Circulating Small Noncoding RNAs Have Specific Expression Patterns in Plasma and Extracellular Vesicles in Myelodysplastic Syndromes and Are Predictive of Patient Outcome

Abstract

Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders with large heterogeneity at the clinical and molecular levels. As diagnostic procedures shift from bone marrow biopsies towards less invasive techniques, circulating small noncoding RNAs (sncRNAs) have become of particular interest as potential novel noninvasive biomarkers of the disease. We aimed to characterize the expression profiles of circulating sncRNAs of MDS patients and to search for specific RNAs applicable as potential biomarkers. We performed small RNA-seq in paired samples of total plasma and plasma-derived extracellular vesicles (EVs) obtained from 42 patients and 17 healthy controls and analyzed the data with respect to the stage of the disease, patient survival, response to azacitidine, mutational status, and RNA editing. Significantly higher amounts of RNA material and a striking imbalance in RNA content between plasma and EVs (more than 400 significantly deregulated sncRNAs) were found in MDS patients compared to healthy controls. Moreover, the RNA content of EV cargo was more homogeneous than that of total plasma, and different RNAs were deregulated in these two types of material. Differential expression analyses identified that many hematopoiesis-related miRNAs (e.g., miR-34a, miR-125a, and miR-150) were significantly increased in MDS and that miRNAs clustered on 14q32 were specifically increased in early MDS. Only low numbers of circulating sncRNAs were significantly associated with somatic mutations in the SF3B1 or DNMT3A genes. Survival analysis defined a signature of four sncRNAs (miR-1237-3p, U33, hsa_piR_019420, and miR-548av-5p measured in EVs) as the most significantly associated with overall survival (HR = 5.866, p < 0.001). In total plasma, we identified five circulating miRNAs (miR-423-5p, miR-126-3p, miR-151a-3p, miR-125a-5p, and miR-199a-3p) whose combined expression levels could predict the response to azacitidine treatment. In conclusion, our data demonstrate that circulating sncRNAs show specific patterns in MDS and that their expression changes during disease progression, providing a rationale for the potential clinical usefulness of circulating sncRNAs in MDS prognosis. However, monitoring sncRNA levels in total plasma or in the EV fraction does not reflect one another, instead, they seem to represent distinctive snapshots of the disease and the data should be interpreted circumspectly with respect to the type of material analyzed.

Expression, Regulation and Function of microRNA as Important Players in the Transition of MDS to Secondary AML and Their Cross Talk to RNA-Binding Proteins

“…This is partially due to the methodical differences and the source of material profiled for miRNA expression as studies included analysis on MDS blasts, bone marrow aspirates with and without stroma cells, peripheral blood specimen plasma, and extracellular microvesicles (MV). Recently, it has been shown that the RNA content of the EV cargo was more homogeneous when compared to total plasma which comprised a different set of deregulated miRNAs [ 84 ]. Even upon sorting of BM cells for the stem cell marker CD34, the CD34 + cell population is still heterogeneous, since immune cells committed in their early developmental phase to a particular lineage and endothelial cells also express CD34 [ 85 ].…”

“…Using this approach, a higher miRNA content in MV of MDS patients compared to healthy controls was found [ 93 ] suggesting that the miRNA cargo of circulating MVs may contribute to the pathophysiology of this disease. Furthermore, the miRNA content differs between total plasma and EVs in MDS versus healthy controls [ 84 ].…”

“…In detail a double knockout of the two miR-15/-16 loci in mice caused the development of AML [ 104 ]. These results could be directly translated into humans, since BM probes from patients with MDS transforming into sAML or from patients with sAML expressed lower levels of both miRNAs when compared to corresponding samples from MDS patients [ 84 , 105 ].…”

The altered transcriptome of pediatric myelodysplastic syndrome revealed by RNA sequencing

“…MDSs are a heterogeneous group of clonal hematopoietic neoplasms. Although recent studies have shown that MDS and AML patients had different gene mutation patterns [1][2][3][4], the molecular underpinnings remain unknown [5][6][7][8][9][10]. To identify DEGs related to the PMDS, we performed RNA-seq in 4 patients with primary PMDS and in 2 control pediatric samples (Additional file 1: Figures S1A-B).…”

The miRNA Profile in Non-Hodgkin’s Lymphoma Patients with Secondary Myelodysplasia

“…MicroRNAs are important regulators of the differentiation and development of HSCs, and so their aberrant expression promote the development of both myeloid and lymphoid neoplasms [9]. The number of many hematopoiesis-associated miRNAs was substantially increased in the extracellular vesicles in MDS plasma [11]. In turn, miRNAs can be transported by exosomes and influence gene expression in BM cells.…”