CoChat
Sign Up
Cited by 28

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

A Comprehensive Study of Vesicular and Non-Vesicular miRNAs from a Volume of Cerebrospinal Fluid Compatible with Clinical Practice

Prieto-Fernández, Endika, Aransay, Ana María, Royo, Félix, González, Esperanza, Lozano, Juan José, Santos-Zorrozua, Borja, Macias-Camara, Nuria, González, Monika, Garay, Raquel Pérez, Benito, Javier, Garcia-Orad, Africa, Falcón-Pérez, Juan Manuel·2019·Theranostics
DOI 10.7150/thno.31502PMC PMC6643433
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.7150/thno.31502

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Figures

Figure 1 Experimental design for comparison of six methods of analyzing miRNAs in bodily fluids. Aliquots of 200 µL of CSF were used to test each of the six methods in triplicate (overall, 18 aliquots were processed). The pellets obtained in each EV enrichment procedure were resuspended in 100 µL of 1X DPBS. Then, total RNA was extracted to perform the downstream analyses (TaqMan RT-qPCR and smallRNAseq). Abbreviations: size-exclusion chromatography (SEC), ultracentrifugation (UC), miRCURY Exosome Isolation Kit from Qiagen (QIA), Total Exosome Isolation Reagent from Invitrogen (INV), mirVana PARIS Kit from Ambion (PAR), and Plasma/Serum RNA Purification Kit from Norgen (NOR).
Figure 1 Experimental design for comparison of six methods of analyzing miRNAs in bodily fluids. Aliquots of 200 µL of CSF were used to test each of the six methods in triplicate (overall, 18 aliquots were processed). The pellets obtained in each EV enrichment procedure were resuspended in 100 µL of 1X DPBS. Then, total RNA was extracted to perform the downstream analyses (TaqMan RT-qPCR and smallRNAseq). Abbreviations: size-exclusion chromatography (SEC), ultracentrifugation (UC), miRCURY Exosome Isolation Kit from Qiagen (QIA), Total Exosome Isolation Reagent from Invitrogen (INV), mirVana PARIS Kit from Ambion (PAR), and Plasma/Serum RNA Purification Kit from Norgen (NOR).CC BY · PubMed Central
Figure 2 Performance of different protocols measured using RT-qPCR. A, the number of TaqMan RT-qPCR replicates (from a total of 12) in which the studied miRNAs were detected. Twelve RT-qPCR reactions were performed for each method (3 EV isolations and miRNA extractions x 2 cDNA synthesis reactions x 2 technical duplicates of each cDNA reaction). B, relative quantification (in comparison with ath-miR-159a) of miR-21-5p, miR-451a, miR-92a-3p, and miR-22-3p and C, of miR-1911-5p, miR-1264, miR-30c-5p, and miR-34b-3p. Abbreviations: ultracentrifugation (UC), miRCURY Exosome Isolation Kit from Qiagen (QIA), Total Exosome Isolation Reagent from Invitrogen (INV), mirVana PARIS Kit from Ambion (PAR), and Plasma/Serum RNA Purification Kit from Norgen (NOR).
Figure 2 Performance of different protocols measured using RT-qPCR. A, the number of TaqMan RT-qPCR replicates (from a total of 12) in which the studied miRNAs were detected. Twelve RT-qPCR reactions were performed for each method (3 EV isolations and miRNA extractions x 2 cDNA synthesis reactions x 2 technical duplicates of each cDNA reaction). B, relative quantification (in comparison with ath-miR-159a) of miR-21-5p, miR-451a, miR-92a-3p, and miR-22-3p and C, of miR-1911-5p, miR-1264, miR-30c-5p, and miR-34b-3p. Abbreviations: ultracentrifugation (UC), miRCURY Exosome Isolation Kit from Qiagen (QIA), Total Exosome Isolation Reagent from Invitrogen (INV), mirVana PARIS Kit from Ambion (PAR), and Plasma/Serum RNA Purification Kit from Norgen (NOR).CC BY · PubMed Central
Figure 3 Size-exclusion chromatography analysis of CSF. A, Western blot analysis of CD63, CD9, neuron-specific enolase (NSE), and human serum albumin (HSA) proteins. Molecular weights are shown in KDa. B, the number of TaqMan RT-qPCR replicates (from a total of 12) in which the studied miRNAs were detected. C, quantification (relative to ath-miR-159a) of miR-21-5p, miR-451a, and miR-92a-3p and D, of miR-1911-5p, miR-22-3p, and miR-30c-5p.
Figure 3 Size-exclusion chromatography analysis of CSF. A, Western blot analysis of CD63, CD9, neuron-specific enolase (NSE), and human serum albumin (HSA) proteins. Molecular weights are shown in KDa. B, the number of TaqMan RT-qPCR replicates (from a total of 12) in which the studied miRNAs were detected. C, quantification (relative to ath-miR-159a) of miR-21-5p, miR-451a, and miR-92a-3p and D, of miR-1911-5p, miR-22-3p, and miR-30c-5p.CC BY · PubMed Central
Figure 4 RNase protection assay. Relative quantification (with respect to ath-miR-159a) of each miRNA evaluated by RT-qPCR. The positive control (CTRL) shows the total abundance of each miRNA in this pool of samples. The samples were also treated with proteinase K and RNase A (PK+RNase) or Triton X-100 and RNase A (TX-100+RNase) to examine the association of miRNAs with the vesicles (and their location inside the vesicles or on their surface). The three conditions were assessed in triplicate.
Figure 4 RNase protection assay. Relative quantification (with respect to ath-miR-159a) of each miRNA evaluated by RT-qPCR. The positive control (CTRL) shows the total abundance of each miRNA in this pool of samples. The samples were also treated with proteinase K and RNase A (PK+RNase) or Triton X-100 and RNase A (TX-100+RNase) to examine the association of miRNAs with the vesicles (and their location inside the vesicles or on their surface). The three conditions were assessed in triplicate.CC BY · PubMed Central
Figure 5 UpSet plot showing the total set size and overlaps between the 281 unique miRNAs and those isolated by each method (PAR, INV, and NOR) or found in the F03 and F09 fractions of the SEC. The number of common miRNAs detected by each method is indicated on the y-axis. The shaded circles connected by solid lines in the lower panel show the intersecting miRNA datasets.
Figure 5 UpSet plot showing the total set size and overlaps between the 281 unique miRNAs and those isolated by each method (PAR, INV, and NOR) or found in the F03 and F09 fractions of the SEC. The number of common miRNAs detected by each method is indicated on the y-axis. The shaded circles connected by solid lines in the lower panel show the intersecting miRNA datasets.CC BY · PubMed Central
Figure 6 A, a pie chart showing the 12 miRNAs detected in the exosomal fraction but not in the F09 fraction of the size-exclusion chromatography. B, the most representative pathways predicted by ConsensusPathDB considering the 3,638 target genes of these 12 miRNAs.
Figure 6 A, a pie chart showing the 12 miRNAs detected in the exosomal fraction but not in the F09 fraction of the size-exclusion chromatography. B, the most representative pathways predicted by ConsensusPathDB considering the 3,638 target genes of these 12 miRNAs.CC BY · PubMed Central
Figure 7 Comparison between the quantification (relative to ath-miR-159a) obtained using RT-qPCR and the normalized smallRNAseq counts (represented on a logarithmic scale) for six reference miRNAs considered and method compared. A, mirVana PARIS Kit from Ambion. B, Total Exosome Isolation Reagent from Invitrogen. C, Plasma/Serum RNA Purification Kit from Norgen. The miR-1264 and miR-34b-3p were not considered. The correlation coefficients between RT-qPCR and smallRNAseq data for each method are also shown (upper panel for each method).
Figure 7 Comparison between the quantification (relative to ath-miR-159a) obtained using RT-qPCR and the normalized smallRNAseq counts (represented on a logarithmic scale) for six reference miRNAs considered and method compared. A, mirVana PARIS Kit from Ambion. B, Total Exosome Isolation Reagent from Invitrogen. C, Plasma/Serum RNA Purification Kit from Norgen. The miR-1264 and miR-34b-3p were not considered. The correlation coefficients between RT-qPCR and smallRNAseq data for each method are also shown (upper panel for each method).CC BY · PubMed Central

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 2 references

Research works printed but not linked: 55

  1. [1]Cunha BA Cerebrospinal fluid (CSF) lactic acid levels: A rapid and reliable way to differentiate viral from bacterial meningitis or concurrent viral/bacterial meningitis J Clin Microbiol 2012 50 211 22203753 PMC3256707
  2. [2]El Kadmiri N Said N Slassi I Biomarkers for alzheimer disease: Classical and novel candidates' review Neuroscience 2018 370 181 90 28729061
  3. [4]Manek R Moghieb A Yang Z Protein biomarkers and neuroproteomics characterization of microvesicles/exosomes from human cerebrospinal fluid following traumatic brain injury Mol Neurobiol 2018 55 6112 28 29188495 PMC6359938
  4. [5]Nevel KS Wilcox JA Robell LJ The utility of liquid biopsy in central nervous system malignancies Curr Oncol Rep 2018 20 60 29876874
  5. [6]Siravegna G Marsoni S Siena S Integrating liquid biopsies into the management of cancer Nat Rev Clin Oncol 2017 14 531 48 28252003
  6. [7]Wang Y Springer S Zhang M Detection of tumor-derived DNA in cerebrospinal fluid of patients with primary tumors of the brain and spinal cord Proc Natl Acad Sci USA 2015 112 9704 09 26195750 PMC4534284
  7. [8]Kopkova A Sana J Fadrus P Cerebrospinal fluid microRNAs as diagnostic biomarkers in brain tumors Clin Chem Lab Med 2018 56 869 79 29451858
  8. [9]Drusco A Bottoni A Lagana A A differentially expressed set of microRNAs in cerebro-spinal fluid (CSF) can diagnose CNS malignancies Oncotarget 2015 6 20829 39 26246487 PMC4673232
  9. [10]Bartel DP MicroRNAs: Genomics, biogenesis, mechanism, and function Cell 2004 116 281 97 14744438
  10. [11]Johanson TM Skinner JP Kumar A The role of microRNAs in lymphopoiesis Int J Hematol 2014 100 246 53 24929847
  11. [12]Calin GA Sevignani C Dumitru CD Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers Proc Natl Acad Sci U S A 2004 101 2999 3004 14973191 PMC365734
  12. [13]Teplyuk NM Mollenhauer B Gabriely G MicroRNAs in cerebrospinal fluid identify glioblastoma and metastatic brain cancers and reflect disease activity Neuro Oncol 2012 14 689 700 22492962 PMC3367845
  13. [14]Baraniskin A Kuhnhenn J Schlegel U Identification of microRNAs in the cerebrospinal fluid as biomarker for the diagnosis of glioma Neuro Oncol 2012 14 29 33 21937590 PMC3245991
  14. [15]Yagi Y Ohkubo T Kawaji H Next-generation sequencing-based small RNA profiling of cerebrospinal fluid exosomes Neurosci Lett 2017 636 48 57 27780738
  15. [16]Yanez-Mo M Siljander PR Andreu Z Biological properties of extracellular vesicles and their physiological functions J Extracell Vesicles 2015 4 27066 25979354 PMC4433489
  16. [17]Lobb RJ Lima LG Moller A Exosomes: Key mediators of metastasis and pre-metastatic niche formation Semin Cell Dev Biol 2017 67 3 10 28077297
  17. [18]Jung KO Youn H Lee CH Visualization of exosome-mediated miR-210 transfer from hypoxic tumor cells Oncotarget 2017 8 9899 910 28038441 PMC5354779
  18. [19]Akers JC Hua W Li H A cerebrospinal fluid microRNA signature as biomarker for glioblastoma Oncotarget 2017 8 68769 779 28978155 PMC5620295
  19. [20]Nagaraj S Zoltowska KM Laskowska-Kaszub K microRNA diagnostic panel for alzheimer's disease and epigenetic trade-off between neurodegeneration and cancer Ageing Res Rev 2019 49 125 43 30391753
  20. [21]Verheul C Kleijn A Lamfers MLM Cerebrospinal fluid biomarkers of malignancies located in the central nervous system Handb Clin Neurol 2017 146 139 69 29110768
  21. [22]Akers JC Ramakrishnan V Kim R miRNA contents of cerebrospinal fluid extracellular vesicles in glioblastoma patients J Neurooncol 2015 123 205 16 25903655 PMC4459648
  22. [23]Shi R Wang PY Li XY Exosomal levels of miRNA-21 from cerebrospinal fluids associated with poor prognosis and tumor recurrence of glioma patients Oncotarget 2015 6 26971 81 26284486 PMC4694967
  23. [24]Tietje A Maron KN Wei Y Cerebrospinal fluid extracellular vesicles undergo age dependent declines and contain known and novel non-coding RNAs PLoS One 2014 9 e113116 25420022 PMC4242609
  24. [25]Liu CG Song J Zhang YQ MicroRNA-193b is a regulator of amyloid precursor protein in the blood and cerebrospinal fluid derived exosomal microRNA-193b is a biomarker of alzheimer's disease Mol Med Rep 2014 10 2395 400 25119742
  25. [26]Riancho J Vazquez-Higuera JL Pozueta A MicroRNA profile in patients with alzheimer's disease: Analysis of miR-9-5p and miR-598 in raw and exosome enriched cerebrospinal fluid samples J Alzheimers Dis 2017 57 483 91 28269782
  26. [27]Goswami S Banerjee A Kumari B Differential expression and significance of circulating microRNAs in cerebrospinal fluid of acute encephalitis patients infected with japanese encephalitis virus Mol Neurobiol 2017 54 1541 51 26860411
  27. [28]Welton JL Loveless S Stone T Cerebrospinal fluid extracellular vesicle enrichment for protein biomarker discovery in neurological disease; multiple sclerosis J Extracell Vesicles 2017 6 1369805 28959386 PMC5614217
  28. [29]Gui Y Liu H Zhang L Altered microRNA profiles in cerebrospinal fluid exosome in parkinson disease and alzheimer disease Oncotarget 2015 6 37043 53 26497684 PMC4741914
  29. [30]Bache S Rasmussen R Rossing M MicroRNA changes in cerebrospinal fluid after subarachnoid hemorrhage Stroke 2017 48 2391 8 28768799 PMC5571886
  30. [31]Sorensen SS Nygaard AB Carlsen AL Elevation of brain-enriched miRNAs in cerebrospinal fluid of patients with acute ischemic stroke Biomark Res 2017 5 24 28702194 PMC5504978
  31. [32]You WD Tang QL Wang L Alteration of microRNA expression in cerebrospinal fluid of unconscious patients after traumatic brain injury and a bioinformatic analysis of related single nucleotide polymorphisms Chin J Traumatol 2016 19 11 5 27033266 PMC4897835
  32. [34]van Harten AC Mulders J Scheltens P Differential expression of microRNA in cerebrospinal fluid as a potential novel biomarker for alzheimer's disease J Alzheimers Dis 2015 47 243 52 26402772
  33. [35]Quintana E Ortega FJ Robles-Cedeno R miRNAs in cerebrospinal fluid identify patients with MS and specifically those with lipid-specific oligoclonal IgM bands Mult Scler 2017 23 1716 26 28067602
  34. [36]Burgos K Malenica I Metpally R Profiles of extracellular miRNA in cerebrospinal fluid and serum from patients with alzheimer's and parkinson's diseases correlate with disease status and features of pathology PLoS One 2014 9 e94839 24797360 PMC4010405
  35. [37]Baraniskin A Kuhnhenn J Schlegel U Identification of microRNAs in the cerebrospinal fluid as marker for primary diffuse large B-cell lymphoma of the central nervous system Blood 2011 117 3140 6 21200023
  36. [38]Bhomia M Balakathiresan NS Wang KK A panel of serum MiRNA biomarkers for the diagnosis of severe to mild traumatic brain injury in humans Sci Rep 2016 6 28148 27338832 PMC4919667
  37. [39]Bergman P Piket E Khademi M Circulating miR-150 in CSF is a novel candidate biomarker for multiple sclerosis Neurol Neuroimmunol Neuroinflamm 2016 3 e219 27144214 PMC4841644
  38. [40]Royo F Schlangen K Palomo L Transcriptome of extracellular vesicles released by hepatocytes PLoS One 2013 8 e68693 23874726 PMC3708910
  39. [41]Shelke GV Lasser C Gho YS Importance of exosome depletion protocols to eliminate functional and RNA-containing extracellular vesicles from fetal bovine serum J Extracell Vesicles 2014 3 10.3402 /jev.v3.24783 PMC4185091 25317276
  40. [42]Langmead B Trapnell C Pop M Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol 2009 10 R25 2009 -10-3-r25 19261174 PMC2690996
  41. [43]Harrow J Frankish A Gonzalez JM GENCODE: The reference human genome annotation for the ENCODE project Genome Res 2012 22 1760 74 22955987 PMC3431492
  42. [44]Robinson MD Oshlack A A scaling normalization method for differential expression analysis of RNA-seq data Genome Biol 2010 11 R25 2010 -11-3-r25 20196867 PMC2864565
  43. [45]Lex A Gehlenborg N Strobelt H UpSet: Visualization of intersecting sets IEEE Trans Vis Comput Graph 2014 20 1983 92 26356912 PMC4720993
  44. [46]Dweep H Gretz N miRWalk2.0: A comprehensive atlas of microRNA-target interactions Nat Methods 2015 12 697 26226356
  45. [47]Kamburov A Stelzl U Lehrach H The ConsensusPathDB interaction database: 2013 update Nucleic Acids Res 2013 41 D793 800 23143270 PMC3531102
  46. [48]Kanehisa M Furumichi M Tanabe M KEGG: New perspectives on genomes, pathways, diseases and drugs Nucleic Acids Res 2017 45 D353 61 27899662 PMC5210567
  47. [49]Fabregat A Jupe S Matthews L The reactome pathway knowledgebase Nucleic Acids Res 2018 46 D649 55 29145629 PMC5753187
  48. [50]Meunier J Lemoine F Soumillon M Birth and expression evolution of mammalian microRNA genes Genome Res 2013 23 34 45 23034410 PMC3530682
  49. [51]Monguio-Tortajada M Roura S Galvez-Monton C Nanosized UCMSC-derived extracellular vesicles but not conditioned medium exclusively inhibit the inflammatory response of stimulated T cells: Implications for nanomedicine Theranostics 2017 7 270 84 28042333 PMC5197063
  50. [52]Gamez-Valero A Monguio-Tortajada M Carreras-Planella L Size-exclusion chromatography-based isolation minimally alters extracellular vesicles' characteristics compared to precipitating agents Sci Rep 2016 6 33641 27640641 PMC5027519
  51. [53]Boing AN van der Pol E Grootemaat AE Single-step isolation of extracellular vesicles by size-exclusion chromatography J Extracell Vesicles 2014 3 10.3402 /jev.v3.23430 PMC4159761 25279113
  52. [54]Reiber H Dynamics of brain-derived proteins in cerebrospinal fluid Clin Chim Acta 2001 310 173 86 11498083
  53. [55]Haque A Polcyn R Matzelle D New insights into the role of neuron-specific enolase in neuro-inflammation, neurodegeneration, and neuroprotection Brain Sci 2018 8 10.3390 /brainsci8020033 PMC5836052 29463007
  54. [56]Yan T Skaftnesmo KO Leiss L Neuronal markers are expressed in human gliomas and NSE knockdown sensitizes glioblastoma cells to radiotherapy and temozolomide BMC Cancer 2011 11 524 22185371 PMC3259117
  55. [57]Anckar J Bonni A Regulation of neuronal morphogenesis and positioning by ubiquitin-specific proteases in the cerebellum PLoS One 2015 10 e0117076 25607801 PMC4301861

Cited by

Sorted by citations

Metadata

Authors
Prieto-Fernández, E., Aransay, A. M., Royo, F., González, E., Lozano, J. J., Santos-Zorrozua, B., Macias-Camara, N., González, M., Garay, R. P., Benito, J., Garcia-Orad, A., & Falcón-Pérez, J. M.
Venue
Theranostics
Publisher
Ivyspring International Publisher
Published
2019
Volume
9
Issue
16
Pages
4567-4579
ISSN
1838-7640
DOI
10.7150/thno.31502
PMC
PMC6643433
Cited by
28
References
2
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review