Cellular and molecular architecture of hematopoietic stem cells and progenitors in genetic models of bone marrow failure
Stephanie Heidemann, Brian Bursic, Sasan Zandi, Hongbing Li, Sagi Abelson, Robert J. Klaassen, Sharon Abish, Meera Rayar, Vicky R. Breakey, Houtan Moshiri, Santhosh Dhanraj, Richard de Borja, Adam Shlien, John E. Dick, Yigal Dror
Stephanie Heidemann, Brian Bursic, Sasan Zandi, Hongbing Li, Sagi Abelson, Robert J. Klaassen, Sharon Abish, Meera Rayar, Vicky R. Breakey, Houtan Moshiri, Santhosh Dhanraj, Richard de Borja, Adam Shlien, John E. Dick, Yigal Dror
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Research Article Hematology Oncology

Cellular and molecular architecture of hematopoietic stem cells and progenitors in genetic models of bone marrow failure

Abstract

Inherited bone marrow failure syndromes, such as Fanconi anemia (FA) and Shwachman-Diamond syndrome (SDS), feature progressive cytopenia and a risk of acute myeloid leukemia (AML). Using deep phenotypic analysis of early progenitors in FA/SDS bone marrow samples, we revealed selective survival of progenitors that phenotypically resembled granulocyte-monocyte progenitors (GMP). Whole-exome and targeted sequencing of GMP-like cells in leukemia-free patients revealed a higher mutation load than in healthy controls and 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, and decreased mutation rates at Xp(C>T)pG sites compared with other Xp(C>T)pX sites and enrichment for Cancer Signature 1 (X indicates any nucleotide). Potential preleukemic targets in the GMP-like cells from patients with FA/SDS included SYNE1, DST, HUWE1, LRP2, NOTCH2, and TP53. Serial analysis of GMPs from an SDS patient who progressed to leukemia 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 2 FA/SDS patients with leukemia was similar to that of FA/SDS patients without transformation. The predicted founding clones in SDS-derived AML harbored mutations in several genes, including TP53, while in FA-derived AML the mutated genes included ARID1B and SFPQ. We describe 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.

Authors

Stephanie Heidemann, Brian Bursic, Sasan Zandi, Hongbing Li, Sagi Abelson, Robert J. Klaassen, Sharon Abish, Meera Rayar, Vicky R. Breakey, Houtan Moshiri, Santhosh Dhanraj, Richard de Borja, Adam Shlien, John E. Dick, Yigal Dror

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Figure 2

Frequency of somatic variants in bone marrow samples from patients with SDS and FA and healthy control subjects.

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Frequency of somatic variants in bone marrow samples from patients with ...
(A) Comparison of average (±SEM) variant rate between FA (n = 6), SDS (n = 7), and healthy control subjects (n = 6). The box plots depict the minimum and maximum values (whiskers), the upper and lower quartiles, and the median. The length of the box represents the interquartile range. Results by Student’s t test are shown. P = 0.0695 by Kruskal-Wallis test with Dunn’s post hoc test when comparing the 3 subject groups. (B–D) Variant rate among controls, FA subjects, and SDS subjects organized according to ages. (E) Allele frequency of the various variants in controls, FA subjects, and SDS subjects. The groups were compared using the Wilcoxon’s signed-rank test. *P < 0.0001. The y axis represents the variant frequency and the x axis represents the variants arranged from those with the highest allele frequency to the lowest. In each group, each number may represent a different variant.