Classification of pediatric acute myeloid leukemia based on miRNA expression profiles

MiRNA expression as outcome predictor in pediatric AML: systematic evaluation of a new model

Accurately predicting patient outcomes is essential for optimizing treatment and improving outcomes in pediatric acute myeloid leukemia (AML). In recent years, microRNAs have emerged as a promising prognostic marker, with a growing body of evidence supporting their potential predictive value. We systematically reviewed all previous studies that have analyzed the expression of microRNAs as predictors of survival in pediatric AML and found 16 microRNAs and 4 microRNA signatures previously proposed as predictors of survival. We then used a public access cohort of 1414 pediatric AML patients from the TARGET project to develop a new predictive model using penalized lasso Cox regression based on microRNA expression. Here we propose a new score based on a 37-microRNA signature that is associated with AML and is able to predict survival more accurately than previous microRNA-based methods.

Identification of Circular RNA Circ_0003256 as a Novel Player in Pediatric Acute Myeloid Leukemia

BACKGROUND

Aberrant expression of circular RNAs (circRNAs) is tightly associated with the pathogenesis of human cancers, including pediatric acute myeloid leukemia (AML). In this report, we sought to define the precise action of circ_0003256 in the pathogenesis of pediatric AML.

MATERIALS AND METHODS

Circ_0003256, microRNA (miR)-582-3p, and protein kinase cAMP-activated catalytic subunit beta (PRKACB) were quantified by quantitative real-time polymerase chain reaction and Western blot. Cell proliferation, cycle distribution, and apoptosis were estimated by MTT, 5-ethynyl-2'-deoxyuridine, and flow cytometry assays, respectively. Direct relationships among circ_0003256, miR-582-3p, and PRKACB were verified by a dual-luciferase reporter and RNA pull-down assays.

RESULTS

Our data indicated that circ_0003256 was highly expressed in pediatric AML patients and cells. Suppression of circ_0003256 hindered cell proliferation and promoted apoptosis in THP-1 and MV4-11 cells. Mechanistically, circ_0003256 contained functional binding sites for miR-582-3p, and circ_0003256 suppression influenced cell behaviors by upregulating miR-582-3p. MiR-582-3p directly targeted and inhibited PRKACB and the inhibition of PRKACB phenocopied miR-582-3p overexpression in regulating cell functional behaviors. Moreover, circ_0003256 involved the posttranscriptional regulation of PRKACB through miR-582-3p.

CONCLUSION

Our findings identify that suppression of circ_0003256 impedes the malignant behaviors of pediatric AML cells by regulating PRKACB expression by competing for shared miR-582-3p.

Exploration of differentially expressed mRNAs and miRNAs for pediatric acute myeloid leukemia

Background: To establish a comprehensive differential gene profile for pediatric acute myeloid leukemia patients (pAML) based on two independent databases and verify the differentially expressed genes using in vitro and in vivo analyses.

Methods: The mRNA and miRNA sequencing information of GSE2191 and GSE35320, clinically recruited pAML individuals, and human AML cell line (NB4 cells) were utilized in the study.

Results: Compared with the control sample, pAML patients demonstrated a total of 778 differentially expressed genes, including 565 upregulated genes and 213 downregulated genes. The genes including ZC3H15, BCLAF1, PPIG, DNTTIP2, SRSF11, KTN1, UBE3A, PRPF40A, TMED5, and GNL2 were the top 10 potential hub genes. At the same time, 12 miRNAs demonstrated remarkable differential expressions in pAML individuals compared with control individuals, as five upregulated and seven downregulated miRNAs. The hsa-miR-133, hsa-miR-181, and hsa-miR-195 were significantly downregulated. Building a miRNA–mRNA regulatory network, hsa-miR-133 regulated ZC3H15, BCLAF1, SRSF11, KTN1, PRPF40A, and GNL2. Using the NB4 cell model, hsa-miR-133 treatment inhibited cell proliferation capacity, which could be attenuated by a single mRNA transfection or a combination of ZC3H15 and BCLAF1. At the same time, hsa-miR-133 mimic treatment could significantly accelerate cell apoptosis in NB4 cells, which was also ZC3H15- and BCLAF1-dependent. The concentrations of ZC3H15 and BCLAF1 were investigated in peripheral blood using the ELISA method for the clinical control and pAML samples. In pAML samples, the expression levels of ZC3H15 and BCLAF1 were significantly enhanced (p < 0.01), regardless of the classification.

Conclusion: Collectively, this study hypothesized several promising candidates for pAML formation.

miR-144-3p Derived from Bone Marrow Mesenchymal Stem Cells (BMSCs) Restrains the Drug Resistance of Acute Myeloid Leukemia (AML)

This study assessed whether miR-144-3p derived from BMSCs restrains the drug resistance of AML. Our study intends to assess miR-144-3p’s role in AML drug resistance. Drug resistance AML cells were transfected with miR-144-3p mimic or NC followed by measuring miR-144-3p level, relation of miR-144-3p with Wnt, cell activity and apoptosis by flow cytometry and the expression of signal proteins by Western Blot. The action of miR-144-3p in inducting drug resistance of K562/AND was more effective. Cell apoptosis and proliferative index was increased by overexpression of miR-144-3p along with significantly down regulated Wnt. In conclusion, the malignant invasion of AML with drug resistance is increased by miR-144-3p derived from BMSCs through regulating the Wnt/β-catenin signal, indicating that miT-144-3p might be a new target for the treatment of AML.

Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures

Background

Accurate cancer classification is essential for correct treatment selection and better prognostication. microRNAs (miRNAs) are small RNA molecules that negatively regulate gene expression, and their dyresgulation is a common disease mechanism in many cancers. Through a clearer understanding of miRNA dysregulation in cancer, improved mechanistic knowledge and better treatments can be sought.

Results

We present a topology-preserving deep learning framework to study miRNA dysregulation in cancer. Our study comprises miRNA expression profiles from 3685 cancer and non-cancer tissue samples and hierarchical annotations on organ and neoplasticity status. Using unsupervised learning, a two-dimensional topological map is trained to cluster similar tissue samples. Labelled samples are used after training to identify clustering accuracy in terms of tissue-of-origin and neoplasticity status. In addition, an approach using activation gradients is developed to determine the attention of the networks to miRNAs that drive the clustering. Using this deep learning framework, we classify the neoplasticity status of held-out test samples with an accuracy of 91.07%, the tissue-of-origin with 86.36%, and combined neoplasticity status and tissue-of-origin with an accuracy of 84.28%. The topological maps display the ability of miRNAs to recognize tissue types and neoplasticity status. Importantly, when our approach identifies samples that do not cluster well with their respective classes, activation gradients provide further insight in cancer subtypes or grades.

Conclusions

An unsupervised deep learning approach is developed for cancer classification and interpretation. This work provides an intuitive approach for understanding molecular properties of cancer and has significant potential for cancer classification and treatment selection.

miRNAs mediated drug resistance in hematological malignancies

Despite improvements in the therapeutic approaches for hematological malignancies in the last decades, refractory disease still occurs, and cancer drug resistance still remains a major hurdle in the clinical management of these cancer patients. The investigation of this problem has been extensive and different mechanism and molecules have been associated with drug resistance. MicroRNAs (miRNAs) have been described as having an important action in the emergence of cancer, including hematological tumors, and as being major players in their progression, aggressiveness and response to treatments. Moreover, miRNAs have been strongly associated with cancer drug resistance and with the modulation of the sensitivity of cancer cells to a wide array of anticancer drugs. Furthermore, this role has also been reported for miRNAs packaged into extracellular vesicles (EVs-miRNAs), which in turn have been described as essential for the horizontal transfer of drug resistance to sensitive cells. Several studies have been suggesting the use of miRNAs as biomarkers for drug response and clinical outcome prediction, as well as promising therapeutic tools in hematological diseases. Indeed, the combination of miRNA-based therapeutic tools with conventional drugs contributes to overcome drug resistance. This review addresses the role of miRNAs in the pathogenesis of hematological malignances, namely multiple myeloma, leukemias and lymphomas, highlighting their important action (either in their cell-free circulating form or within circulating EVs) in drug resistance and their potential clinical applications.

MiRNA Dysregulation in Childhood Hematological Cancer

For decades, cancer biology focused largely on the protein-encoding genes that have clear roles in tumor development or progression: cell-cycle control, apoptotic evasion, genome instability, drug resistance, or signaling pathways that stimulate growth, angiogenesis, or metastasis. MicroRNAs (miRNAs), however, represent one of the more abundant classes of cell modulators in multicellular organisms and largely contribute to regulating gene expression. Many of the ~2500 miRNAs discovered to date in humans regulate vital biological processes, and their aberrant expression results in pathological and malignant outcomes. In this review, we highlight what has been learned about the roles of miRNAs in some of the most common human pediatric leukemias and lymphomas, along with their value as diagnostic/prognostic factors.

MicroRNA-155 expression and function in AML: An evolving paradigm

Acute myeloid leukemia (AML) arises when immature myeloid blast cells acquire multiple, recurrent genetic and epigenetic changes that result in dysregulated proliferation. Acute leukemia is the most common form of pediatric cancer, with AML accounting for ~20% of all leukemias in children. The genomic aberrations that drive AML inhibit myeloid differentiation and activate signal transduction pathways that drive proliferation. MicroRNAs, a class of small (~22 nucleotide) noncoding RNAs that posttranscriptionally suppress the expression of specifically targeted transcripts, are also frequently dysregulated in AML, which may prove useful for the purposes of disease classification, prognosis, and future therapeutic approaches. MicroRNA expression profiles are associated with patient prognosis and responses to standard chemotherapy, including predicting therapy resistance in AML. miR-155 is the primary focus of this review because it has been repeatedly associated with poorer survival across multiple cohorts of adult and pediatric AML. We discuss some novel features of miR-155 expression in AML, in particular how the levels of expression can critically influence function. Understanding the role of microRNAs in AML and the ways in which microRNA expression influences AML biology is one means to develop novel and more targeted therapies.