Immunoaffinity Research Articles

Cross validation of pharmacokinetic bioanalytical methods: Experimental and statistical design

Pharmacokinetic (PK) analysis is an integral part of drug development. Health agency guidance provides development and validation recommendations for PK bioanalytical methods run in one laboratory. However, as a drug development program progresses, a PK bioanalytical method may need to be run in more than one laboratory. Additionally, a PK bioanalytical method format may change and a new method platform may be validated and implemented during the drug development cycle. Here we describe the cross validation strategy for comparisons of two validated bioanalytical methods used to generate PK data within the same study or across different studies. Current guidance for cross validations is limited and, therefore, Genentech, Inc. has developed a cross validation experimental strategy that utilizes incurred samples along with a comprehensive statistical analysis. One hundred incurred study samples over the applicable range of concentrations are selected based on four quartiles (Q) of in-study concentration levels. The samples are assayed once in the two bioanalytical methods. Bioanalytical method equivalency is assessed for the 100 samples based on pre-specified acceptability criterion: the two methods are considered equivalent if the percent differences in the lower and upper bound limits of the 90 % confidence interval (CI) are both within ±30 %. Quartile by concentration analysis using the same criterion may also need to be performed. A Bland-Altman plot of the percent difference of sample concentrations versus the mean concentration of each sample is also created to help further characterize the data. This strategy is a robust assessment of PK bioanalytical method equivalency and includes subgroup analyses by concentration to assess for biases. This strategy was implemented in two case studies: 1) two different laboratories using the same bioanalytical method and 2) a bioanalytical method platform change from enzyme-linked immunosorbent assay (ELISA) to multiplexing immunoaffinity (IA) liquid chromatography tandem mass spectrometry (IA LC-MS/MS).

Improving the Sensitivity of Protein Quantification by Immunoaffinity Liquid Chromatography─Triple Quadrupole Mass Spectrometry Using an Iterative Transition Summing Technique.

The desire to reach ever-diminishing lower limits of quantification (LLOQ) to probe changes in low abundance protein targets has led to enormous progress in sample preparation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) instrumentation. To maximize signal and reduce noise, many approaches have been employed, including specific immunoaffinity (IA) enrichment and reducing the LC flow to the nanoflow (nLC) level; however, additional sensitivity gains may still be required. Recently, a technique termed "echo summing" has been described for small-molecular-weight analytes on a triple quadrupole (QqQ) MS where multiple iterations of the same, single selected reaction monitoring (SRM) transition are collected, summed, and integrated, yielding significant analyte dependent signal-to-noise (S/N) improvements. Herein, the direct applicability of echo summing to protein quantification by sequential IA combined with nLC-MS/MS (IA-nLC-MS/MS) is described for a beta nerve growth factor (NGF) and a soluble asialoglycoprotein receptor (sASGPR) assay from human serum. Five iterations of echo summing outperformed traditional collection in relative average accuracy (-1.5 ± 7.7 vs -41.7 ± 10.7% bias) and precision (7.8 vs 18.4% coefficient of variation (CV)) of the low-end quality control (QC) sample (N = 4) for NGF and improved functional sensitivity of serially diluted serum QC samples (N = 5 each population) approximately 2-fold (1.96 and 2.00-fold) for two peptides of sASGPR. Echo summing also extended the minimum quantifiable QC level for sASGPR 4-fold lower. Similar gains are believed to be achievable for most protein IA-nLC-MS/MS assays.

Precursor carboxy-silica for functionalization with interactive ligands. IV. Carbodiimide assisted preparation of immobilized antibody stationary phases for high performance immuno-affinity chromatography of human serum

In this Part IV of the article series dealing with the functionalization of the precursor carboxy silica with various chromatographic ligands, immuno affinity (IA) columns were prepared with immobilized anti-apolipoprotein B (AAP B) and anti-haptoglobin (AHP) antibodies for use in immuno affinity chromatography (IAC) in the aim of selectivily capturing their corresponding antigens from healthy and cancer human sera. Diseased human serum with adenocarcinoma cancer was selected as a typical diseased biological fluid. Besides preferentially capturing their corresponding antigens, the AAP B column captured from disease-free and cancer sera, 34 proteins and 33 proteins, respectively, while the AHP column enriched 38 and 47 proteins, respectively. This nonspecific binding can be attributed to the many proteins human serum have, which could mediate protein–protein interactions thus leading to the so-called “sponge effect”. This kind of behavior can be exploited positively in the determination of differentially expressed proteins (DEPs) for diseased serum with respect to healthy serum and in turn allow the identification of an array of potential biomarkers for cancer. In fact, For AHP column, 13 upregulated and 22 downregulated proteins were identified whereas for AAP B column the numbers were 23 and 10, respectively. The DEPs identified with both columns match those reported in the literature for other types of cancers. The different expression of proteins in each IAC column can be related to the variability of protein–protein interactions. In addition, an array of a few biomarkers is more indicative of a certain disease than a single biomarker.

Quantification of the lung cancer tumor marker CYFRA 21-1 using protein precipitation, immunoaffinity bottom-up LC-MS/MS.

Numerous studies have proven the potential of cytokeratin 19 fragment 21-1 (CYFRA 21-1) detection in the (early) diagnosis and treatment monitoring of non-small cell lung cancer (NSCLC). Conventional immunoassays for CYFRA 21-1 quantification are however prone to interferences and lack diagnostic sensitivity and standardization. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an emerging approach based on a different, often superior, detection principle, which may improve the clinical applicability of CYFRA 21-1 in cancer diagnostics. Therefore, we developed and validated a protein precipitation, immunoaffinity (IA) LC-MS/MS assay for quantitative analysis of serum CYFRA 21-1. Selective sample preparation was performed using ammonium sulfate (AS) precipitation, IA purification, tryptic digestion and LC-MS/MS quantification using a signature peptide and isotopically labeled internal standard. The workflow was optimized and validated according to EMA guidelines and results were compared to a conventional immunoassay. Significant interference effects were seen during IA purification, which were sufficiently solved by performing AS precipitation prior to IA purification. A linear calibration curve was obtained in the range of 1.0-100 ng/mL (R2=0.98). Accuracy and precision were well within acceptance criteria. In sera of patients suspected of lung cancer, the method showed good correlation with the immunoassay. A robust AS precipitation-IA LC-MS/MS assay for the quantification of serum CYFRA 21-1 was developed. With this assay, the clinically added value of LC-MS/MS-based detection over immunoassays can be further explored.

Analysis of Neuron–Specific enolase isozymes in human serum using immunoaffinity purification and liquid chromatography–tandem mass spectrometry quantification

Neuron–specific enolase (NSE) is a promising small–cell lung cancer (SCLC) biomarker composed of αγ and γγ isozyme dimers. As the conventional immunoassays are prone to interferences and cannot differentiate between the isozymes, we developed a multiplex immunoaffinity (IA) liquid chromatography–tandem mass spectrometry (LC–MS/MS) assay for the quantification of NSEα and NSEγ in human serum. A calibrator was prepared by performing cold denaturation of recombinantly expressed αα and γγ enolase dimers to induce a new dimer equilibrium that was determined to be approximately 1αγ:1γγ:1αα. Selective sample purification was achieved by performing IA extraction using an antibody specific towards NSEγ. The isolated αγ and γγ dimers were denatured and trypsin digested to allow quantification of the selected signature peptides and their corresponding isotopically labelled peptide internal standard. The obtained linear dynamic ranges were determined to be 1.5–56 ng/mL and 0.64–167 ng/mL for NSEα and NSEγ (R2 = 0.88 and 0.97 respectively). Validation of the assay showed acceptable accuracy and precision for NSEα and NSEγ. The method was successfully applied to patient serum in which both isozymes were detected. Compared to the conventional immunoassay, substantially lower total NSE concentrations were measured in IA LC–MS/MS. With this multiplex IA LC-MS/MS assay, the clinical value of quantifying the individual isozymes can be explored. In addition, together with the calibrator described here, it may be applied to standardize NSE immunoassays across different platforms.

Current Developments of Analytical Methodologies for Aflatoxins' Determination in Food during the Last Decade (2013-2022), with a Particular Focus on Nuts and Nut Products.

This review aims to provide a clear overview of the most important analytical development in aflatoxins analysis during the last decade (2013-2022) with a particular focus on nuts and nuts-related products. Aflatoxins (AFs), a group of mycotoxins produced mainly by certain strains of the genus Aspergillus fungi, are known to impose a serious threat to human health. Indeed, AFs are considered carcinogenic to humans, group 1, by the International Agency for Research on Cancer (IARC). Since these toxins can be found in different food commodities, food control organizations worldwide impose maximum levels of AFs for commodities affected by this threat. Thus, they represent a cumbersome issue in terms of quality control, analytical result reliability, and economical losses. It is, therefore, mandatory for food industries to perform analysis on potentially contaminated commodities before the trade. A full perspective of the whole analytical workflow, considering each crucial step during AFs investigation, namely sampling, sample preparation, separation, and detection, will be presented to the reader, focusing on the main challenges related to the topic. A discussion will be primarily held regarding sample preparation methodologies such as partitioning, solid phase extraction (SPE), and immunoaffinity (IA) related methods. This will be followed by an overview of the leading analytical techniques for the detection of aflatoxins, in particular liquid chromatography (LC) coupled to a fluorescence detector (FLD) and/or mass spectrometry (MS). Moreover, the focus on the analytical procedure will not be specific only to traditional methodologies, such as LC, but also to new direct approaches based on imaging and the ability to detect AFs, reducing the need for sample preparation and separative techniques.

HDL Isolated by Immunoaffinity, Ultracentrifugation, or Precipitation is Compositionally and Functionally Distinct

The HDL proteome has been widely recognized as an important mediator of HDL function. While a variety of HDL isolation methods exist, their impact on the HDL proteome and its associated function remain largely unknown. Here, we compared three of the most common methods for HDL isolation, namely immunoaffinity (IA), density gradient ultracentrifugation (UC), and dextran-sulfate precipitation (DS), in terms of their effects on the HDL proteome and associated functionalities. We used state-of-the-art mass spectrometry to identify 171 proteins across all three isolation methods. IA-HDL contained higher levels of paraoxonase 1, apoB, clusterin, vitronectin, and fibronectin, while UC-HDL had higher levels of apoA2, apoC3, and α-1-antytrypsin. DS-HDL was enriched with apoA4 and complement proteins, while the apoA2 content was very low. Importantly, size-exclusion chromatography analysis showed that IA-HDL isolates contained subspecies in the size range above 12 nm, which were entirely absent in UC-HDL and DS-HDL isolates. Analysis of these subspecies indicated that they primarily consisted of apoA1, IGκC, apoC1, and clusterin. Functional analysis revealed that paraoxonase 1 activity was almost completely lost in IA-HDL, despite high paraoxonase content. We observed that the elution conditions, using 3M thiocyanate, during IA resulted in an almost complete loss of paraoxonase 1 activity. Notably, the cholesterol efflux capacity of UC-HDL and DS-HDL was significantly higher compared to IA-HDL. Together, our data clearly demonstrate that the isolation procedure has a substantial impact on the composition, subclass distribution, and functionality of HDL. In summary, our data show that the isolation procedure has a significant impact on the composition, subclass distribution and functionality of HDL. Our data can be helpful in the comparison, replication and analysis of proteomic datasets of HDL.

A Flexible Multiplatform Bioanalytical Strategy for Measurement of Total Circulating Shed Target Receptors: Application to Soluble B Cell Maturation Antigen Levels in the Presence of a Bispecific Antibody Drug.

B cell maturation antigen (BCMA) is a membrane-bound receptor that is overexpressed on multiple myeloma cells and can be targeted with biotherapeutics. Soluble shed forms of membrane-associated receptors in circulation can act as a drug sink, especially when it is present in high molar ratio compared to drug concentration, potentially derailing the intended pharmacological mechanism and impacting pharmacokinetic (PK) measurements and efficacious dose predictions. In this study, we present a bioanalytical strategy for assessing dynamic levels of total soluble BCMA before and during treatment with a bispecific antibody targeting BCMA and CD3. Implementation of a ligand binding assay was not successful due to extensive bispecific antibody interference. Instead, we explored two types of immunoaffinity (IA) liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays, one at the protein level and one at the surrogate peptide level. Ultimately, the protein-level IA-LC-MS/MS method was optimized for use in a cynomolgus monkey PK/pharmacodynamic study. In addition, we demonstrated that the method was easily adapted for use with human samples in preparation for translation to the clinic. This work demonstrates the benefit of flexibility and agility in bioanalytical method development in early drug development. Multiplatform suitability assessments enable rapid, resource-sparing identification and qualification of clinically translatable assays. We recommend early adoption of this strategy to provide enough time for critical reagent development and assay validation for analysis of shed targets.

Conjugation Site Influences Antibody-Conjugated Drug PK Assays: Case Studies for Disulfide-Linked, Self-Immolating Next-Generation Antibody Drug Conjugates.

Immunoaffinity (IA) LC-MS/MS pharmacokinetic (PK) assays are widely used in the field for antibody drug conjugates (ADCs) containing peptide linkers that are enzymatically cleavable, such as MC-ValCit-PAB. Conjugate PK assay strategies for these ADCs involve cleavage with cathepsin B or papain to release and measure the antibody-conjugated drug (acDrug) concentration. However, robust acDrug PK methods for disulfide-linked self-immolating ADCs are lacking as they are a different conjugation modality. We developed acDrug PK assays for next-generation disulfide-linked ADCs involving immunoaffinity capture, chemical cleavage, and LC-MS/MS. Disulfide-linked ADCs captured from plasma were chemically reduced at basic pH to release the linker-drug, followed by self-immolation to liberate the active drug, and quantified by MRM LC-MS/MS. Herein, we detail the development and optimization of this chemical cleavage acDrug PK assay, resulting in robust accuracy and precision (±20%). The conjugation site of the linker-drug on the antibody was found to affect the kinetics of drug release. Multiple biophysical and chemical characteristics, such as tertiary structure, fractional solvent accessibility, pKa of the conjugation site, surrounding residue's pI, and electrostatic charge, may directly impact the drug release kinetics. Similar site-specific stability has been previously reported for ADCs in vivo. The assay development and qualification data for this original assay format are presented along with its application to multiple in vitro and in vivo studies across species.

Residual Analysis of Aflatoxins in Spice by HPLC Coupled with Solid-Phase Dispersive Extraction and Solid-Phase Fluorescence Derivatization Method.

Aflatoxins (AFs) are carcinogenic mycotoxins. A simple, quick, and accurate method for the micro-analysis of AFs in foodstuffs, especially spices, is needed. A sophisticated pretreatment method that combines solid-phase dispersive extraction (SPDE) and solid-phase fluorescence derivatization using immunoaffinity (IA) gel as the solid phase was developed to analyze AFs in spices simply, quickly, and sensitively by liquid chromatography with fluorescence detection. White and black pepper samples were extracted with a mixed solution of methanol/water (4:1) and then diluted with 7% aqueous solution of Triton-X. The solution was subjected to cleanup by SPDE using IA gel. Trifluoroacetic acid was added to the IA gel for on-site solid-phase fluorescence derivatization. Chromatograms containing well-separated peaks and few interference peaks from contaminants were obtained. The method detection limit of AFs in white and black pepper was 0.15-0.29 ng/g. Repeatability and intermediate precision were <10% and <15%, respectively, and accuracy was 61.7-87.8%. In addition, inter-laboratory precision was <29% and mean recovery was 61.5-76.7%. A favorable z-score of |Z| ≦ 1 was obtained in seven laboratories, although one laboratory gave 2 < |Z| < 3. The validity, reliability, practicality, and robustness of the developed method were verified. By using SPDE and solid-phase fluorescence derivatization in combination for AF analysis, fluorescence derivatization during cleanup was realized, leading to simplification of the pretreatment operation.

Polymeric monolithic microcartridges with gold nanoparticles for the analysis of protein biomarkers by on-line solid-phase extraction capillary electrophoresis-mass spectrometry

In this study, polymeric monoliths with gold nanoparticles (AuNP@monolith) were investigated as microcartridges for the analysis of protein biomarkers by on-line solid-phase extraction capillary electrophoresis-mass spectrometry (SPE-CE-MS). “Plug-and-play” microcartridges (7 mm) were prepared from a glycidyl methacrylate (GMA)-based monolithic capillary column (5 cm x 250 µm i.d.), which was modified with ammonia and subsequently functionalized with gold nanoparticles (AuNPs). The performance of these novel microcartridges was evaluated with human transthyretin (TTR), which is a protein related to different types of familial amyloidotic polyneuropathies (FAP). Protein retention depended on the isoelectric point of the protein (TTR pI~5.4) and elution was achieved with a basic phosphate solution. Under the optimized conditions, limits of detection (LODs) for TTR by AuNP@monolith-SPE-CE-MS were 50 times lower than by CE-MS (5 vs 250 mg•L−1, with an ion trap (IT) mass spectrometer). The sensitivity enhancement was similar compared to SPE-CE-MS using immunoaffinity (IA) microcartridges with intact antibodies against TTR. Linearity, repeatability in migration times and peak areas, reusability, reproducibility and application to serum samples were also evaluated.

Routine and novel methods for isolation of extracellular vesicles

Extracellular vesicles (EV) play an important role in many physiological and pathological processes. Three main classes of EV are recognized, based on their biogenesis: exosomes, microvesicles and apoptotic bodies. Exosomes are extracellular-vesicles of 30 to 150 nm found in many bodily fluids (blood, urine, milk, cerebrospinal fluid, etc.). Due to their cellular origin and role in physiological and pathological processes, exosomes present in body fluids are considered a unique source of non-invasive and clinically relevant biomarkers. Analysis of exosomes can provide insight into the state of the parent-cell from which they originated. However, there is great heterogeneity in the methodologies used for exosome purification affecting the results of downstream analysis. The most commonly used methods for purification are based on ultracentrifugation (UC), ultrafiltration (UF) and precipitation. However, these are hard to standardize, leading to confounding and misleading results during downstream analyses, especially when highly-sensitive techniques such as mass spectrometry are used. Furthermore, loss of certain fractions or damage of EVs can lead to loss in obtained protein and RNA profile. Consequently, there is an emerging need to obtain consensus protocols for exosome isolation and identification of specific sub-populations. This manuscript will critically review the most commonly used techniques for EV purification such as UC, UF, size-exclusion, precipitation and immunoaffinity (IA) methods. We will also review the use of nano-antibodies for the development of novel IA protocols and identification of new EV biomarkers.

Analytical techniques for determination of mycotoxins in barley, malt and beer: A review

The increasing interest in defining the content of mycotoxins is related to the development of methods for their determination. Several methods of determination have been published. This paper describes analytical procedures such as (a) sample preparation – sampling and homogenization, (b) extraction and purification – solid phase extraction (SPE), a QuEChERS method (acronymic name from quick, easy, cheap, effective, rugged and safe), solid-liquid extraction (SLE) and immuno affinity extraction (IAE). It also provides a review of, (c) instruments, and other analytical methods such as thin layer chromatography (TLC), enzyme linked immune sorbent assay (ELISA) and liquid chromatography (LC), gas chromatography (GC) with different detectors for determination of mycotoxin in barley, malt and beer are discussed.

Multimycotoxin Analysis by LC-MS/MS in Cereal Food and Feed: Comparison of Different Approaches for Extraction, Purification, and Calibration

Twelve different approaches commonly used for the simultaneous LC tandem MS (MS/MS) determination of mycotoxins (deoxynivalenol, aflatoxins, ochratoxin A, T-2 and HT-2 toxins, fumonisins, and zearalenone) were tested in cereals and feed materials. They comprised different extraction solvents, types of cleanup [solid-phase extraction, QuEChERS, and immunoaffinity (IMA)], and calibration approaches (external or matrix-matched). The percentage of mycotoxins with acceptable recovery, according to Regulation (EC) No. 401/2006, ranged from 9 to 100%. The approach giving the highest percentage of acceptable results was selected and further tested for corn, rice, and feed spiked at three different mycotoxin levels (low, medium, and high). The method is based on extraction with MeOH-water (70 + 30, v/v) and cleanup with two multiantibody IMA columns. For corn and rice spiked at low mycotoxin levels, a significant matrix effect was observed and was compensated by using 13C calibration. At higher mycotoxin levels (medium and high), matrix effects were negligible as no significant differences were observed for the majority of recovery results calculated by 13C calibration and external calibration. Although the proposed method still needs improvement in terms of accuracy and, to a lesser extent, precision, it was successfully tested with four proficiency tests in buckwheat, corn, rice, and feed, giving acceptable z-scores for 97% (34 out of 35) of results.

Canonical and selective approaches in exosome purification and their implications for diagnostic accuracy

: Extracellular vesicles (EVs) play a pivotal role in cell to cell signalling in both physiological and pathological conditions. Based on their biogenesis, three main classes of EVs are recognized: exosomes, microvesicles and apoptotic bodies. Exosomes are cell-derived vesicles (EVs) present in many body fluids (blood, urine, milk, cerebrospinal fluid) ranging in size from 30 to 150 nm. Due to their involvement in numerous physiological and pathological events, cell derived exosomes in bodily fluids represent a unique source of clinically relevant and non-invasive biomarkers. Since biomolecule content present in exosomes reflects the state of the parent cell, exosome analysis and characterization may provide valuable information about the presence of aberrant processes in the cells from which they originated. Because of the large and heterogeneous scientific community working with exosomes, several purification strategies have been applied so far, which yield EV fractions largely differing for quantity and quality. Most of the present exosome isolation approaches based on ultracentrifugation (UC), ultrafiltration (UF) or precipitation, are inefficient and hard to standardize, thereby creating low reproducibility in sample quality and potentially misleading results because highly sensitivity downstream analytical techniques, such as mass spectrometry, can detect even minute traces of co-isolated contaminants. Furthermore, loss of certain exosomal fractions during purification process or damage of exosomal membrane integrity can also alter final protein and RNA profiles. As a consequence, there is a strong interest in consensus principles for the exosome purification and the search for reliable methods for selective isolation of EV sub-populations. In the present manuscript, we critically overview the most commonly used techniques used for exosome preparation such as ultra-centrifugation, size-based isolation methods, precipitation and immunoaffinity (IA) and their respective applicability for purification of exosomes from clinically relevant samples.

Quantitation of a Therapeutic Antibody in Serum Using Intact Sequential Affinity Capture, Trypsin Digestion, and LC-MS/MS.

Large molecule quantitation by LC-MS/MS commonly relies on bottom-up or so-called surrogate peptide measurements to infer the whole-molecule concentration. This can lead to questions about what is actually being measured in the assay (intact drug and/or other drug related material). An intact sequential affinity capture (ISAC) assay was developed utilizing two different immunoaffinity (IA) reagents. The reagents were selective for the heavy and light chain of a monoclonal antibody, which when used consecutively, ensures that only the intact form of the antibody is represented by the surrogate peptide. The approach provided comparable results to a traditional sandwich IA assay indicating similar capture populations. The use of an initial ISAC assessment of affinity capture purification, should add a degree of confidence in the use of a single IA-LC-MS/MS quantitation assay.

Canonical and selective approaches in exosome purification and their implications for diagnostic accuracy

Extracellular vesicles (EVs) play a pivotal role in cell to cell signalling in both physiological and pathological conditions. Based on their biogenesis, three main classes of EVs are recognized: exosomes, microvesicles and apoptotic bodies. Exosomes are cell-derived vesicles (EVs) present in many body fluids (blood, urine, milk, cerebrospinal fluid) ranging in size from 30 to 150 nm. Due to their involvement in numerous physiological and pathological events, cell derived exosomes in bodily fluids represent a unique source of clinically relevant and non-invasive biomarkers. Since biomolecule content present in exosomes reflects the state of the parent cell, exosome analysis and characterization may provide valuable information about the presence of aberrant processes in the cells from which they originated. Because of the large and heterogeneous scientific community working with exosomes, several purification strategies have been applied so far, which yield EV fractions largely differing for quantity and quality. Most of the present exosome isolation approaches based on ultracentrifugation (UC), ultrafiltration (UF) or precipitation, are inefficient and hard to standardize, thereby creating low reproducibility in sample quality and potentially misleading results because highly sensitivity downstream analytical techniques, such as mass spectrometry, can detect even minute traces of co-isolated contaminants. Furthermore, loss of certain exosomal fractions during purification process or damage of exosomal membrane integrity can also alter final protein and RNA profiles. As a consequence, there is a strong interest in consensus principles for the exosome purification and the search for reliable methods for selective isolation of EV sub-populations. In the present manuscript, we critically overview the most commonly used techniques used for exosome preparation such as ultra-centrifugation, size-based isolation methods, precipitation and immunoaffinity (IA) and their respective applicability for purification of exosomes from clinically relevant samples.

Immuno Affinity SELEX for Simple, Rapid, and Cost-Effective Aptamer Enrichment and Identification against Aflatoxin B1.

Aflatoxins are naturally occurring mycotoxins that contaminate food and agro commodities, leading to acute and chronic health conditions in human and animals. In the present work, an attempt was made to generate high-affinity single stranded DNA aptamers that specifically bind to Aflatoxin B1 (AFB1) by a modified Systemic Evolution of Ligands by Exponential Enrichment (SELEX) procedure with the aid of Immunoaffinity columns. Ten rounds of SELEX and alternating three counter SELEX rounds with a cocktail of related and other mycotoxins were performed to enhance the specificity. Resultant 105 aptamers were clustered into 12 groups according to their primary sequence homology. Candidates with lowest Gibbs free energy (dG value) and unique stem loop structures were selected for further characterization. Aptamers, AFLA5, AFLA53, and AFLA71 exhibiting lower Kd values (50.45 ± 11.06, 48.29 ± 9.45, and 85.02 ± 25.74 nM) were chosen for development of ELONA and determination of purification ability of toxin. The detection limit (LOD) of AFLA5 and AFLA71 was 20 and 40 ng/ml, respectively. HPLC analysis implied that selected aptamers were able to recover and quantify 82.2 to 96.21% (LOQ – 53.74 ng) and 78.3 to 94.22% (LOQ – 66.75 ng) of AFB1 from spiked corn samples, respectively. These findings indicate, immunoaffinity based SELEX can pave an alternative approach to screen aptamers against mycotoxin detection and purification.

Validation of a biotherapeutic immunoaffinity-LC-MS/MS assay in monkey serum: 'plug-and-play' across seven molecules.

Biotherapeutics development requires validated assays in biological matrices for pharmacokinetic assessment. Historically, ligand-binding assays have been the predominant platform available. Recently, alternative hybrid methods, combining ligand-binding analyte enrichment with LC-MS detection have emerged. Methodology & results: The validation of an immunoaffinity (IA)-LC-MS/MS method to quantify a monoclonal antibody biotherapeutic in cynomolgus monkey serum is described. This method includes immunoaffinity capture of the antibody in serum, followed by enzymatic digestion and detection of a framework peptide. Using similar method conditions, six additional biotherapeutic assays were readily validated in different nonhuman mammalian species, including mouse, rat and monkey. The immunoaffinity-LC-MS/MS assay validation results across seven antibody therapeutics, using comparable conditions, illustrate the 'plug-and-play' nature of the IA-LC-MS/MS mAb framework peptide assay format.

Large-scale implementation of sequential protein and peptide immunoaffinity enrichment LC/nanoLC-MS/MS for human β-nerve growth factor.

A previously described immunoaffinity (IA)-LC-MS/MS assay for human β-nerve growth factor (β-NGF) was implemented to support large-scale sample testing for multiple clinical trials. Methodology & results: The procedure was modified to increase throughput by simultaneous preparation of two 96-well plates and LC duty-cycle reduction. Robustness of the LC method and nano-ESI was ensured during large-scale assay execution by closely monitoring and, if needed, replacing system components prior to failure. Following validation, the assay was used to analyze approximately 19,000 samples from multiple clinical studies over several years. Routine implementation of the β-NGF IA-LC-MS/MS assay supported drug development programs. This optimized assay format now serves as a template for other clinical protein biomarker assays.