AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding

Abstract

CCTC-binding factor (CTCF) is a key regulator of gene expression through organization of the chromatin structure. Still, it is unclear how CTCF binding is perturbed in leukemia or in cancer in general. We studied CTCF binding by chromatin immunoprecipitation sequencing in cells from patients with acute myeloid leukemia (AML) and in normal bone marrow (NBM) in the context of gene expression, DNA methylation, and azacitidine exposure. CTCF binding was increased in AML compared with NBM. Aberrant CTCF binding was enriched for motifs for key myeloid transcription factors such as CEBPA, PU.1, and RUNX1. AML with TET2 mutations was characterized by a particularly strong gain of CTCF binding, highly enriched for gain in promoter regions, while AML in general was enriched for changes at enhancers. There was a strong anticorrelation between CTCF binding and DNA methylation. Gain of CTCF occupancy was associated with increased gene expression; however, the genomic location (promoter vs distal regions) and enrichment of motifs (for repressing vs activating cofactors) were decisive for the gene expression pattern. Knockdown of CTCF in K562 cells caused loss of CTCF binding and transcriptional repression of genes with changed CTCF binding in AML, as well as loss of RUNX1 binding at RUNX1/CTCF-binding sites. In addition, CTCF knockdown caused increased differentiation. Azacitidine exposure caused major changes in CTCF occupancy in AML patient cells, partly by restoring a CTCF-binding pattern similar to NBM. We conclude that AML displays an aberrant increase in CTCF occupancy that targets key genes for AML development and impacts gene expression.

Assessing acute myeloid leukemia susceptibility in rearrangement‐driven patients by DNA breakage at topoisomerase II and CCCTC‐binding factor/cohesin binding sites

“…We found that predisposed patients, when compared to nonfusion patients, had significantly more DNA breakage at a select group of TOP2‐sensitive, CTCF‐, RAD21‐, and SMC3‐binding sites. A recent study found that CTCF binding was increased in AML patients when compared to normal bone marrow cells, further implicating CTCF in AML pathogenesis 59 . More importantly, DNA breakage at these TOP2‐sensitive sites specifically increased in a dose‐dependent manner, and increased DNA breakage in etoposide‐treated samples was also associated with stronger protein binding at CTCF, RAD21, and SMC3 sites.…”

“…A recent study found that CTCF binding was increased in AML patients when compared to normal bone marrow cells, further implicating CTCF in AML pathogenesis. 59 More importantly, DNA breakage at these TOP2-sensitive sites specifically increased in a dose-dependent manner, and increased DNA breakage in etoposide-treated samples was also associated with stronger protein binding at CTCF, RAD21, and SMC3 sites. We are also intrigued by the difference in etoposide response among the 34 shared sites (by TOP2, CTCF, RAD21, and SMC3).…”

<p>Identification of Long Non-Coding RNA <em>SNHG</em> Family as Promising Prognostic Biomarkers in Acute Myeloid Leukemia</p>

“…Evidences have shown that somatic gene mutations such as RUNX1 mutation affected transcription activation in AML. 18 In our study, we further identified the association between SNHG7/12 and common gene mutations such as IDH1/2, RUNX1 and NPM1 mutations in patients with AML. However, the potential connections between SNHG7/12 expression and these gene mutations remain poorly defined.…”

Three-dimensional Genome Organization Maps in Normal Haematopoietic Stem Cells and Acute Myeloid Leukemia

“…One question arising is how can we perturb chromatin interactions in cancer? Aza-cytidine, a drug commonly used in AML treatment, has recently been shown to alter CTCF levels (37). We speculate that these drugs may work in part by leading to alterations in chromatin interactions, such as the FIRE at MEIS1 , leading to downregulation of gene expression.…”