Convergence of oncogenic cooperation at single-cell and single-gene levels drives leukemic transformation

Yuxuan Liu,Stephen S Chung,Zhimin Gu,Jian Xu,Junhua Lyu,Pranita Kaphle,Wenhuo Hu,Kathryn E Dickerson,Hui Cao,Yuannyu Zhang

doi:10.1038/s41467-021-26582-4

Abstract

Cancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression. Using a mouse model harboring NRasG12D and EZH2 mutations that recapitulates leukemic progression, we employ single-cell transcriptomic profiling to map cellular composition and gene expression alterations in healthy or diseased bone marrows during leukemogenesis. At cellular level, NRasG12D induces myeloid lineage-biased differentiation and EZH2-deficiency impairs myeloid cell maturation, whereas they cooperate to promote myeloid neoplasms with dysregulated transcriptional programs. At gene level, NRasG12D and EZH2-deficiency independently and synergistically deregulate gene expression. We integrate results from histopathology, leukemia repopulation, and leukemia-initiating cell assays to validate transcriptome-based cellular profiles. We use this resource to relate developmental hierarchies to leukemia phenotypes, evaluate oncogenic cooperation at single-cell and single-gene levels, and identify GEM as a regulator of leukemia-initiating cells. Our studies establish an integrative approach to deconvolute cancer evolution at single-cell resolution in vivo.

Highlights

Cancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression
We validated myeloproliferative neoplasms (MPNs) progression to acute myeloid leukemia (AML) by flow cytometry and histopathological analyses in previous studies[11], establishing a genetically defined leukemia model induced by functional cooperation between oncogenic signaling and epigenetic dysregulation
To determine the regulatory mechanisms by which NRasG12D and EZH2-deficiency cooperate to control aberrant leukemia-initiating cells (LICs) activity, we focused on genes synergistically activated by G12D and E2-KO in hematopoietic stem cell (HSC)/multipotent progenitor (MPP) cells, which are known to enrich for LICs46

Summary

Introduction

Cancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression. While mice harboring NRasG12D alone developed indolent myeloproliferative neoplasms (MPNs) and EZH2 deletion alone had minimal effects on hematopoiesis, combined NRasG12D and EZH2 mutations cooperatively induced MPN progression to lethal AML11 This genetic model permits the identification of molecular pathways controlling MPN progression to acute leukemia and the analysis of the functional cooperation between distinct oncogenic drivers in disease pathophysiology, especially at the single-cell level. We integrate results from histopathology, flow cytometry, leukemia repopulating activity, and leukemiainitiating cell assays to validate the transcriptome-based cellular profiles We use these approaches to relate developmental hierarchies to leukemia phenotypes, to evaluate functional cooperation between distinct oncogenic drivers at single-cell and single-gene levels, and to identify regulators of leukemia-initiating cells

Methods

Results

Conclusion