Stage-Specific Human Induced Pluripotent Stem Cells Map the Progression of Myeloid Transformation to Transplantable Leukemia

Abstract

SUMMARY Myeloid malignancy is increasingly viewed as a disease spectrum, comprising hematopoietic disorders that extend across a phenotypic continuum ranging from clonal hematopoiesis to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). In this study, we derived a collection of iPSC lines capturing a range of disease stages encompassing preleukemia, low-risk MDS, high-risk MDS and secondary AML. Upon differentiation, we found hematopoietic phenotypes of graded severity and/or stage specificity that together delineate a phenotypic roadmap of disease progression culminating in serially transplantable leukemia. We also show that disease stage transitions, both reversal and progression, can be modeled in this system using genetic correction or introduction of mutations via CRISPR/Cas9, and that this iPSC-based approach can be used to uncover disease stage-specific responses to drugs. Our study therefore provides insight into the cellular events demarcating the initiation and progression of myeloid transformation and a new platform for testing genetic and pharmacological interventions.

Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of leukemia

“…Reassuringly, our phenotypic analyses here show that the gene edited iPSCs recapitulated the in vitro and in vivo phenotypes that we previously characterized in patient-derived iPSCs capturing all disease stages (encompassing disease-free, CH, low-risk MDS, high-risk MDS and sAML) 12 . Importantly, a critical limitation of the previous patient-derived progression models was the diverse genetic backgrounds of the different patients from which those iPSC lines were derived, which precluded analyses towards identifying stage-specific transcriptional and chromatin changes.…”

“…Normal iPSC-HSPCs notoriously fail to engraft in xenograft assays 28 . We have previously shown that hematopoietic cells from iPSCs derived from patients with CH and MDS also fail to engraft 12 and we therefore expected that P, A, and SA cells would not support engraftment, as our findings here indeed show. In striking contrast, we and others have shown that it is only iPSCs derived from AML patients that can produce HSPCs with engraftment potential 12,16 .…”

“…We have previously shown that hematopoietic cells from iPSCs derived from patients with CH and MDS also fail to engraft 12 and we therefore expected that P, A, and SA cells would not support engraftment, as our findings here indeed show. In striking contrast, we and others have shown that it is only iPSCs derived from AML patients that can produce HSPCs with engraftment potential 12,16 . This engraftment was predominantly myeloid, similarly to that of the SAR and SARF cells we present here, and unlike normal primary HSPC engraftment in the xenograft setting, which is heavily biased towards the B cell lineage 29 .…”

“…Leveraging the ability to obtain homogeneous populations of clonal iPSC-HSPCs upon hematopoietic differentiation, we perform integrative genomics analyses of their transcriptome and chromatin landscapes and identify AML targets for early intervention. stages from CH to MDS and AML 12,16 , with single mutant cells representing a CH stage, double mutant cells an MDS stage and triple mutant cells a leukemia (Fig. 1j).…”

Identification of drugs for leukaemia differentiation therapy by network pharmacology

“…The ectopic overexpression of these TFs in Ph⁺ B-cell acute lymphoblastic leukaemia (B-ALL) blasts 4 or primary chronic myeloid leukaemia (CML) cells in blast crisis 5 can induce them to undergo myeloid differentiation and lose their leukaemia-initiating potential. In addition, patient-derived AML or CML blasts can be reprogrammed into an iPSC-like state using the Yamanaka TFs (SOX2, KLF4, MYC, and OCT4) 7,8,9 , and subsequently re-differentiated into therapy-sensitive leukaemic cells. However, additional evidence suggests that leukaemias may depend on other TFs to establish the block in differentiation 10,11,12 , and that expression of certain oncogenic TFs may even be subtype-specific 13 .…”