Quantification of Insulin Analogs by Liquid Chromatography-High-Resolution Mass Spectrometry.

Administration of exogenous insulin or insulin analogs is a common cause of hypoglycemia. The etiology of hypoglycemic episodes can be investigated by the measurement of insulin. However, frequently used synthetic insulin analogs show variable reactivity with immunoassays designed for the quantification of human insulin and may produce misleading results. To overcome this challenge, mass spectrometric methods can be applied to differentiate and accurately quantify insulin and its analogs. Here we describe a liquid chromatography-tandem high-resolution accurate mass (LC-HRAM) for the highly specific and independent quantification of insulin and its synthetic analogs including aspart, detemir, glargine, glulisine, and lispro. This method utilizes antibody affinity extraction followed by analysis on a high-resolution accurate mass spectrometer.

Differentiation of Common IGF-1 Variants Using HRMS COM Determination with Follow-Up MS/MS Verification.

Insulin-like growth factor 1 (IGF-1), a peptide hormone regulator of growth hormone (GH), has common variants with differing functionality. These variants are a result of single amino acid changes in the peptide that can lead to significant changes in the resulting protein. The standard method of evaluating any of these variants is by using tandem mass spectrometry (MS/MS) methods. A novel method has been developed to evaluate some variants solely by high-resolution mass spectrometry (HRMS) of the intact peptide by calculating the center of mass (COM) of the [M + 7H]+7 isotopic distribution. This has allowed differentiation between the nonfunctional V44M variant and the A67T/A70T functional variants without the need for MS/MS. However, MS/MS is still needed to differentiate between the A67T and A70T variants. In this chapter we outline the LC-HRMS method for IGF-1 analysis with the inclusion of COM calculations and subsequent MS/MS differentiation.

Detection of 13C-Mannitol and Other Saccharides Using Tandem Mass Spectrometry for Evaluation of Intestinal Permeability or Leaky Gut.

Urine tests for intestinal permeability typically detect the secretion of administered saccharides with relatively different absorptions over a designated time period to determine severity of disease. Traditionally, a disaccharide/monosaccharide ratio such as lactulose/mannitol is used. Due to the potential for contamination of mannitol from different foods and commercial products causing an elevated baseline measurement, 13C mannitol can be used instead. In this chapter, a method of detecting various administered saccharides in urine for the evaluation of intestinal permeability is described. Three monosaccharides and two disaccharides are included so researchers can choose which combinations best fit their needs. Here lactulose, mannitol, 13C mannitol, rhamnose, and sucralose levels are separated and detected in urine using HPLC separation and MS/MS analysis.

Quantification of Parathyroid Hormone and its Fragments in Serum by Liquid Chromatography-High-Resolution Mass Spectrometry.

Parathyroid hormone (PTH), an 84-amino acid peptide hormone, is a major regulator of calcium homeostasis. Quantification of PTH in serum is used clinically to investigate calcium imbalances and for monitoring osteodystrophy in patients with renal failure. In addition to intact PTH, several PTH fragments are found in circulation. Recent studies have shown that accurate quantification of PTH fragments may provide valuable clinical information in certain scenarios. In this chapter, a high-resolution mass spectrometry-based method for quantification of PTH (1-84) and its fragments is described. This method involves immunoaffinity capture of intact PTH and PTH-fragments followed by liquid chromatography-high-resolution mass spectrometry (LC-HRMS).

Limited Correlation between SARS-CoV-2 Serologic Assays for Identification of High-Titer COVID-19 Convalescent Plasma Using FDA Thresholds.

In August 2020, the Food and Drug Administration (FDA) Emergency Use Authorization (EUA) for COVID-19 convalescent plasma (CCP) specified 12 authorized serologic assays and associated assay-specific cutoff values for the selection of high-titer CCP for use in hospitalized patients. The criteria used for establishing these cutoff values remains unclear. Here, we compare the overall agreement and concordance of five serologic assays included in the August 2020 FDA EUA at both the manufacturer-recommended qualitative cutoff thresholds and at the FDA-indicated thresholds for high-titer CCP, using serum samples collected as part of the CCP Expanded Access Program (EAP). The qualitative positive percent agreement (PPA) across assays ranged from 92.3% to 98.8%. However, the high-titer categorization across assays varied significantly, with the PPA ranging from 26.5% to 82.7%. The Roche anti-NC ECLIA provided the lowest agreement compared to all other assays. Efforts to optimize high-titer cutoffs could reduce, although not eliminate, the discordance across assays. The consequences of using nonstandardized assays are apparent in our study, and the high-titer cutoffs chosen for each assay are not directly comparable to each other. The generalized findings in our study will be relevant to any future use of convalescent plasma for either COVID-19 or future pandemics of newly emerged pathogens. IMPORTANCE COVID-19 convalescent plasma (CCP) was one of the first therapeutic options available for the treatment of SARS-CoV-2 infections and continues to be used selectively for immunosuppressed patients. Given the emergence of novel SARS-CoV-2 variants which are resistant to treatment with available monoclonal antibody (MAb) therapy, CCP remains an important therapeutic consideration. The FDA has released several emergency use authorizations (EUA) that have specified which serological assays can be used for qualification of CCP, as well as assay-specific cutoffs that must be used to identify high-titer CCP. In this study, a cohort of donor CCP was assessed across multiple serological assays which received FDA EUA for qualification of CCP. This study indicates a high degree of discordance across the assays used to qualify CCP for clinical use, which may have precluded the optimal use of CCP, including during clinical trials. This study highlights the need for assay standardization early in the development of serological assays for emerging pathogens.

Correlation of ANA Characteristics with pANCA IFA Interference.

BACKGROUND: Antineutrophil cytoplasmic antibody (ANCA) testing by the indirect immunofluorescence assay (IFA) is important for the diagnosis of autoimmune vasculitis. A common analytical interference for ANCA-IFA is the presence of an antinuclear antibody (ANA), which can cause an apparent perinuclear ANCA (pANCA) result on ethanol-fixed neutrophils. Here, the association of ANA patterns, titers, and concentrations with pANCA interference is investigated. METHODS: Samples positive for ANA by IFA with homogeneous, speckled, dense fine speckled (DFS), and centromere patterns were tested for ANA by enzyme immunoassay (EIA)] and for ANCA by IFA on ethanol-fixed neutrophils. Titers and concentrations were determined for the ANA-IFA and EIA, respectively, and correlated with the frequency of pANCA interpretations. RESULTS: For ANA-EIA positive samples (≥1.1U), 20.0% led to a pANCA interpretation compared to 5.1% for negative samples (≤1.0U). For samples positive by ANA-IFA, 12.9% resulted in a pANCA interpretation. Interference on pANCA correlated with ANA-IFA titer, with ANA titers ≥1:1280 identified as pANCA positive in 20.9% of samples compared to 9.7% for titers <1:1280. There was also a correlation with ANA pattern, as homogeneous samples were most likely to be called positive for pANCA (31.7%), followed by speckled (8.8%), DFS (6.8%), and centromere (3.6%). CONCLUSIONS: Positivity for ANA by EIA is associated with increased prevalence of pANCA interpretation. Samples positive for ANA by IFA also demonstrated this association, particularly with higher-titer, homogeneous patterns. Laboratories can use this information to determine an optimal workflow for when investigating potential pANCA interferences.

Small RNA Biosensor Design Strategy To Mitigate Off-Analyte Response.

Several bottlenecks in the design of current sensor technologies for small noncoding RNA must be addressed. The small size of the sensors and the large number of other nucleotides that may have sequence similarity makes selectivity a real concern. Many of the current sensors have one strand with an exposed region called a toehold. The toehold serves as a place for the analyte nucleic acid strand to bind and initiate competitive displacement of sensors' secondary strands. Since the toehold region is not protected, any endogenous oligonucleotide sequences that are similar or only different by a few nucleic acids will interact with the toehold and cause false signals. To address sensor selectivity, we investigated how the toehold location in the sensor impacts the sensitivity and selectivity for the analyte of interest. We will discuss the differences in sensitivity and selectivity for a miR-146a-5p biosensor in the presence of different naturally occurring mismatch sequences. We found that altering the toehold location lowered the rate of the false signal from off-analyte microRNA by upward of 20 percentage points. Detection limits as low as 56 pM were observed when the sensor concentration was 5 nM. The findings herein are broadly applicable to other small and large RNAs as well as other types of sensing platforms.

Performance of nano-assembly logic gates with a DNA multi-hairpin motif.

DNA nano-assemblies have far-reaching implications for molecular computers. Boolean logic gates made from DNA respond to specific combinations of chemical or molecular inputs. In complex samples an assortment of other chemicals and molecules may interfere with the gate's recognition and response mechanisms. For logic gates to accept an increasing number of inputs, while maintaining selectivity, their design must only respond when specific input combinations are available simultaneously. Here we present proof-of-principle for a fluorescent-based nano-assembly logic gate for three inputs. Central to the gate's design is a multi-hairpin motif that distinguishes it from other works in this area. The multi-hairpin motif facilitates a larger and increasing number of inputs and a place to generate FRET-based signal enhancement. We will show the nano-assembly logic gate worked in aqueous buffer and in crude MCF-7 cell lysate. We will demonstrate the gate's selectivity against off-analyte cocktails. Finally, multi-hairpin motifs with different chemical and physical properties were evaluated to test their logic capabilities. Future work will demonstrate the gate's ability to visually identify specific combinations of oligonucleotides called small non-coding RNAs (ncRNAs) in cells. This nano-assembly logic gate for small ncRNA has far reaching cellular computation and single-cell analysis applicability. The gate can be used for basic cellular analysis, computing and observing the unique molecular expression patterns in tumor microenvironments, and advancing the field of therapeutics.

Förster resonance energy transfer to impart signal-on and -off capabilities in a single microRNA biosensor.

Many studies have found that over- or under-expression of biomolecules called microRNAs (miRNA) regulates several diseases. Biosensors are in need to visually identify the relative expression level of miRNA to determine the direction these miRNA change in cells and tissues. Our established reporter+probe miRNA biosensor design requires that miRNA outcompete and displace the reporter from the probe. Once displaced, the reporter folds into a hairpin structure to force together a pair of Förster Resonance Energy Transfer (FRET) dyes. The donor and acceptor signal changes can be used to indicate the over-/under-expression of miRNA. The bright signal from the donor will indicate miRNA under-expression; the bright acceptor signal will indicate miRNA over-expression. Since close proximity of the dyes to each other and nucleic acids often quench fluorescence, polyethylene glycol spacers were added in-between the dyes and nucleic acids. We compared reporter designs with and without spacers to investigate the effects on the following analytical metrics: (1) extent of signal change, (2) limits of detection and quantitation, and (3) sensitivity. Systematic errors and amount of reporter+probe biosensor formed were evaluated for one of the biosensors. Cy3|Cy5 and 6-carboxyfluorescein (6-FAM)|ATTO 633 dye pairs on reporters containing spacers showed an increase in the acceptor signal change by ∼190 and ∼484%, respectively, compared to no spacers. Transduction mechanisms that enhance and quench the signal both showed LODs that ranged from 3-17 nanomolar (nM) with 100 nM of the biosensor.

Molecular structure and thermodynamic predictions to create highly sensitive microRNA biosensors.

Many studies have established microRNAs (miRNAs) as post-transcriptional regulators in a variety of intracellular molecular processes. Abnormal changes in miRNA have been associated with several diseases. However, these changes are sometimes subtle and occur at nanomolar levels or lower. Several biosensing hurdles for in situ cellular/tissue analysis of miRNA limit detection of small amounts of miRNA. Of these limitations the most challenging are selectivity and sensor degradation creating high background signals and false signals. Recently we developed a reporter+probe biosensor for let-7a that showed potential to mitigate false signal from sensor degradation. Here we designed reporter+probe biosensors for miR-26a-2-3p and miR-27a-5p to better understand the effect of thermodynamics and molecular structures of the biosensor constituents on the analytical performance. Signal changes from interactions between Cy3 and Cy5 on the reporters were used to understand structural aspects of the reporter designs. Theoretical thermodynamic values, single stranded conformations, hetero- and homodimerization structures, and equilibrium concentrations of the reporters and probes were used to interpret the experimental observations. Studies of the sensitivity and selectivity revealed 5-9 nM detection limits in the presence and absence of interfering off-analyte miRNAs. These studies will aid in determining how to rationally design reporter+probe biosensors to overcome hurdles associated with highly sensitive miRNA biosensing.

Detection of miRNA using a double-strand displacement biosensor with a self-complementary fluorescent reporter.

Design of rapid, selective, and sensitive DNA and ribonucleic acid (RNA) biosensors capable of minimizing false positives from nuclease degradation is crucial for translational research and clinical diagnostics. We present proof-of-principle studies of an innovative micro-ribonucleic acid (miRNA) reporter-probe biosensor that displaces a self-complementary reporter, while target miRNA binds to the probe. The freed reporter folds into a hairpin structure to induce a decrease in the fluorescent signal. The self-complementarity of the reporter facilitates the reduction of false positives from nuclease degradation. Nanomolar limits of detection and quantitation were capable with this proof-of-principle design. Detection of miRNA occurs within 10 min and does not require any additional hybridization, labeling, or rinsing steps. The potential for medical applications of the reporter-probe biosensor is demonstrated by selective detection of a cancer regulating microRNA, Lethal-7 (Let-7a). Mechanisms for transporting the biosensor across the cell membrane will be the focus of future work.