Biology subjects

Hakobyan, M.

Publications and source records attributed to Hakobyan, M..

3 recordsLinked to original sources

bioRxiv2024

High interleukin-3 concentrations prime murine myeloid progenitor cells towards granulocytic differentiation

Impaired differentiation a key feature of many hematopoietic malignancies. To decipher the molecular processes underlying malignant transformation, it is important to understand the mechanisms regulating hematopoietic differentiation. Cell lines derived from transformed hematopoietic progenitors or from leukemia patients have proven to be valuable model systems for mechanistic investigations of hematopoiesis. In the present work, we investigated the cell-intrinsic differentiation capacity of the interleukin 3 (IL-3) dependent murine myeloid progenitor cell line 32D. We demonstrated that 32D cells have a cell-intrinsic granulocytic differentiation potential which requires the presence of high IL-3 concentrations in order to induce granulocytic priming. We also show that 32D cells still proliferate at comparable rates but lack granulocytic priming in the presence of intermediate IL-3 concentrations. This phenotypic plasticity is fully reversible and entirely depends on the IL-3 concentrations present in the culture media. RNA-seq analysis revealed that, among other myeloid genes, the expression of Csf3r is strongly induced exclusively in the presence of high IL-3 concentrations, likely explaining the granulocytic differentiation in response to G-CSF treatment. Together, our work provides detailed cellular and molecular insights into the phenotypic plasticity of 32D cells driven by different IL-3 concentrations and suggest culture conditions for different experimental set ups. Key pointsO_LI32D cells represent a murine myeloid cell line with endogenous granulocytic differentiation potential. C_LIO_LI32D cells present molecular and functional plasticity depending on their culture conditions. C_LIO_LIHigh IL-3 culture conditions prime 32D cells towards the granulocytic lineage. C_LIO_LILow IL-3 culture conditions lead to a reversible loss of the granulocytic differentiation potential of 32D cells while fully maintaining their proliferative activity. C_LI

molecular biology↗

bioRxiv2023

Oncogenic RAS-Pathway Activation Drives Oncofetal Reprogramming and Creates Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia

Aberrant fetal gene expression facilitates tumor-specific cellular plasticity by hijacking molecular programs of embryogenesis1. Persistent fetal gene signatures in childhood malignancies are typically explained by their prenatal origins2-6. In contrast, reactivation of fetal gene expression is considered a consequence of oncofetal reprogramming (OFR) in adult malignancies and is associated with aggressive disease7-10. To date, OFR has not been described in the context of childhood malignancies. Here, we performed a comprehensive multi-layered molecular characterization of juvenile myelomonocytic leukemia (JMML) and identified OFR as a hallmark of aggressive JMML. We observed that hematopoietic stem cells (HSCs) aberrantly express mixed developmental programs in JMML. Expression of fetal gene signatures combined with a postnatal epigenetic landscape suggested OFR, which was validated in a JMML mouse model, demonstrating that postnatal activation of RAS signaling is sufficient to induce fetal gene signatures. Integrative analysis identified the fetal HSC maturation marker CD52 as a novel therapeutic target for aggressive JMML. Anti-CD52 treatment depleted human JMML HSCs and disrupted disease propagation in vivo. In summary, this study implicates OFR, defined as postnatal acquisition of fetal transcription signatures, in the pathobiology of a childhood malignancy. We provide evidence for the direct involvement of oncogenic RAS signaling in OFR. Finally, we demonstrate how OFR can be leveraged for the development of novel treatment strategies. Highlights{blacksquare} Epigenomic and transcriptomic landscape of juvenile myelomonocytic leukemia (JMML) in the context of hematopoietic development. {blacksquare}The presence of fetal transcription signatures in childhood malignancies is not indicative of a developmental maturation block. {blacksquare}High-risk JMML is characterized by oncofetal reprogramming of postnatal hematopoietic stem cells (HSCs). {blacksquare}RAS-pathway mutations induce fetal-like gene expression signatures in murine postnatal HSCs. {blacksquare}The fetal maturation marker CD52 is a novel therapeutic target in high-risk JMML.

cancer biology↗

bioRxiv2022

Dynamic DNA methylation reveals novel cis-regulatory elements in murine hematopoiesis

BackgroundThe differentiation of hematopoietic stem and progenitor cells (HSPCs) to terminally differentiated immune cells is accompanied by large-scale remodeling of the DNA methylation landscape. While significant insights into the molecular mechanisms of hematopoietic tissue regeneration were derived from mouse models, profiling of DNA methylation changes has been hampered by high cost or low resolution using the methods available. This problem has been overcome by the recent development of the Infinium Mouse Methylation BeadChip (MMBC) array, facilitating methylation profiling of the mouse genome at single CpG resolution at affordable cost. ResultsWe extended the RnBeads package to provide a computational framework for the analysis of MMBC data. This framework was applied to a newly generated MMBC reference map of mouse hematopoiesis encompassing nine different cell types. The analysis of dynamically regulated CpG sites showed progressive and unidirectional DNA methylation changes from HSPCs to differentiated hematopoietic cells and allowed the identification of lineage- and cell type-specific DNA methylation programs. Comparison to previously published catalogues of cis-regulatory elements (CREs) revealed 12,856 novel putative CREs which were dynamically regulated by DNA methylation (mdCREs). These mdCREs were predominantly associated with patterns of cell type-specific DNA hypomethylation and could be identified as epigenetic control regions regulating the expression of key hematopoietic genes during differentiation. ConclusionsWe established a publicly available analysis pipeline for MMBC datasets and provide a DNA methylation atlas of mouse hematopoiesis. This resource allowed us to identify novel putative CREs involved in hematopoiesis and will serve as a platform to study epigenetic regulation of normal and malignant hematopoiesis.

genomics↗