Pathogenic human variant that dislocates GATA2 zinc fingers disrupts hematopoietic gene expression and signaling networks
Mabel Minji Jung, … , Sunduz Keles, Emery H. Bresnick
Mabel Minji Jung, … , Sunduz Keles, Emery H. Bresnick
Published February 21, 2023
Citation Information: J Clin Invest. 2023;133(7):e162685. https://doi.org/10.1172/JCI162685.
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Pathogenic human variant that dislocates GATA2 zinc fingers disrupts hematopoietic gene expression and signaling networks

Abstract

Although certain human genetic variants are conspicuously loss of function, decoding the impact of many variants is challenging. Previously, we described a patient with leukemia predisposition syndrome (GATA2 deficiency) with a germline GATA2 variant that inserts 9 amino acids between the 2 zinc fingers (9aa-Ins). Here, we conducted mechanistic analyses using genomic technologies and a genetic rescue system with Gata2 enhancer–mutant hematopoietic progenitor cells to compare how GATA2 and 9aa-Ins function genome-wide. Despite nuclear localization, 9aa-Ins was severely defective in occupying and remodeling chromatin and regulating transcription. Variation of the inter–zinc finger spacer length revealed that insertions were more deleterious to activation than repression. GATA2 deficiency generated a lineage-diverting gene expression program and a hematopoiesis-disrupting signaling network in progenitors with reduced granulocyte-macrophage colony-stimulating factor (GM-CSF) and elevated IL-6 signaling. As insufficient GM-CSF signaling caused pulmonary alveolar proteinosis and excessive IL-6 signaling promoted bone marrow failure and GATA2 deficiency patient phenotypes, these results provide insight into mechanisms underlying GATA2-linked pathologies.

Authors

Mabel Minji Jung, Siqi Shen, Giovanni A. Botten, Thomas Olender, Koichi R. Katsumura, Kirby D. Johnson, Alexandra A. Soukup, Peng Liu, Qingzhou Zhang, Zena D. Jensvold, Peter W. Lewis, Robert A. Beagrie, Jason K.K. Low, Lihua Yang, Joel P. Mackay, Lucy A. Godley, Marjorie Brand, Jian Xu, Sunduz Keles, Emery H. Bresnick

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Figure 5

Multiomic analysis with GATA2 disease variant reveals principles of GATA2 function through chromatin.

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Multiomic analysis with GATA2 disease variant reveals principles of GATA...
(A) PCA quantifying multidimensional scaling distances between differential chromatin accessibility (ATAC-Seq, GEO GSE201968) with n = 4 biological replicates of hi–77–/– empty, hi–77–/– GATA2, hi–77–/– 9aa-Ins. Venn diagram depicts overlap. (B) Chromatin transitions of genes activated or repressed by GATA2, both GATA2 and 9aa-Ins, or only 9aa-Ins. Number of genes comprised by each group is shown above the graphs. (C) GATA2 and 9aa-Ins impact on chromatin accessibility. hi–77–/– GATA2/hi–77–/– empty signal or hi–77–/– 9aa-Ins/hi–77–/– empty signal was determined at genes activated/repressed by only GATA2, GATA2 and 9aa-Ins, and only 9aa-Ins conditions by amalgamation of ATAC-Seq peaks linked to DEGs. Statistical calculations to measure chromatin accessibility (>0 or <0 for differential accessibility) used Wilcoxon’s rank sum test. Comparisons between 2 groups used Wilcoxon’s signed rank test. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001. (D) Motif enrichment analysis at differentially accessible loci activated or repressed by only GATA2, GATA2 and 9aa-Ins, or only 9aa-Ins. Number of peaks comprised by each group is on the left of the heatmap. Peaks less than 100 kb from the start site were analyzed.