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Pandey D, Ghosh D. Proteomics-based host-specific biomarkers for tuberculosis: The future of TB diagnosis. J Proteomics 2024; 305:105245. [PMID: 38942234 DOI: 10.1016/j.jprot.2024.105245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Tuberculosis (TB) is an infectious disease that remains one of the major global public health concerns. Early detection of Active Pulmonary TB is therefore of utmost importance for controlling lethality and disease spreading. Currently available TB diagnostics can be broadly categorized into microscopy, culture-based, and molecular approaches, all of which come with compromised sensitivity, limited efficacy, and high expenses. Hence, rapid, sensitive, and affordable diagnostic methods for TB is the current prerequisite for disease management. This review summarizes the proteomics investigations for host-specific biomarkers from serum, sputum, saliva, and urine samples of TB patients, along with patients having comorbidity. Thorough data mining from available literature led us to conclude that the host-specific proteins involved in immunity and defense, metabolic regulation, cellular adhesion, and motility, inflammatory responses, and tissue remodelling have shown significant deregulation upon Mycobacterium tuberculosis (Mtb) infection. Notably, the immunoregulatory protein orosomucoid (ORM) was up-regulated in active TB compared to non-TB individuals, as observed in multiple studies from diverse sample types. Mannose receptor C type 2 (MRC2) was identified as an upregulated, treatment response biomarker in two independent serum proteomics investigations. Thorough mechanistic investigation on these candidate proteins would be fascinating to dig into potential drug targets and customized therapeutics for TB patients, along with their diagnostic potentials.
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Affiliation(s)
- Divya Pandey
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, UPES, Dehradun 248007, Uttarakhand, India
| | - Dipanjana Ghosh
- School of Biomolecular Engineering & Biotechnology, Rajiv Gandhi Technological University, Airport Bypass Road, Bhopal 462033, India.
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Huangfu S, Yu X, Sun Z, Jiang B, Chen H. Chemical reagents for the enrichment of modified peptides in MS-based identification. Chem Commun (Camb) 2024; 60:1509-1516. [PMID: 38224214 DOI: 10.1039/d3cc05260e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Chemical reagents with special groups as enrichable handles have empowered the ability to label and enrich modified peptides. Here is an overview of different chemical reagents with affinity tags to isolate labeled peptides and the latest developments of enrichment strategies. Biotin is the most used affinity tag due to its high interaction with avidin. To decrease the unfavorable influence of biotin for its poor efficiency in ionization and fragmentation in downstream MS analysis, cleavable moieties were installed between the reactive groups and biotin to release labeled peptides from the biotin. To minimize the steric hindrance of biotin, a two-step method was developed, for which alkyne- or azide-tagged linkers were firstly used to label peptides and then biotin was installed through click chemistry. Recently, new linkers using a small phosphonic acid as the affinity tag for IMAC or TiO2 enrichment have been developed and successfully used to isolate chemically labeled peptides in XL-MS. A stable P-C instead of P-O bond was introduced to linkers to differentiate labeled and endogenous phosphopeptides. Furthermore, a membrane-permeable phosphonate-containing reagent was reported, which facilitated the study of living systems. Taking a cue from classic chemical reactions, stable metal-complex intermediates, including cobalt and palladium complexes, have been developed as peptide purification systems. Advanced enrichment strategies have also been proposed, such as the two-stage IMAC enrichment method and biotin-based two-step reaction strategy, allowing the reduction of unwanted peptides and improvements for the analysis of specific labeled peptides. Finally, future trends in the area are briefly discussed.
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Affiliation(s)
- Shangwei Huangfu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China
| | - Xianqiang Yu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China
| | - Ziyu Sun
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.
- School of Physical Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China
| | - Hongli Chen
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.
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Tripathi R, Guglani A, Ghorpade R, Wang B. Biotin conjugates in targeted drug delivery: is it mediated by a biotin transporter, a yet to be identified receptor, or (an)other unknown mechanism(s)? J Enzyme Inhib Med Chem 2023; 38:2276663. [PMID: 37955285 PMCID: PMC10653662 DOI: 10.1080/14756366.2023.2276663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/24/2023] [Indexed: 11/14/2023] Open
Abstract
Conjugation of drugs with biotin is a widely studied strategy for targeted drug delivery. The structure-activity relationship (SAR) studies through H3-biotin competition experiments conclude with the presence of a free carboxylic acid being essential for its uptake via the sodium-dependent multivitamin transporter (SMVT, the major biotin transporter). However, biotin conjugation with a payload requires modification of the carboxylic acid to an amide or ester group. Then, there is the question as to how/whether the uptake of biotin conjugates goes through the SMVT. If not, then what is the mechanism? Herein, we present known uptake mechanisms of biotin and its applications reported in the literature. We also critically analyse possible uptake mechanism(s) of biotin conjugates to address the disconnect between the results from SMVT-based SAR and "biotin-facilitated" targeted drug delivery. We believe understanding the uptake mechanism of biotin conjugates is critical for their future applications and further development.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Anchala Guglani
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Rujuta Ghorpade
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
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Wu W, Zheng J, Wang R, Wang Y. Ion channels regulate energy homeostasis and the progression of metabolic disorders: Novel mechanisms and pharmacology of their modulators. Biochem Pharmacol 2023; 218:115863. [PMID: 37863328 DOI: 10.1016/j.bcp.2023.115863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
The progression of metabolic diseases, featured by dysregulated metabolic signaling pathways, is orchestrated by numerous signaling networks. Among the regulators, ion channels transport ions across the membranes and trigger downstream signaling transduction. They critically regulate energy homeostasis and pathogenesis of metabolic diseases and are potential therapeutic targets for treating metabolic disorders. Ion channel blockers have been used to treat diabetes for decades by stimulating insulin secretion, yet with hypoglycemia and other adverse effects. It calls for deeper understanding of the largely elusive regulatory mechanisms, which facilitates the identification of new therapeutic targets and safe drugs against ion channels. In the article, we critically assess the two principal regulatory mechanisms, protein-channel interaction and post-translational modification on the activities of ion channels to modulate energy homeostasis and metabolic disorders through multiple novel mechanisms. Moreover, we discuss the multidisciplinary methods that provide the tools for elucidation of the regulatory mechanisms mediating metabolic disorders by ion channels. In terms of translational perspective, the mechanistic analysis of recently validated ion channels that regulate insulin resistance, body weight control, and adverse effects of current ion channel antagonists are discussed in details. Their small molecule modulators serve as promising new drug candidates to combat metabolic disorders.
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Affiliation(s)
- Wenyi Wu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Jianan Zheng
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, China.
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Li Y, Kanao E, Yamano T, Ishihama Y, Imami K. TurboID-EV: Proteomic Mapping of Recipient Cellular Proteins Proximal to Small Extracellular Vesicles. Anal Chem 2023; 95:14159-14164. [PMID: 37709279 PMCID: PMC10534987 DOI: 10.1021/acs.analchem.3c01015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
Extracellular vesicles (EVs), including exosomes, have been recognized as key mediators of intercellular communications through donor EV and recipient cell interaction. Until now, most studies have focused on the development of analytical tools to separate EVs and their applications for the molecular profiling of EV cargo. However, we lack a complete picture of the mechanism of EV uptake by the recipient cells. Here, we developed the TurboID-EV system with the engineered biotin ligase TurboID, tethered to the EV membrane, which allowed us to track the footprints of EVs during and after EV uptake by the proximity-dependent biotinylation of recipient cellular proteins. To analyze biotinylated recipient proteins from low amounts of input cells (corresponding to ∼10 μg of proteins), we developed an integrated proteomic workflow that combined stable isotope labeling with amino acids in cultured cells (SILAC), fluorescence-activated cell sorting, spintip-based streptavidin affinity purification, and mass spectrometry. Using this method, we successfully identified 456 biotinylated recipient proteins, including not only well-known proteins involved in endocytosis and macropinocytosis but also other membrane-associated proteins such as desmoplakin and junction plakoglobin. The TurboID-EV system should be readily applicable to various EV subtypes and recipient cell types, providing a promising tool to dissect the specificity of EV uptake mechanisms on a proteome-wide scale.
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Affiliation(s)
- Yuka Li
- Department
of Molecular Systems BioAnalysis, Department of Proteomics and Drug
Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Eisuke Kanao
- Laboratory
of Clinical and Analytical Chemistry, National
Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
- Department
of Proteomics and Drug Discovery, Graduate School of Pharmaceutical
Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Tomoyoshi Yamano
- Department
of Immunology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa 920-1164, Japan
- WPI
Nano Life Science Institute (NanoLSI), Kanazawa
University, Kanazawa 920-1164, Japan
| | - Yasushi Ishihama
- Department
of Molecular Systems BioAnalysis, Department of Proteomics and Drug
Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory
of Clinical and Analytical Chemistry, National
Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
- Department
of Proteomics and Drug Discovery, Graduate School of Pharmaceutical
Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Koshi Imami
- Department
of Molecular Systems BioAnalysis, Department of Proteomics and Drug
Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- PRESTO,
Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo 102-0075, Japan
- Proteome
Homeostasis Research Unit, RIKEN Center
for Integrative Medical Sciences, Yokohama 230-0045, Japan
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Veenstra BT, Veenstra TD. Proteomic applications in identifying protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:1-48. [PMID: 38220421 DOI: 10.1016/bs.apcsb.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
There are many things that can be used to characterize a protein. Size, isoelectric point, hydrophobicity, structure (primary to quaternary), and subcellular location are just a few parameters that are used. The most important feature of a protein, however, is its function. While there are many experiments that can indicate a protein's role, identifying the molecules it interacts with is probably the most definitive way of determining its function. Owing to technology limitations, protein interactions have historically been identified on a one molecule per experiment basis. The advent of high throughput multiplexed proteomic technologies in the 1990s, however, made identifying hundreds and thousands of proteins interactions within single experiments feasible. These proteomic technologies have dramatically increased the rate at which protein-protein interactions (PPIs) are discovered. While the improvement in mass spectrometry technology was an early driving force in the rapid pace of identifying PPIs, advances in sample preparation and chromatography have recently been propelling the field. In this chapter, we will discuss the importance of identifying PPIs and describe current state-of-the-art technologies that demonstrate what is currently possible in this important area of biological research.
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Affiliation(s)
- Benjamin T Veenstra
- Department of Math and Sciences, Cedarville University, Cedarville, OH, United States
| | - Timothy D Veenstra
- School of Pharmacy, Cedarville University, Cedarville, OH, United States.
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Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. J Biol Chem 2022; 298:102343. [PMID: 35933017 PMCID: PMC9437848 DOI: 10.1016/j.jbc.2022.102343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.
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Affiliation(s)
- Murat Artan
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
| | - Markus Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter (VBC), Vienna, Austria
| | - Weiqiang Chen
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter (VBC), Vienna, Austria
| | - Mario de Bono
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
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