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Omics Analysis of Pancreatic Cancer Platelets Reveals Active “Education”, including Dysregulation of Splicing Signature and Inhibition of SPARC by Modified Forms of miRNAs

ABSTRACT: PDAC cells can activate platelets and change their RNA and protein content, thus, we performed an integrative study investigating the biological processes of differentially spliced mRNAs and expressed miRNAs, as well as proteins. To focus on these “dangerous liaisons”, we used benign disease as a background noise correction for putative inflammatory signals. Gene set enrichment analysis on differential miRNAs, RNA transcripts and proteins revealed an enrichment of RNA splicing, mRNA processing and translation initiation on miRNAs and proteins and depletion on RNA transcripts, as previously described. Furthermore, we provide a new repertoire of PDAC and benign platelet-ome, visualized by the R shiny application, to be exploited for future studies. In conclusion, our data show that platelets change their biological repertoire in the presence of PDAC, through dysregulation of miRNAs and splicing factors, supporting the presence of de novo protein machinery that can “educate” the platelet. This has major clinical implications since the emerging molecules could provide important innovative PDAC biomarkers in the context of liquid biopsies.

ORGANISM(S): Homo sapiens

PROVIDER: GSE160252 | GEO | 2021/01/19

REPOSITORIES: GEO

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Omics Analysis of Pancreatic Cancer Platelets Reveals Active “Education”, including Dysregulation of Splicing Signature and Inhibition of SPARC by Modified Forms of miRNAs

Project description:Pancreatic ductal adenocarcinoma (PDAC) is associated with hypercoagulation, but molecular mechanisms underlying PDAC/platelets interaction remain controversial. PDAC cells can activate platelets and change their RNA and protein content, thus, we performed an integrative study investigating the biological processes of differentially spliced mRNAs and expressed miRNAs, as well as proteins. To focus on these “dangerous liaisons”, we used benign disease as a background noise correction for putative inflammatory signals. Gene set enrichment analysis on differential miRNAs, RNA transcripts and proteins revealed an enrichment of RNA splicing, mRNA processing and translation initiation on miRNAs and proteins and depletion on RNA transcripts, as previously described. Moreover, correlation analyses revealed a specific regulation on SPARC RNA transcripts by isomiRs involved in cancer signaling, suggesting a specific modulation/”education” in PDAC platelets. We identified HBA1, HBD, CA1 and AGT as protein markers in PDAC platelets. In conclusion, our data show that platelets change their biological repertoire in the presence of PDAC, through dysregulation of miRNAs and splicing factors, supporting the presence of a clear de novo protein machinery that can “educate” the platelet.

2021-09-09 | PXD022514 | Pride

Platelet microRNA-mRNA Co-Expression Profiles Correlate with Platelet Reactivity

Project description:MicroRNAs (miRNAs) regulate cell physiology by altering protein expression, but the biology of platelet miRNAs is largely unexplored. We tested whether platelet miRNA levels were associated with platelet reactivity by genome-wide profiling using platelet RNA from 19 healthy subjects. We found that human platelets express 284 miRNAs. Unsupervised hierarchical clustering of miRNA profiles resulted in 2 groups of subjects that appeared to cluster by platelet aggregation phenotypes. Seventy-four miRNAs were differentially expressed (DE) between subjects grouped according to platelet aggregation to epinephrine, a subset of which predicted the platelet reactivity response. Using whole genome mRNA expression data on these same subjects, we computationally generated a high-priority list of miRNA-mRNA pairs in which the DE platelet miRNAs had binding sites in 3'UTRs of DE mRNAs, and the levels were negatively correlated. Three miRNA-mRNA pairs (miR-200b:PRKAR2B, miR-495:KLHL5 and miR-107:CLOCK) were selected from this list and all 3 miRNAs knocked down protein expression from the target mRNA. Reduced activation from platelets lacking PRKAR2B supported these findings. In summary, (1) platelet miRNAs are able to repress expression of platelet proteins, (2) miRNA profiles are associated with and may predict platelet reactivity, and (3) bioinformatic approaches can successfully identify functional miRNAs in platelets. Total RNA from the platelets of 19 donors was harvested and labeled with Hy3. Reference RNA (a pool of all samples) was labeled with Hy5. This submission represents the miRNA expression component of the study.

2011-09-26 | E-GEOD-27917 | biostudies-arrayexpress

Platelet-secreted microRNA-223 promotes endothelial cell apoptosis induced by advanced glycation end products via targeting the insulin-like growth factor 1 receptor

Project description:Platelets contain abundant miRNAs, however, the biogenesis pathway of miRNAs in anucleate platelets is unclear. Platelet-rich plasma was diluted in washing buffer and the platelet suspension was centrifuged to isolated pure platelets.Finally, platelets were recovered in suspension buffer at the concentration of 4–5×10^8 platelets/ml. Aliquots of the platelet suspensions were activated in the presence of 2.5 mM CaCl2 with 0ng/ml or 1 ng/ml thrombopoietin (TPO)

2014-02-04 | E-GEOD-51453 | biostudies-arrayexpress

Platelet microRNA-mRNA Co-Expression Profiles Correlate with Platelet Reactivity

2011-09-27 | GSE27917 | GEO

Small RNA Sequencing of Different Blood Compartments

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2022-04-12 | GSE200251 | GEO

Platelet microRNA expression profiles of acute coronary syndrome patients with high and low platelet reactivity

Project description:To explore the diverse platelet microRNA (miRNA) expression between high platelet reactivity (HPR) and low platelet reactivity (LPR) patients with acute coronary syndromes (ACS), we enrolled a cohort of ACS patients and performed miRNA expression profiling of platelets from four HPR and four LPR patients using human miRNA microarray system. VerifyNow P2Y12 assay was applied to indentify HPR and LPR. Venous blood was drawn from the patients and was centrifuged to prepare platelets. Among the candidate differentially expressed miRNAs, miR-15b expression was further confirmed to be lower in platelets of 22 HPR patients than 17 LPR by quantitative reverse-transcription polymerase chain reaction (RT-qPCR). We enrolled a consecutive cohort of 290 ACS patients and assessed the platelet reactivity using VerifyNow P2Y12 assay. In this study, HPR was defined as M-bM-^IM-%300 platelet reactivity unit (PRU) while LPR <170 PRU. miRNA microarray analysis was performed in platelets of four HPR and four LPR patients with ACS.

2014-07-17 | E-GEOD-59488 | biostudies-arrayexpress

Platelet miRNA expression from patients of PDAC and healthy donors

Project description:Platelets can change their expression of mRNA and miRNAs when educated by tumors. In this assay we assesed the diferential expression of miRNA between healthy individuals and patients suffering pancreatic cancer (PDAC) Platelets form 4 healthy donors, 4 PDAC patient blood and 4 PDAC patient pancreatic drainage were collected to asses differential expression

2022-05-17 | GSE203122 | GEO

Platelet micro-RNA expression in type 2 diabetes mellitus

Project description:Results Platelets in non-diabetic patients demonstrated miRNA expression profiles comparable to previously published data. The miRNA expression profiles of platelets in diabetics were similar. Statistical analysis unveiled only three miRNAs (miR-377-5p, miR-628-3p, miR-3137) with high reselection probabilities in resampling techniques, corresponding to signatures with only modest discriminatory performance. Functional annotation of predicted targets for these miRNAs pointed towards an influence of diabetes mellitus on mRNA processing. Conclusions/interpretation We did not find any major differences in platelet miRNA profiles between diabetics and non-diabetics. Minor differences pertained to miRNAs associated with mRNA processing. Thus, previously described differences in plasma miRNAs between diabetic and nondiabetic patients cannot be explained by plain changes in the platelet miRNA profile. Platelet miRNA profiles were assessed in clinically stable diabetic and nondiabetic patients (each n=30). Platelet miRNA was isolated from leucocyte-depleted platelet-rich plasma, and miRNA profiling was performed using LNA micro-array technology (miRBase 18.0, containing 1,917 human miRNAs). Effects of diabetes mellitus were explored by univariate statistical tests for each miRNA, adjusted for potential confounders, and by developing a multivariable signature, which was evaluated by resampling techniques. Platelet phenotype was assessed by light transmission aggregometry and impedance aggregometry.

2014-03-14 | E-GEOD-44093 | biostudies-arrayexpress

Thrombin-reduced miR-27b attenuates platelet angiogenic activities via enhancing platelet de novo synthesis of anti-angiogenic thrombospondin-1

Project description:To identify if platelet activation would result in altered platelet miRNA profile, not only in total RNA sample, also in AGO2-immunoprecipitation(AGO2-IP) products. To determinate if altered platelet miRNAs could regulate de novo protein synthesis of angiogenic factors in activated platelets, and even more importantly, if miRNA-regulated platelet angiogenic factor synthesis could result in changes of platelet angiogenic activities.

2017-03-14 | GSE96533 | GEO

Murine platelet miRNA pattern and its regulation by a MK/platelet-specific genetic ablation of Dicer.

Project description:Purpose: To assess the platelet miRNA pattern which is regulated in a Dicer-dependent manner, we conducted a global screen of platelet miRNA expression of murine platelets from Dicerlox/lox and DicerPf4∆/Pf4∆ mice using Next-generation deep sequencing analysis. Methods: Platelets were isolated from 10- to 12-week-old Dicerlox/lox and DicerPf4Δ/Pf4Δ mice of male sex. Total RNA including miRNA was isolated from murine platelets using the QIAsymphony RNA Kit. The sequencing library was prepared using the QIAseq miRNA Library Kit with 10 to 20 ng input. The libraries were pooled in an equimolar fashion and sequenced on a NovaSeq6000 as paired-end reads with a sequencing depth of >12 Mio clusters (i.e. read-pairs) per sample. Results: we were able to detect a total of 427 miRNAs in these platelets, of which 81 were significantly regulated (> |0.5| logFC threshold) in a Dicer-dependent manner. The majority of miRNAs were significantly downregulated, but a smaller proportion of miRNAs was slightly, but significantly upregulated in platelets lacking Dicer. Conclusions: this study discloses differential expression patterns of further platelet miRNAs that potentially link multiple intercellular processes and pathways implicated in several stages of the pathogenesis of myocardial I/R injury

2023-03-03 | GSE184523 | GEO

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