Comparative miRNA Expression Profiling of Circulating Exosomes From MGUS and Smoldering Multiple Myeloma Patients

Abstract Abstract 3975 Introduction. Exosomes are small vesicles (50–100 nm) of endocytic origin, which are released in the extra-cellular milieu by several cell types. It is known that cell-to-cell communication is partially mediated by exosomes. The role of exosomes has been shown in tumor progression, due to their ability to carry and transfer microRNAs (miRNAs) to the recipient cells. In this study, we sought to examine the role of circulating exosomes in modulating transition from a monoclonal gammopathy of undermined significance (MGUS) stage to a smoldering myeloma (SMM) stage. Method. Exosomes were collected from peripheral blood obtained from healthy individuals (n=4), MGUS patients (n=4) and SMM patients (n=4), using ultracentrifugation; and further studied by using electron microscopy and immunogold labeling for the detection of CD63 and CD81. miRNA profiling has been performed using nCounter miRNA expression assay (Nanostring® Technologies, Seattle WA). Bioinformatic software tools (TargetScan, MIRDB) were used to predict the target genes of identified miRNA and define their function. Results. Circulating exosomes were studied at ultrastructural level showing positivity for CD81 and CD63, as demonstrated by immunogold labeling and electron microscopy. We identified 16 miRNAs differentially expressed in circulating exosome obtained from MGUS patients compared to healthy subjects (p < 0.05): specifically, higher expression of miR-450a, -30e, -125a, -300 and lower expression of miR-185, -150, -98 were observed in MGUS- compared to heatly individual-derived circulating exosomes. Interestingly, miR-30e and -150 are important for modulation of NK cell activity by targeting perforin and c-Myb, respectively. We furthermore compared the miRNA expression profiling between MGUS and SMM circulating exosomes; and found 11 miRNAs differentially expressed (p < 0.05). Specifically, higher expression of miR-107 and lower expression of miR-28, -32, -548a, -939, -99a, -345, -125a, -587, -323b and -92a were observed in SMM- compared to MGUS-derived circulating exosomes. Among the de-regulated miRNAs, miR-99a, -345, -92a and -28 are known to act as tumor suppressors in prior publications. Moreover, predicted targets for miR-107 include genes involved in molding the bone marrow microenvironment. Indeed, miR-107 is known to decrease hypoxia-inducible factor-1 β (HIF-1β), miR-125a correlated with the expression level of matrix metalloproteinase 11 (MMP11), and vascular endothelial growth factor A (VEGF-A) and miR-548a regulates the expression of MMP2. Conclusion. These findings indicate that circulating exosomes differ between normal, MGUS and SMM patients, and could potentially be involved in modulating the host microenvironment for specific homing of clonal plasma cells to the bone marrow; thus providing a better understanding of the epigenetic changes responsible for the transition from an MGUS stage to a SMM stage. Disclosures: Ghobrial: Millennium: Advisory Board Other; Novartis: Advisory Board, Advisory Board Other.

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Identification of Differentially Expressed MicroRNAs in Osteosarcoma

Sarcoma ◽

10.1155/2011/732690 ◽

2011 ◽

Vol 2011 ◽

pp. 1-6 ◽

Cited By ~ 90

Author(s):

Rishi R. Lulla ◽

Fabricio F. Costa ◽

Jared M. Bischof ◽

Pauline M. Chou ◽

Maria de F. Bonaldo ◽

...

Keyword(s):

High Throughput ◽

Mirna Expression ◽

Expression Profiling ◽

Differentially Expressed ◽

Pcr Analysis ◽

Osteosarcoma Cell ◽

Human Osteoblasts ◽

Normal Human ◽

Mirna Expression Profiling

A limited number of reports have investigated the role of microRNAs in osteosarcoma. In this study, we performed miRNA expression profiling of osteosarcoma cell lines, tumor samples, and normal human osteoblasts. Twenty-two differentially expressed microRNAs were identified using high throughput real-time PCR analysis, and 4 (miR-135b, miR-150, miR-542-5p, and miR-652) were confirmed and validated in a different group of tumors. Both miR-135b and miR-150 have been previously shown to be important in cancer. We hypothesize that dysregulation of differentially expressed microRNAs may contribute to tumorigenesis. They might also represent molecular biomarkers or targets for drug development in osteosarcoma.

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Mirna Expression Profiling and Proteomic Analysis Of Circulating Exosomes From Multiple Myeloma Patients

Blood ◽

10.1182/blood.v122.21.3086.3086 ◽

2013 ◽

Vol 122 (21) ◽

pp. 3086-3086

Author(s):

Salomon Manier ◽

Erica N Boswell ◽

Siobhan Glavey ◽

Antonio Sacco ◽

Patricia Maiso ◽

...

Keyword(s):

Electron Microscopy ◽

Mass Spectrometry ◽

Multiple Myeloma ◽

Mirna Expression ◽

Proteomic Analysis ◽

Research Funding ◽

Advisory Board ◽

Immunogold Labeling ◽

Healthy Donors ◽

Lower Expression

Abstract Introduction Exosomes are small vesicles (50-100 nm) of endocytic origin, which are released in the extra-cellular milieu by several cell types. It is known that cell-to-cell communication is partially mediated by exosomes. Exosomes play a role in tumor progression where they have been shown to carry and transfer microRNAs (miRNAs) and proteins to the recipient cells. In this study, we sought to characterize circulating exosomes in terms of their ability to modulate the microenvironment, leading to Multiple Myeloma (MM) progression. Method Exosomes were collected from peripheral blood obtained from healthy individuals (n=5), MGUS patients (n=5) and MM patients (n=10), using ultracentrifugation. Further characterization was carried out using electron microscopy and immunogold labeling for the detection of CD63 and CD81 and for the size using Nanosight® analysis. MiRNA were isolated using miRNeasy mini kit (Qiagen®) and profiling has been performed using nCounter miRNA expression assay (Nanostring® Technologies, Seattle WA). Bioinformatic software tools (TargetScan, MIRDB) were used to predict the target genes of identified miRNA to define their function. Proteins were isolated from exosomes following lysis and precipitated by acetone before in-solution trypsin digestion and ZipTip® purification. Proteomic analysis was performed using mass spectrometry (BIDMC Mass Spectrometry, ObiTrap Elite®). Spectral count numbers were determined with a false discovery rate (FDR) less than 0.5%. Results Circulating exosomes were studied at ultrastructural level showing positivity for CD81 and CD63, as demonstrated by immunogold labeling and electron microscopy. Exosome number and size did not differ based on clinical stage on Nanosight® analysis. We identified 16 miRNAs differentially expressed in circulating exosomes obtained from MGUS patients compared to healthy subjects (FC >2 or <-2; p<0.05): specifically, higher expression of miR-450a, -30e, -125a, -300 and lower expression of miR-185, -150, -98 were observed in MGUS- compared to healthy individual-derived circulating exosomes. Interestingly, miR-30e and -150 modulate NK cell activity by targeting perforin and c-Myb, respectively. We found 96 miRNAs differentially expressed in circulating exosomes from MM patients as compared to healthy donors: specifically lower expression of Let-7 family members, miR-150, -15a and higher expression of miR-125b, -144 and -363 were observed. Interestingly, miR-15a is involved in angiogenesis regulating VEGFA and FGF2. Let-7 family members are tumor suppressors targeting k-Ras and c-Myc and miR-150 regulates CXCR-4 expression. Moreover, these patterns have been described in MM cells suggesting that circulating exosomes in MM are mainly released from MM cells and could play a role in modulating the tumor micro-environment. The mass spectrometry analysis was performed on protein derived from circulating exosomes from 5 healthy donors, 5 MGUS and 10 MM patients. 272 proteins were identified in circulating exosomes including proteins highly associated with exosomes such as CD9, HSP70, Rab proteins (Rab7a; Rab5; Rab27b) and annexins. Comparing MM exosomal proteins to healthy donor exosomal proteins, we found significantly distinctive peptide counts for fibronectin (FC=3.5; p=0.002), AMBP protein (FC=3; p=0.001) and Ig gamma-1 chain C region (FC=2.5; p=0.006). Interestingly, fibronectin expression level in the microenvironment has been reported to be associated with tumor proliferation and drug resistance in MM. Conclusion These findings indicate that circulating exosomes differ between normal, MGUS and MM patients in terms of miRNA and protein content. Circulating exosomes could potentially be involved in modulating the host microenvironment for specific homing of clonal plasma cells to the bone marrow; thus providing a better understanding of the epigenetic changes responsible for the transition to MM stage. Disclosures: Leleu: CELGENE: Honoraria; JANSSEN: Honoraria. Ghobrial:Onyx: Advisoryboard Other; BMS: Advisory board, Advisory board Other, Research Funding; Noxxon: Research Funding; Sanofi: Research Funding.

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Serum microRNA Expression Profiling in Malaria Patients and Bioinformatic Analysis of Hsa-miR-106b-5p

10.21203/rs.3.rs-680474/v1 ◽

2021 ◽

Author(s):

Jiacong Peng ◽

Xiaohong Peng ◽

Ying Wang ◽

Liping Jiang ◽

Dayu Li ◽

...

Keyword(s):

Signal Transduction ◽

Mirna Expression ◽

Expression Profiling ◽

Target Genes ◽

Small Gtpase ◽

Differentially Expressed ◽

Ppi Network ◽

Kegg Analysis ◽

Significant Difference ◽

Mirna Expression Profiling

Abstract BackgroundMalaria, caused by Plasmodium, is one of the three major infectious diseases that seriously endangers public health. Resistance to anti-malarial drugs and insecticides has made the prevention and control of malaria shown little improvement in the last four years. This study aimed to explore the changes in microRNA (miRNA) expression profiling of malaria patient and predict malaria-related miRNA by bioinformatics methods to provide theoretical basis for further verification of the correlation between specific miRNAs and immune regulation of malaria.MethodsSerum of patients infected by Plasmodium falciparum and healthy people from Myanmar border area was collected. miRNA expression profiling was obtained by RT-qPCR. Then the differentially expressed miRNA was screened and target genes were predicted by four miRNA databases (TargetScan, DIANA-microT, miRDB, and miRTarbase) and an intersection of target genes was obtained by Venn analysis. GO and KEGG analysis were performed for the overlapping target genes via Metascape. The results were further visualized by Cytoscape. Finally, Protein-protein interaction (PPI) network of predicted overlapping target genes was built by STRING.ResultsAmong the 341 tested serum miRNAs, 64 were differentially expressed in malaria patients (P<0.05), 27 miRNAs were up-regulated and 37 miRNAs were down-regulated. The miRNA with the most significant difference was hsa-miR-106b-5p (FC=14.871, adjusted.P.value<0.01); GO and KEGG analysis found that its overlapping predicted target gene set was remarkably enriched in biological functions such as GO:0007264~small GTPase mediated signal transduction, GO:0051056~regulation of small GTPase mediated signal transduction, GO:0051020~GTPase binding, GO:0048514~blood vessel morphogenesis(P<0.01) and signal pathway such as hsa04144: Endocytosis, hsa01521:EGFR tyrosine kinase inhibitor resistance, hsa05212:Pancreatic cancer (P<0.01); Besides, a PPI network containing 39 predicted target genes of hsa-miR-106b-5p was constructed, and 5 hub genes VEGFA, STAT3, RACGAP1, OCRL, and RBBP7 have been selected.ConclusionThe bioinformatics analysis results indicated that hsa-miR-106b-5p has a great relationship with malaria, it plays a part in inhibiting the emergence of ARTs resistance in Plasmodium and tumor progression, which may be achieved by regulating vascular morphogenesis, endocytosis, and VEGFA. The underlying mechanism needs to be further elucidated. We believe that this finding will facilitate an in-depth research on the association between malaria and miRNA.

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miRNA expression profiling uncovers a role of miR‐302b‐3p in regulating skin fibroblasts senescence

Journal of Cellular Biochemistry ◽

10.1002/jcb.28862 ◽

2019 ◽

Vol 121 (1) ◽

pp. 70-80 ◽

Cited By ~ 3

Author(s):

Jingyong Tan ◽

Longyuan Hu ◽

Xin Yang ◽

Xin Zhang ◽

Canshen Wei ◽

...

Keyword(s):

Mirna Expression ◽

Expression Profiling ◽

Skin Fibroblasts ◽

Mirna Expression Profiling

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miRNA Expression Profiling in Mesenchymal Stromal/Stem Cells Derived from G-CSF Primed Bone Marrows

Blood ◽

10.1182/blood.v124.21.5140.5140 ◽

2014 ◽

Vol 124 (21) ◽

pp. 5140-5140

Author(s):

Aysen Gunel-Ozcan ◽

Ilgin Cagnan ◽

Emin Kansu ◽

Duygu Uckan

Keyword(s):

Stem Cells ◽

Bone Marrow ◽

Mirna Expression ◽

Expression Profiling ◽

Conflicts Of Interest ◽

Hematopoietic Stem ◽

Molecular Control ◽

Healthy Donors ◽

Mirna Expression Profiling ◽

Stromal Stem Cells

Abstract Regulatory microRNAs (miRNAs) are involved in the molecular control of hematopoiesis and diseases that result from aberrations during this process. Bone marrow (BM) transplantation is a commonly used therapy for patients with certain hematopoietic diseases. Prior to BM transplantation, donors are occasionally treated with granulocyte colony-stimulating factor (G-CSF) to increase the number of hematopoietic stem or progenitor cells in the collected stem cell product. Here we aimed to assess the effects of G-CSF priming on miRNA expression of BM derived mesenchymal stromal/stem cells (BM-MSCs) from healthy donors. Previously isolated and characterized BM-MSCs from 3 days G-CSF (10 μg/kg/d) treated (n=5) and untreated (n=8) healthy donors were used for miRNA expression profiling with Affymetrix GeneChip 2.0 Array. Following Robust Multi-array Average (RMA) normalization, data analysis was carried out in Partek Genomics Suite software package (Partek Incorporated). Differentially expressed miRNAs between G-CSF primed and unprimed groups were determined (p<0.05, fold change ±1.5). A total of 2156 miRNAs were upregulated whereas 2436 miRNAs were downregulated after in-vivo G-CSF priming. The expression of hp_hsa-mir-1238 and has-miR-3180-3p non-coding RNAs was significantly increased in G-CSF primed BM-MSCs (p<0.001). Modular enrichment analysis of hsa-miR-3180-3p predicted target genes by GeneCodis 3 software revealed that some may play a role in different types of cancer such as small cell lung cancer (Adjusted p-value: 8.47338e-7, 0.000382029). Our data indicate that G-CSF treatment changes miRNA expression of bone marrow stromal cells (MSCs) and this change might be important to evaluate for long-term biosafety. Disclosures No relevant conflicts of interest to declare.

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Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

Current Bioinformatics ◽

10.2174/1574893615999200508091615 ◽

2020 ◽

Vol 15 ◽

Author(s):

Na Wang ◽

Yukun Li ◽

Sijing Liu ◽

Liu Gao ◽

Chang Liu ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Bioinformatics Analysis ◽

Differentially Expressed ◽

Functional Study ◽

Regulation Network ◽

Glucagon Like Peptide 1 ◽

G Protein Coupled ◽

Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

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Identification of novel MiRNAs and MiRNA expression profiling during grain development in indica rice

BMC Genomics ◽

10.1186/1471-2164-13-264 ◽

2012 ◽

Vol 13 (1) ◽

pp. 264 ◽

Cited By ~ 49

Author(s):

Ying Lan ◽

Ning Su ◽

Yi Shen ◽

Rongzhi Zhang ◽

Fuqing Wu ◽

...

Keyword(s):

Mirna Expression ◽

Expression Profiling ◽

Indica Rice ◽

Grain Development ◽

Mirna Expression Profiling

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Left-Sided Colorectal Cancer Distinct in Indigenous African Patients Compared to Other Ethnic Groups in South Africa.

10.21203/rs.3.rs-845611/v1 ◽

2021 ◽

Author(s):

M. McCabe ◽

C. Penny ◽

P. Magangane ◽

S. Mirza ◽

Y. Perner

Keyword(s):

Colorectal Cancer ◽

South Africa ◽

Ethnic Groups ◽

Mirna Expression ◽

Expression Profiling ◽

Expression Patterns ◽

Molecular Characteristics ◽

Anatomical Site ◽

Molecular Features ◽

Mirna Expression Profiling

Abstract Introduction: A large proportion of indigenous African (IA) colorectal cancer (CRC) patients in South Africa are young (<50years), with no unique histopathological or molecular characteristics. Anatomical site as well as microsatellite instability (MSI) status have shown to be associated with different clinicopathological and molecular features. This study aimed to ascertain key histopathological and miRNA expression patterns in microsatellite stable (MSS) and low-frequency MSI (MSI-L) patients, to provide insight into the mechanism of the disease. Methods: A retrospective cohort (2011-2015) of MSS/MSI-L CRC patient samples diagnosed at Charlotte Maxeke Johannesburg Academic Hospital was analyzed. Samples were categorized by site [Right colon cancer (RCC) versus left (LCC)], ethnicity [IA versus other ethnic groups (OEG)] and MSI status (MSI-L vs MSS). T-test, Fischer’s exact and Chi-square tests were conducted. Additional miRNA expression profiling was performed on IA patient samples. Results: IA patients with LCC demonstrated an increased prevalence in males, sigmoid colon, signet-ring-cell morphology, MSI-L with BAT25/26 marker instability and advanced disease association. MiRNA expression profiling revealed unique clustering, with dysregulation of let-7 and miRNA-125. Conclusion: This study revealed distinct histopathological features for LCC, and suggests BAT25/26, miRNAs let-7a-5p and miRNA-125a/b-5p as negative prognostic markers in African CRC patients. Larger confirmatory studies are recommended.

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