Omics Technologies to Decipher Regulatory Networks in Granulocytic Cell Differentiation.

Svetlana Novikova,Konstantin Yarygin,Alexey Lupatov,Victor Zgoda,Olga Tikhonova,Tatiana Farafonova,Igor Vakhrushev,Leonid Kurbatov

doi:10.3390/biom11060907

Svetlana Novikova, Konstantin Yarygin + Show 6 more

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https://doi.org/10.3390/biom11060907

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Journal: Biomolecules	Publication Date: Jun 18, 2021
Citations: 8	License type: CC BY 4.0

Affiliation: Institute of Biomedical Chemistry

Abstract

Induced granulocytic differentiation of human leukemic cells under all-trans-retinoid acid (ATRA) treatment underlies differentiation therapy of acute myeloid leukemia. Knowing the regulation of this process it is possible to identify potential targets for antileukemic drugs and develop novel approaches to differentiation therapy. In this study, we have performed transcriptomic and proteomic profiling to reveal up- and down-regulated transcripts and proteins during time-course experiments. Using data on differentially expressed transcripts and proteins we have applied upstream regulator search and obtained transcriptome- and proteome-based regulatory networks of induced granulocytic differentiation that cover both up-regulated (HIC1, NFKBIA, and CASP9) and down-regulated (PARP1, VDR, and RXRA) elements. To verify the designed network we measured HIC1 and PARP1 protein abundance during granulocytic differentiation by selected reaction monitoring (SRM) using stable isotopically labeled peptide standards. We also revealed that transcription factor CEBPB and LYN kinase were involved in differentiation onset, and evaluated their protein levels by SRM technique. Obtained results indicate that the omics data reflect involvement of the DNA repair system and the MAPK kinase cascade as well as show the balance between the processes of the cell survival and apoptosis in a p53-independent manner. The differentially expressed transcripts and proteins, predicted transcriptional factors, and key molecules such as HIC1, CEBPB, LYN, and PARP1 may be considered as potential targets for differentiation therapy of acute myeloid leukemia.

Highlights

Cell differentiation is a fundamental process of the development, growth, reproduction of multicellular organisms
Various mutations impair granulocytic differentiation resulting in highly heterogeneous acute myeloid leukemia (AML), which could be cured by high dosage of all-trans-retinoid acid (ATRA)
To obtain the transcriptomic data, HL-60 cells were harvested at 3 h, 24 h, and 96 h after ATRA treatment followed by mRNA microarray profiling

Summary

Introduction

Cell differentiation is a fundamental process of the development, growth, reproduction of multicellular organisms. Regulation of cell differentiation has been for decades and remains an important task for investigation due to its importance in cancer and many other diseases therapy. Leukemic cells that are induced to differentiate under all-trans-retinoid acid (ATRA) treatment make a convenient model for studying of cell maturation in vitro. ATRA in physiological dosage binds and activates a heterodimer receptor RAR/RXR followed by release of histone deacetylases (HDACs) and transcription co-repressors (N-CoR or SMRT), and by recruitment of transcription co-activators (NcoA1/SRC-1, CBP/p300, p/CIP, and ACTR) [1]. Containing genes, which are repressed by nonactive RAR/RXR, trigger the further cascade of molecular events leading to myeloid precursor’s maturation into functional granulocytes. Various mutations impair granulocytic differentiation resulting in highly heterogeneous acute myeloid leukemia (AML), which could be cured by high dosage of ATRA.

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