-genetic determinants of malignant clonal fitness at single-cell resolution. Nature 2022;601:125–31.

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