High-sensitivity workflow for LC-MS-based analysis of GalNAc-conjugated oligonucleotides: a case study

Preconcentration and purification of oligonucleotides from heat-treated human plasma by anion-exchange microextraction devices coupled to high performance liquid chromatography-mass spectrometry

BACKGROUND

Methodologies that preconcentrate high quality nucleic acids (NAs) for downstream assays are essential for their accurate and reproducible analysis by mass spectrometry (MS). Established methods rely on solid-phase extraction that involves numerous steps and user intervention or liquid-liquid extractions that are time-consuming and employ toxic organic solvents. A promising alternative methodology involves anion-exchange microextraction sorbents that selectively isolate NAs through electrostatic interactions with the negatively charged phosphodiester backbone. The microextraction devices recover and preconcentrate NAs using a salt-containing solution, which is generally incompatible with MS analysis.

RESULTS

Six anion-exchange microextraction sorbents featuring monomers derived from 2-aminoethyl methacrylate were synthesized and examined in this study to understand the interactions that take place between NAs and the ammonium cationic moiety. Sorbent affinities for bovine serum albumin, small single-stranded oligonucleotides, RNA, short double-stranded DNA), and 2000 bp dsDNA were determined. Recoveries of an oligonucleotide and 2000 bp dsDNA were measured and examined in salt solutions of varied concentration, anion species, and organic additives. High oligonucleotide preconcentration factors of 8.6 ± 0.2 were obtained for the sorbent featuring two cationic ammonium moieties on each monomer using 500.0 mM ammonium perchlorate. A separate sorbent composed of dimethyl ethyl ammonium moieties produced a preconcentration factor of 4.6 ± 0.2 using only 31.25 mM ammonium perchlorate. The sorbents were demonstrated in the complete workflow in which an analog antisense oligonucleotide was spiked into human plasma and purified, enabling successful molecular weight analysis.

SIGNIFICANCE

This study demonstrates the compatibility of microextraction recovery solutions comprised of ammonium perchlorate with reversed-phase and hydrophilic interaction chromatographic separations and time-of-flight MS for characterization of oligonucleotides. The combination of anion-exchange microextraction sorbents and HPLC-TOF-MS enables the purification, preconcentration, and identification of a oligonucleotides from heat-treated human plasma. The compatibility of the salt-containing recovery solutions with chromatographic separation modalities highlights that anion-exchange microextraction devices are a complete and compelling sample preparation methodology for oligonucleotides.

Review on the bioanalysis of non-virus-based gene therapeutics

Over the past years, gene therapeutics have held great promise for treating many inherited and acquired diseases. The increasing number of approved gene therapeutics and developing clinical pipelines demonstrate the potential to treat diseases by modifying their genetic blueprints in vivo. Compared with conventional treatments targeting proteins rather than underlying causes, gene therapeutics can achieve enduring or curative effects via gene activation, inhibition, and editing. However, the delivery of DNA/RNA to the target cell to alter the gene expression is a complex process that involves, crossing numerous barriers in both the extracellular and intracellular environment. Generally, the delivery strategies can be divided into viral-based and non-viral-based vectors. This review summarizes various bioanalysis strategies that support the non-virus-based gene therapeutics research, including pharmacokinetics (PK)/toxicokinetics (TK), biodistribution, immunogenicity evaluations for the gene cargo, vector, and possible expressed protein, and highlights the challenges and future perspectives of bioanalysis strategies in non-virus-based gene therapeutics. This review may provide new insights and directions for the development of emerging bioanalytical methods, offering technical support and a research foundation for innovative gene therapy treatments.

Observations from a decade of oligonucleotide bioanalysis by LC-MS

There is a growing need for efficient bioanalysis of oligonucleotide therapeutics. This broad class of molecules presents numerous challenges relative to traditional small molecule therapeutics. Methodologies including ligand-binding assays or polymerase chain reaction may be fit-for-purpose in many instances, but liquid chromatography coupled to mass spectrometry (LC-MS) often delivers the best balance of sensitivity and selectivity. Over the last decade, we have engaged with many such molecules and derived insights into challenges and solutions. Herein, we provide four case studies illustrating challenges we have encountered. These issues include low or variable analyte recovery, poor resolution from related species, chromatographic abnormalities or challenging sensitivity. We present a summary of considerations, based on these experiences, to assist others working in the area.

Rapid Intact Mass Analysis and Evaluation of the Separation Potential of Microfluidic Capillary Electrophoresis Mass Spectrometry for Oligonucleotides

Oligonucleotide characterization is a rapidly advancing field in the biopharmaceutical industry. Understanding critical quality attributes, such as intact mass and impurities, requires a toolbox of analytical techniques, which commonly includes liquid chromatography-mass spectrometry (LC-MS). Oligonucleotide LC-MS analysis frequently requires sample run times upward of 15 min to achieve separation of multiple oligonucleotide species. Additionally, LC methods frequently employ mobile phase additives such as triethylamine and 1,1,1,3,3,3-hexafluoro-2-propanol that are not always desired for use in MS instrumentation. Here, microfluidic capillary electrophoresis mass spectrometry (CE-MS) via ZipChip technology was employed to enable rapid intact mass analysis of oligonucleotide single strands. Baseline separation of equal length oligonucleotides was achieved in less than 4 min. Additionally, the potential of the ZipChip platform for separation of oligonucleotide full-length products (FLPs) and their impurities was evaluated.

Bioanalysis of Oligonucleotide by LC-MS: Effects of Ion Pairing Regents and Recent Advances in Ion-Pairing-Free Analytical Strategies

Oligonucleotides (OGNs) are relatively new modalities that offer unique opportunities to expand the therapeutic targets. Reliable and high-throughput bioanalytical methods are pivotal for preclinical and clinical investigations of therapeutic OGNs. Liquid chromatography-mass spectrometry (LC-MS) is now evolving into being the method of choice for the bioanalysis of OGNs. Ion paring reversed-phase liquid chromatography (IP-RPLC) has been widely used in sample preparation and LC-MS analysis of OGNs; however, there are technical issues associated with these methods. IP-free methods, such as hydrophilic interaction liquid chromatography (HILIC) and anion-exchange techniques, have emerged as promising approaches for the bioanalysis of OGNs. In this review, the state-of-the-art IP-RPLC-MS bioanalytical methods of OGNs and their metabolites published in the past 10 years (2012-2022) are critically reviewed. Recent advances in IP-reagent-free LC-MS bioanalysis methods are discussed. Finally, we describe future opportunities for developing new methods that can be used for the comprehensive bioanalysis of OGNs.