NKL homeobox gene activities in normal and malignant myeloid cells.

Stefan Nagel,Maren Kaufmann,Michaela Scherr,Iris Dallmann,Claudia Pommerenke,Corinna Meyer,Hans G Drexler,Max Koeppel,Roderick A F Macleod,Francesco Bertolini

doi:10.1371/journal.pone.0226212

Abstract

Recently, we have documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in early hematopoiesis and in lymphopoiesis, which spotlights genes deregulated in lymphoid malignancies. Here, we enlarge this map to include normal NKL homeobox gene expressions in myelopoiesis by analyzing public expression profiling data and primary samples from developing and mature myeloid cells. We thus uncovered differential activities of six NKL homeobox genes, namely DLX2, HHEX, HLX, HMX1, NKX3-1 and VENTX. We further examined public expression profiling data of 251 acute myeloid leukemia (AML) and 183 myelodysplastic syndrome (MDS) patients, thereby identifying 24 deregulated genes. These results revealed frequent deregulation of NKL homeobox genes in myeloid malignancies. For detailed analysis we focused on NKL homeobox gene NANOG, which acts as a stem cell factor and is correspondingly expressed alone in hematopoietic progenitor cells. We detected aberrant expression of NANOG in a small subset of AML patients and in AML cell line NOMO-1, which served as a model. Karyotyping and genomic profiling discounted rearrangements of the NANOG locus at 12p13. But gene expression analyses of AML patients and AML cell lines after knockdown and overexpression of NANOG revealed regulators and target genes. Accordingly, NKL homeobox genes HHEX, DLX5 and DLX6, stem cell factors STAT3 and TET2, and the NOTCH-pathway were located upstream of NANOG while NKL homeobox genes HLX and VENTX, transcription factors KLF4 and MYB, and anti-apoptosis-factor MIR17HG represented target genes. In conclusion, we have extended the NKL-code to the myeloid lineage and thus identified several NKL homeobox genes deregulated in AML and MDS. These data indicate a common oncogenic role of NKL homeobox genes in both lymphoid and myeloid malignancies. For misexpressed NANOG we identified an aberrant regulatory network, which contributes to the understanding of the oncogenic activity of NKL homeobox genes.

Highlights

Human hematopoiesis starts with hematopoietic stem/progenitor cells (HSPC) residing in specific niches in the bone marrow
While HHEX, HLX and VENTX were expressed in most samples HMX1 expression was restricted to the erythropoietic lineage, DLX2 to mature mast cells and monocytes, and NKX3-1 to mature granulocytes and monocytes
To identify aberrantly expressed NKL homeobox genes in myeloid malignancies we screened public expression profiling data of 251 acute myeloid leukemia (AML) and 183 myelodysplastic syndrome (MDS) patient samples using datasets GSE15434 (S2 Fig) and GSE19429 (S3 Fig), respectively. This examination revealed 18 deregulated NKL homeobox genes in AML patients with normal karyotype and 14 in MDS patients (Table 1). We found in these AML and MDS patients 24 deregulated NKL homeobox genes, including BARHL1, BARX1, DLX1, DLX2, DLX3, DLX4, DLX6, EMX1, EMX2, HHEX, HLX, HMX1, HMX2, MSX1, MSX2, NANOG, NKX1-1, NKX2-3, NKX2-5, NKX3-1, NKX3-2, NKX6-3, VAX2 and VENTX

Summary

Introduction

Human hematopoiesis starts with hematopoietic stem/progenitor cells (HSPC) residing in specific niches in the bone marrow. These cells undergo self-renewal and generate lymphoid primed multipotent progenitors (LMPP), which supply both the lymphoid and myeloid lineage. Derived common lymphoid progenitors (CLP) and common myeloid progenitors (CMP) populate the entire casts of lymphocytes and myeloid blood cells, respectively [1]. Additional myeloid blood cells are mast cells and monocytes the latter of, which are able to differentiate into dendritic cells in the bone marrow or into macrophages in non-hematopoietic tissues [2]. Alternative hematopoietic models exist, which differ in the positioning and developmental potential of LMPPs and CMPs [3,4,5]. Chromosomal rearrangements, gene mutations, aberrant signalling pathways or alternative mechanisms drive the deregulation of particular developmental genes, which mediate an arrest of differentiation, enhanced survival and/ or sustained proliferation [1,6,7]

Methods

Results

Conclusion