Direct identification of microribonucleic acid miR-451 from plasma using liquid chromatography mass spectrometry

Basiri, Babak; Sutton, J. Michael; Hooshfar, Shirin; Byrnes, Charnel C.; Murph, Mandi M.; Bartlett, Michael G.

doi:10.1016/j.chroma.2018.11.029

Cited by 32 publications

(26 citation statements)

References 58 publications

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“…In Figure , it can be seen that the model can accurately predict the trend for ssRNA even though the model was built with only data from ssDNA. In fact, this agrees with data recently obtained in our lab regarding analysis of microRNAs from biological systems using a non‐traditional ion pair for improved sensitivity and lower adduction during mass spectral analysis …”

Section: Resultssupporting

confidence: 92%

“…In fact, this agrees with data recently obtained in our lab regarding analysis of microRNAs from biological systems using a non-traditional ion pair for improved sensitivity and lower adduction during mass spectral analysis. 44 Next, we were curious to find if the model would hold up against a slightly different oligonucleotide modificationa phosphorothioate backbone. Phosphorothioates contain a substitution in the phosphodiester backbone replacing one of the oxygen atoms with a sulfur.…”

Section: Resultsmentioning

confidence: 99%

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Modeling cationic adduction of oligonucleotides using electrospray desorption ionization

Sutton

Bartlett

2020

Rapid Comm Mass Spectrometry

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Rationale Cationic adduction causes poor sensitivity and increases spectral complexity during mass spectral analysis of oligonucleotides and alkylamines are used to reduce this adduction. It is unclear the effect of the physiochemical properties of the alkylamines on the reduction of the cationic adduction. Methods All samples were directly infused into a Synapt G2 HDMS quadrupole time‐of‐flight (TOF) hybrid mass spectrometer in negative ion electrospray ionization mode through the native built‐in fluidics system. The infusion flow rate was set to 50 μL/min. The TOFMS tuning parameters were as follows: capillary voltage −2.0 kV, cone voltage 25 V, extraction cone voltage 2 V, source temperature 125°C, desolvation temperature 450°C, cone gas flow rate 0 L/h, and desolvation gas (nitrogen) flow rate 1000 L/h. Results A quantitative model was created to predict the optimized alkylamine for MS analysis, while a qualitative model was generated to explain the most important physiochemical properties: proton affinity (13.83%), gas‐phase basicity (11.79%), pKa (11.47%), boiling point (10.73%), MW (10.3%), Henry's Law Constant (9.56%), and partition coefficient (logP) (9.44%). The quantitative model was applied to RNA (microRNA) and a phosphorothioate and predicts the trend of cationic adduction. Conclusions Two models are described to understand the physiochemical properties that contribute to the adduction and to provide users a quick mathematical tool to predict the best choice of alkylamine to lower cationic adduction and decrease spectral complexity while enhancing sensitivity.

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Section: Resultssupporting

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Modeling cationic adduction of oligonucleotides using electrospray desorption ionization

Sutton

Bartlett

2020

Rapid Comm Mass Spectrometry

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“…5b). One of the strengths of this approach is that it greatly reduces the number of sample transfer steps that are involved in sample preparation (McGinnis, Cummings, & Bartlett, 2013; Basiri et al, 2019). Since it has been previously noted that nonspecific adsorptive losses become quite significant at lower concentrations of oligonucleotides, processes that can minimize this problem are attractive.…”

Section: Bioanalysis Of Oligonucleotides and Their Metabolitesmentioning

confidence: 99%

“…To help preserve oligonucleotides during the proteinase digestion, compounds that inhibit nucleases activity can be added such as ethylenediamine tetraacetic acid (EDTA) which can sequester metal atoms that are critical cofactors for several families of nucleases (Dattagupta et al, 1975; Hilz, Wiegers, & Adamietz, 1975). When well optimized, proteinase K digestion can be accomplished in 3 hr (McGinnis, Cummings, & Bartlett, 2013; Basiri et al, 2019).…”

Section: Bioanalysis Of Oligonucleotides and Their Metabolitesmentioning

confidence: 99%

“…The other real challenge of this approach for bioanalysis is that it is so selective that it makes the use of an internal standard difficult. This particular problem has been addressed recently by Basiri et al (2019) who showed that it was possible to actually use the biotinylated capture strand as an internal standard with excellent performance.…”

Section: Bioanalysis Of Oligonucleotides and Their Metabolitesmentioning

confidence: 99%

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Bioanalysis and Biotransformation of Oligonucleotide Therapeutics by Liquid Chromatography‐mass Spectrometry

Sutton

Kim

Zahar

et al. 2020

Mass Spectrometry Reviews

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Since 2016, eight new oligonucleotide therapies have been approved which has led to increased interest in oligonucleotide analysis. There is a particular need for powerful bioanalytical tools to study the metabolism and biotransformation of these molecules. This review provides the background on the biological basis of these molecules as currently used in therapies. The article also reviews the current state of analytical methodology including state of the art sample preparation techniques, liquid chromatography‐mass spectrometry methods, and the current limits of detection/quantitation. Finally, the article summarizes the challenges in oligonucleotide bioanalysis and provides future perspectives for this emerging field. © 2020 John Wiley & Sons Ltd.

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Exploring the theranostic potentials of miRNA and epigenetic networks in autoimmune diseases: A comprehensive review

Nag,

Mitra,

Tripathi

et al. 2023

Immunity Inflam & Disease

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BackgroundAutoimmune diseases (AD) are severe pathophysiological ailments that are stimulated by an exaggerated immunogenic response towards self‐antigens, which can cause systemic or site‐specific organ damage. An array of complex genetic and epigenetic facets majorly contributes to the progression of AD, thus providing significant insight into the regulatory mechanism of microRNA (miRNA). miRNAs are short, non‐coding RNAs that have been identified as essential contributors to the post‐transcriptional regulation of host genome expression and as crucial regulators of a myriad of biological processes such as immune homeostasis, T helper cell differentiation, central and peripheral tolerance, and immune cell development.AimsThis article tends to deliberate and conceptualize the brief pathogenesis and pertinent epigenetic regulatory mechanism as well as miRNA networks majorly affecting five different ADs namely rheumatoid arthritis (RA), type 1 diabetes, multiple sclerosis (MS), systemic lupus erythematosus (SLE) and inflammatory bowel disorder (IBD) thereby providing novel miRNA‐based theranostic interventions.Results & DiscussionPertaining to the differential expression of miRNA attributed in target tissues and cellular bodies of innate and adaptive immunity, a paradigm of scientific expeditions suggests an optimistic correlation between immunogenic dysfunction and miRNA alterations.ConclusionTherefore, it is not astonishing that dysregulations in miRNA expression patterns are now recognized in a wide spectrum of disorders, establishing themselves as potential biomarkers and therapeutic targets. Owing to its theranostic potencies, miRNA targets have been widely utilized in the development of biosensors and other therapeutic molecules originating from the same.

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Direct identification of microribonucleic acid miR-451 from plasma using liquid chromatography mass spectrometry

Cited by 32 publications

References 58 publications

Modeling cationic adduction of oligonucleotides using electrospray desorption ionization

Modeling cationic adduction of oligonucleotides using electrospray desorption ionization

Bioanalysis and Biotransformation of Oligonucleotide Therapeutics by Liquid Chromatography‐mass Spectrometry

Exploring the theranostic potentials of miRNA and epigenetic networks in autoimmune diseases: A comprehensive review

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