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Rollo D, Kulkarni A, Yu K, Fabris D. Investigating the Merits of Microfluidic Capillary Zone Electrophoresis-Mass Spectrometry (CZE-MS) in the Bottom-Up Characterization of Larger RNAs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:561-574. [PMID: 38350102 DOI: 10.1021/jasms.3c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Established bottom-up approaches for the characterization of nucleic acids (NAs) rely on the strand-cleavage activity of nucleotide-specific endonucleases to generate smaller oligonucleotides amenable to gas-phase sequencing. The complexity of these hydrolytic mixtures calls for the utilization of a front-end separation to facilitate full mass spectrometric (MS) characterization. This report explored the merits of microfluidic capillary zone electrophoresis (CZE) as a possible alternative to common liquid chromatography techniques. An oligonucleotide ladder was initially employed to investigate the roles of fundamental analyte features and experimental parameters in determining the outcome of CZE-MS analyses. The results demonstrated the ability to fully resolve the various rungs into discrete electrophoretic peaks with full-width half-height (FWHH) resolution that was visibly affected by the overall amount of material injected into the system. Analogous results were obtained from a digestion mixture prepared by treating yeast tRNAPhe (75 nt) with RNase T1, which provided several well-resolved peaks in spite of the increasing sample heterogeneity. The regular shapes of such peaks, however, belied the fact that most of them contained sets of comigrating species, as shown by the corresponding MS spectra. Even though it was not possible to segregate each species into an individual electrophoretic peak, the analysis still proved capable of unambiguously identifying a total of 29 hydrolytic products, which were sufficient to cover 96% of the tRNAPhe's sequence. Their masses accurately reflected the presence of modified nucleotides characteristic of this type of substrate. The analysis of a digestion mixture obtained from the 364 nt HIV-1 5'-UTR proved to be more challenging. The electropherogram displayed fewer well-resolved peaks and significantly greater incidence of product comigration. In this case, fractionating the highly heterogeneous mixture into discrete bands helped reduce signal suppression and detection bias. As a result, the corresponding MS data enabled the assignment of 248 products out of the possible 513 predicted from the 5'-UTR sequence, which afforded 100% sequence coverage. This figure represented a significant improvement over the 36 total products identified earlier under suboptimal conditions, which afforded only 57% coverage, or the 83 observed by direct infusion nanospray-MS (72%). These results provided a measure of the excellent potential of the technique to support the bottom-up characterization of progressively larger NA samples, such as putative NA therapeutics and mRNA vaccines.
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Affiliation(s)
- Daniele Rollo
- University of Connecticut, Storrs, Connecticut 06269, United States
| | | | - Kate Yu
- 908 Devices, Boston, Massachusetts 02210, United States
| | - Daniele Fabris
- University of Connecticut, Storrs, Connecticut 06269, United States
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Naghdi E, Moran GE, Reinau ME, De Malsche W, Neusüß C. Concepts and recent advances in microchip electrophoresis coupled to mass spectrometry: Technologies and applications. Electrophoresis 2023; 44:246-267. [PMID: 35977423 DOI: 10.1002/elps.202200179] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/11/2022] [Accepted: 08/13/2022] [Indexed: 02/01/2023]
Abstract
The online coupling of microchip electrophoresis (ME) as a fast, highly efficient, and low-cost miniaturized separation technique to mass spectrometry (MS) as an information-rich and sensitive characterization technique results in ME-MS an attractive tool for various applications. In this paper, we review the basic concepts and latest advances in technology for ME coupled to MS during the period of 2016-2021, covering microchip materials, structures, fabrication techniques, and interfacing to electrospray ionization (ESI)-MS and matrix-assisted laser desorption/ionization-MS. Two critical issues in coupling ME and ESI-MS include the electrical connection used to define the electrophoretic field strength along the separation channel and the generation of the electrospray for MS detection, as well as, a miniaturized ESI-tip. The recent commercialization of ME-MS in zone electrophoresis and isoelectric focusing modes has led to the widespread application of these techniques in academia and industry. Here we summarize recent applications of ME-MS for the separation and detection of antibodies, proteins, peptides, carbohydrates, metabolites, and so on. Throughout the paper these applications are discussed in the context of benefits and limitations of ME-MS in comparison to alternative techniques.
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Affiliation(s)
- Elahe Naghdi
- Department of Chemistry, Aalen University, Aalen, Germany
| | - Griffin E Moran
- Novo Nordisk A/S, Global Research Technologies, Maaloev, Denmark
| | | | - Wim De Malsche
- µFlow group, Department of Chemical Engineering, Vrije Universiteit Brussel, Brussels, Belgium
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Whitson HE, Colton C, El Khoury J, Gate D, Goate A, Heneka MT, Kaddurah-Daouk R, Klein RS, Shinohara ML, Sisodia S, Spudich SS, Stevens B, Tanzi R, Ting JP, Garden G. Infection and inflammation: New perspectives on Alzheimer's disease. Brain Behav Immun Health 2022; 22:100462. [PMID: 36118272 PMCID: PMC9475126 DOI: 10.1016/j.bbih.2022.100462] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/10/2022] [Indexed: 11/24/2022] Open
Abstract
Neuroinflammation has been recognized as a component of Alzheimer's Disease (AD) pathology since the original descriptions by Alois Alzheimer and a role for infections in AD pathogenesis has long been hypothesized. More recently, this hypothesis has gained strength as human genetics and experimental data suggest key roles for inflammatory cells in AD pathogenesis. To review this topic, Duke/University of North Carolina (Duke/UNC) Alzheimer's Disease Research Center hosted a virtual symposium: "Infection and Inflammation: New Perspectives on Alzheimer's Disease (AD)." Participants considered current evidence for and against the hypothesis that AD could be caused or exacerbated by infection or commensal microbes. Discussion focused on connecting microglial transcriptional states to functional states, mouse models that better mimic human immunity, the potential involvement of inflammasome signaling, metabolic alterations, self-reactive T cells, gut microbes and fungal infections, and lessons learned from Covid-19 patients with neurologic symptoms. The content presented in the symposium, and major topics raised in discussions are reviewed in this summary of the proceedings.
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Affiliation(s)
- Heather E. Whitson
- Duke Center for the Study of Aging and Human Development, Duke University School of Medicine, Busse Bldg Rm 3502, Durham, NC, 27710, USA
- Durham VA Medical Center, Geriatric Research Education and Clinical Center, 508 Fulton Street, Durham, NC, 27705, USA
| | - Carol Colton
- Department of Neurology, Duke University School of Medicine, 3116 N Duke St, Durham, NM, 27704, USA
| | - Joseph El Khoury
- Center for Immunology & Inflammatory Diseases, Division of Infectious Diseases, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA
| | - David Gate
- The Ken & Ruth Davee Dept of Neurology, Northwestern University Feinberg School of Medicine, 303 E Chicago Ave, Ward 12-140, Chicago, IL 60611, USA
| | - Alison Goate
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029-6574, USA
| | - Michael T. Heneka
- Dept of Neurodegenerative Disease and Geriatric Psychiatry/Neurology, University of Bonn Medical Center, Sigmund-Freud Str. 25, 53127, Bonn, Germany
| | - Rima Kaddurah-Daouk
- Dept of Psychiatry and Behavioral Sciences, Dept of Medicine, Duke Institute of Brain Sciences, Duke University School of Medicine, DUMC Box 3903, Blue Zone, South, Durham, NC, 27710, USA
| | - Robyn S. Klein
- Center for Neuroimmunology & Neuroinfectious Diseases, Depts of Medicine, Pathology & Immunology, and Neuroscience, Washington University School of Medicine, 660 S Euclid Ave, Box 8015, St. Louis, MO, 63110, USA
| | - Mari L. Shinohara
- Dept of Immunology, Duke University School of Medicine, 207 Research Dr, Box 3010, Durham, NC, 27710, USA
| | - Sangram Sisodia
- Dept of Neurobiology, University of Chicago, Abbott Memorial Hall, 947 East 58th St, MC 0928, Chicago, IL, 60637, USA
| | - Serena S. Spudich
- Dept of Neurology, Yale School of Medicine, PO Box 208018, New Haven, CT, 06520, USA
| | - Beth Stevens
- F.M. Kirby Neurobiology Center, Children's Hospital Boston, 300 Longwood Ave, Center for Life Sciences 12th Floor, Boston, MA, 02115, USA
| | - Rudolph Tanzi
- McCance Center for Brain Health, Massachusetts General Hospital, 114 16th St, Charlestown, MA, 02129, USA
| | - Jenny P. Ting
- Depts of Genetics, Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for Translational Immunology, UNC School of Medicine, 125 Mason Farm Road, 6th Floor Marsico Hall, Chapel Hill, NC, 27599-7290, USA
| | - Gwenn Garden
- Dept of Neurology, UNC School of Medicine, Physicians Office Building, 170 Manning Drive, Campus Box 7025, Chapel Hill, NC, 27599-7025, USA
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