Cellular and Molecular Architecture of Hematopoietic Stem Cells and Progenitors in Genetic Models of Bone Marrow Failure

Inherited bone marrow failure syndromes (IBMFSs) such as Fanconi Anemia (FA) and Shwachman-Diamond syndrome (SDS) feature progressive cytopenia and a risk of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). Using deep immunophenotypic analysis of hematopoietic stem cells (HSCs) and early progenitors in bone marrow samples from 13 FA/SDS patients without MDS/AML and 6 healthy controls, we revealed relative survival of progenitors that phenotypically resembled granulocyte-monocyte progenitors (GMP) in the patients. In contrast, HSCs, multipotent progenitors, common myeloid progenitors and megakaryocyte-erythroid progenitors were remarkably reduced in FA/SDS patients compared to controls. Whole exome and targeted sequencing of GMP-like cells in leukemia-free patients revealed a prominently higher mutation load in FA/SDS patient samples than in healthy controls. Patient samples also manifested molecular changes that are characteristic of AML: increased G>A/C>T variants, decreased A>G/T>C variants, increased trinucleotide mutations at Xp(C>T)pT, decreased lower mutation rates at Xp(C>T)pG sites compared to other Xp(C>T)pX sites and enrichment for cancer signature 1. AML cells have previously been reported as commonly harboring this cancer signature. Potential pre-leukemic targets in the GMP-like cells from FA/SDS patients included SYNE1, DST, HUWE1, LRP2, NOTCH2 and TP53. Serial analysis of GMPs from a SDS patient, who progressed to AML revealed a gradual increase in mutational burden, enrichment of G>A/C>T signature and emergence of new clones. Interestingly, the molecular signature of marrow cells from two FA/SDS patients with AML was similar to that of FA/SDS without transformation. The predicted founding clones in SDS-AML harbored mutations in several genes including TP53, while in FA-AML the mutated genes included ARID1B and SFPQ. In conclusion, we described an architectural change in the hematopoietic hierarchy of FA/SDS with remarkable preservation of GMP-like populations harboring unique mutation signatures. GMP-like cells might represent a cellular reservoir for clonal evolution.