Dataset Information

MiRNome profiling of LSC-enriched CD34⁺CD38^-CD26⁺ fraction in Ph⁺ CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool.

ABSTRACT: Chronic myeloid leukemia (CML) is a myeloid stem cell neoplasm characterized by an expansion of myeloid progenitor cells and the presence of BCR-ABL1 oncoprotein. Since the introduction of specific BCR-ABL1 tyrosine kinase inhibitors (TKI), overall survival has improved significantly. However, under long-term therapy patients may have residual disease that originates from TKI-resistant leukemic stem cells (LSC). In this work, we analyzed the miRNome of LSC-enriched CD34⁺CD38^-CD26⁺ and normal hematopoietic stem cells (HSC) fractions obtained from the same chronic phase (CP) CML patients, and stem and progenitor cells obtained from healthy donors (HD) by next-generation sequencing. We detected a global decrease of microRNA levels in LSC-enriched CD34⁺CD38^-CD26⁺ and HSC fractions from CML-CP patients, and decreased levels of microRNAs and snoRNAs from a genomic cluster in chromosome 14, suggesting a mechanism of silencing of multiple non-coding RNAs. Surprisingly, HSC from CML-CP patients, despite the absence of BCR-ABL1 expression, showed an altered miRNome. We confirmed by RT-qPCR that the levels of miR-196a-5p were increased more than nine-fold in CD26⁺ (BCR-ABL1 ⁺ ) vs. CD26^- (BCR-ABL1 ^-) CD34⁺CD38^- fractions from CML-CP patients at diagnosis, and in silico analysis revealed a significant association to lipid metabolism and hematopoiesis functions. In the light of recent descriptions of increased oxidative metabolism in CML LSC-enriched fractions, these results serve as a guide for future functional studies that evaluate the role of microRNAs in this process. Metabolic vulnerabilities in LSCs open the road for new therapeutic strategies. This is the first report of the miRNome of CML-CP CD34⁺CD38^- fractions that distinguishes between CD26⁺ (BCR-ABL1 ⁺ ) and their CD26^- (BCR-ABL1 ^- ) counterparts, providing valuable data for future studies.

SUBMITTER: Ruiz MS

PROVIDER: S-EPMC7869017 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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miRNome profiling of LSC-enriched CD34+CD38-CD26+ fraction in Ph+ CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool.

Ruiz María Sol MS Sánchez María Belén MB Bonecker Simone S Furtado Carolina C Koile Daniel D Yankilevich Patricio P Cranco Santiago S Custidiano María Del Rosario MDR Freitas Josefina J Moiraghi Beatriz B Pérez Mariel Ana MA Pavlovsky Carolina C Varela Ana Inés AI Ventriglia Verónica V Sánchez Ávalos Julio César JC Larripa Irene I Zalcberg Ilana I Mordoh José J Valent Peter P Bianchini Michele M

Frontiers in pharmacology 20210111

Chronic myeloid leukemia (CML) is a myeloid stem cell neoplasm characterized by an expansion of myeloid progenitor cells and the presence of BCR-ABL1 oncoprotein. Since the introduction of specific BCR-ABL1 tyrosine kinase inhibitors (TKI), overall survival has improved significantly. However, under long-term therapy patients may have residual disease that originates from TKI-resistant leukemic stem cells (LSC). In this work, we analyzed the miRNome of LSC-enriched CD34+CD38-</su ...[more]

PMID: 33569005

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Project description:BACKGROUND: BCR-ABL1+ chronic myeloid leukemia (CML) is characterized by abnormal production of leukemic stem (LSC) and progenitor cells and their spread from the bone marrow into the blood resulting in extramedullary myeloproliferation. So far, little is known about specific markers and functions of LSC in CML. METHODS: We examined the phenotype and function of CD34+/CD38─/Lin─ CML LSC by a multi-parameter screen approach employing antibody-phenotyping, mRNA expression profiling, and functional studies, including LSC repopulation experiments in irradiated NOD-SCID-IL-2Rgamma-/- (NSG) mice, followed by marker-validation using diverse control-cohorts and follow-up samples of CML patients treated with imatinib. RESULTS: Of all LSC markers examined, dipeptidylpeptidase IV (DPPIV=CD26) was identified as specific and functionally relevant surface marker-enzyme on CD34+/CD38─ CML LSC. CD26 was not detected on normal CD34+/CD38─ stem cells or LSC in other hematopoietic malignancies. The percentage of CD26+ CML LSC decreased to undetectable levels during successful treatment with imatinib in all patients (p<0.001). Whereas the sorted CD26─ stem cells obtained from CML patients engrafted irradiated NSG mice with multilineage BCR-ABL1-negative hematopoiesis, CD26+ LSC engrafted NSG mice with BCR-ABL1+ cells. Functionally, CD26 was identified as target-enzyme disrupting the SDF-1alpha-CXCR4-axis by cleaving SDF-1alpha a chemotaxin for CXCR4+ stem cells. Whereas CD26 was found to inhibit SDF-1alpha-induced migration, CD26-targeting gliptins reverted this effect and blocked the mobilization of CML LSC in a stroma co-culture assay. CONCLUSIONS: CD26 is a robust biomarker of LSC and a useful tool for their quantification and isolation in patients with BCR/ABL1+ CML. Moreover, CD26 expression may explain the extramedullary spread of LSC in CML. To define specific mRNA expression patterns and to identify specific LSC markers in CML LSC, gene array analyses were performed. RNA was isolated from sorted CD34+/CD45+/CD38─ CML LSC, CD34+/CD45+/CD38+ CML progenitor cells, CML MNC, sorted CD34+/CD38─ cord blood (CB) SC, CB-derived CD34+/CD38+ progenitor cells, and CB MNC. Total RNA was extracted from sorted cells using RNeasy Micro-Kit (Qiagen) and used (100 ng total RNA) for Gene Chip analyses. Preparation of terminal-labeled cRNA, hybridization to genome-wide human PrimeView GeneChips (Affymetrix, Santa Clara, CA, USA) and scanning of arrays were carried out according to the manufacturer's protocols (https://www.affymetrix.com). Robust Multichip Average (RMA) signal extraction and normalization were performed according to http://www.bioconductor.org/ as described.18 Differences in mRNA expression levels (from multiple paired samples) were calculated as mRNA ratio of i) CML LSC versus CB SC, ii) CML LSC versus CD34+/CD38+ CML progenitors, and normal cord blood SC versus cord blood progenitors. To calculate differential gene expression between individual sample groups where appropriate, we performed a statistical comparison using the LIMMA package as described previously. Briefly, LIMMA estimates the fold change between predefined sample groups by fitting a linear model and using an empirical Bayes method to moderate the standard errors of the estimated log-fold changes for each probe set.

Dataset Information

MiRNome profiling of LSC-enriched CD34⁺CD38^-CD26⁺ fraction in Ph⁺ CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool.

Publications

miRNome profiling of LSC-enriched CD34<sup>+</sup>CD38<sup>-</sup>CD26<sup>+</sup> fraction in Ph<sup>+</sup> CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool.

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OmicsDI is part of the ELIXIR infrastructure

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Dataset Information

MiRNome profiling of LSC-enriched CD34+CD38-CD26+ fraction in Ph+ CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool.

Publications

miRNome profiling of LSC-enriched CD34<sup>+</sup>CD38<sup>-</sup>CD26<sup>+</sup> fraction in Ph<sup>+</sup> CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

MiRNome profiling of LSC-enriched CD34⁺CD38^-CD26⁺ fraction in Ph⁺ CML-CP samples from Argentinean patients: a potential new pharmacogenomic tool.