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Guzmán-Lorite M, Rosu F, Marina ML, García MC, Gabelica V. miRNA and DNA analysis by negative ion electron transfer dissociation and infrared multiple-photon dissociation mass spectrometry. Anal Chim Acta 2024; 1299:342431. [PMID: 38499418 DOI: 10.1016/j.aca.2024.342431] [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: 10/04/2023] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND The use of simple and hybrid fragmentation techniques for the identification of molecules in tandem mass spectrometry provides different and complementary information on the structure of molecules. Nevertheless, these techniques have not been as widely explored for oligonucleotides as for peptides or proteins. The analysis of microRNAs (miRNAs) warrants special attention, given their regulatory role and their relationship with several diseases. The application of different fragmentation techniques will be very interesting for their identification. RESULTS Four synthetic miRNAs and a DNA sequence were fragmented in an ESI-FT-ICR mass spectrometer using both simple and hybrid fragmentation techniques: CID, nETD followed by CID, IRMPD, and, for the first time, nETD in combination with IRMPD. The main fragmentation channel was base loss. The use of nETD-IRMPD resulted in d/z, a/w, and c/y ions at higher intensities. Moreover, nETD-IRMPD provided high sequence coverage and low internal fragmentation. Native MS analysis revealed that only miR159 and the DNA sequence formed stable dimers under physiological ionic strength. The use of organic co-solvents or additives resulted in a lower sequence coverage due to lesser overall ionization efficiency. NOVELTY This work demonstrates that the combination of nETD and IRMPD for miRNA fragmentation constitutes a suitable alternative to common fragmentation methods. This strategy resulted in efficient fragmentation of [miRNA]5- using low irradiation times and fewer internal fragments while ensuring a high sequence coverage. Moreover, given that such low charge states predominate upon spraying in physiological-like conditions, native MS can be applied for obtaining structural information at the same time.
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Affiliation(s)
- Miriam Guzmán-Lorite
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain
| | - Frédéric Rosu
- Université de Bordeaux, CNRS, INSERM, IECB, UAR3033, US01, F-33600, Pessac, France
| | - María Luisa Marina
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain; Universidad de Alcalá, Instituto de Investigación Química "Andrés M. Del Río", Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain
| | - María Concepción García
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain; Universidad de Alcalá, Instituto de Investigación Química "Andrés M. Del Río", Ctra. Madrid-Barcelona Km. 33.600, 28871, Alcalá de Henares (Madrid), Spain.
| | - Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM, IECB, UAR3033, US01, F-33600, Pessac, France; Université de Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600, Pessac, France
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Yuen BPN, Wong KS, So YM, Kwok WH, Cheung HW, Wan TSM, Ho ENM, Wong WT. Gene Doping Control Analysis of Human Erythropoietin Transgene in Equine Plasma by PCR-Liquid Chromatography High-Resolution Tandem Mass Spectrometry. Anal Chem 2024; 96:5307-5314. [PMID: 38504497 DOI: 10.1021/acs.analchem.4c00247] [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: 03/21/2024]
Abstract
Gene doping involves the misuse of genetic materials to alter an athlete's performance, which is banned at all times in both human and equine sports. Quantitative polymerase chain reaction (qPCR) assays have been used to control the misuse of transgenes in equine sports. Our laboratory recently developed and implemented duplex as well as multiplex qPCR assays for transgenes detection. To further advance gene doping control, we have developed for the first time a sensitive and definitive PCR-liquid chromatography high-resolution tandem mass spectrometry (PCR-LC-HRMS/MS) method for transgene detection with an estimated limit of detection of below 100 copies/mL for the human erythropoietin (hEPO) transgene in equine plasma. The method involved magnetic-glass-particle-based extraction of DNA from equine plasma prior to PCR amplification with 2'-deoxyuridine 5'-triphosphate (dUTP) followed by treatments with uracil DNA glycosylase and hot piperidine for selective cleavage to give small oligonucleotide fragments. The resulting DNA fragments were then analyzed by LC-HRMS/MS. The applicability of this method has been demonstrated by the successful detection of hEPO transgene in a blood sample collected from a gelding (castrated male horse) that had been administered the transgene. This novel approach not only serves as a complementary method for transgene detection but also paves the way for developing a generic PCR-LC-HRMS/MS method for the detection of multiple transgenes.
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Affiliation(s)
- Bruce Pui-Nam Yuen
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Kin-Sing Wong
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Yat-Ming So
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Wai Him Kwok
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Hiu Wing Cheung
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Terence See Ming Wan
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Emmie Ngai-Man Ho
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Wing-Tak Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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4
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Pereira SAP, Romano-deGea J, Barbosa AI, Costa Lima SA, Dyson PJ, Saraiva MLMFS. Fine-tuning the cytotoxicity of ruthenium(II) arene compounds to enhance selectivity against breast cancers. Dalton Trans 2023; 52:11679-11690. [PMID: 37552495 PMCID: PMC10442743 DOI: 10.1039/d3dt02037a] [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: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/09/2023]
Abstract
Ruthenium-based complexes have been suggested as promising anticancer drugs exhibiting reduced general toxicity compared to platinum-based drugs. In particular, Ru(η6-arene)(PTA)Cl2 (PTA = 1,3,5-triaza-7-phosphaadamantane), or RAPTA, complexes have demonstrated efficacy against breast cancer by suppressing metastasis, tumorigenicity, and inhibiting the replication of the human tumor suppressor gene BRCA1. However, RAPTA compounds have limited cytotoxicity, and therefore comparatively high doses are required. This study explores the activity of a series of RAPTA-like ruthenium(II) arene compounds against MCF-7 and MDA-MB-231 breast cancer cell lines and [Ru(η6-toluene)(PPh3)2Cl]+ was identified as a promising candidate. Notably, [Ru(η6-toluene)(PPh3)2Cl]Cl was found to be remarkably stable and highly cytotoxic, and selective to breast cancer cells. The minor groove of DNA was identified as a relevant target.
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Affiliation(s)
- Sarah A P Pereira
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Jan Romano-deGea
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Ana Isabel Barbosa
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
| | - Sofia A Costa Lima
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
| | - Paul J Dyson
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - M Lúcia M F S Saraiva
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, no 228, 4050-313 Porto, Portugal.
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Liu XY, Ji X, Heinis C, Waser J. Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization. Angew Chem Int Ed Engl 2023; 62:e202306036. [PMID: 37311172 DOI: 10.1002/anie.202306036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Herein, we report a novel strategy for the modification of peptides based on the introduction of highly reactive hypervalent iodine reagents-ethynylbenziodoxolones (EBXs)-onto peptides. These peptide-EBXs can be readily accessed, by both solution- and solid-phase peptide synthesis (SPPS). They can be used to couple the peptide to other peptides or a protein through reaction with Cys, leading to thioalkynes in organic solvents and hypervalent iodine adducts in water buffer. Furthermore, a photocatalytic decarboxylative coupling to the C-terminus of peptides was developed using an organic dye and was also successful in an intramolecular fashion, leading to macrocyclic peptides with unprecedented crosslinking. A rigid linear aryl alkyne linker was essential to achieve high affinity for Keap1 at the Nrf2 binding site with potential protein-protein interaction inhibition.
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Affiliation(s)
- Xing-Yu Liu
- Laboratory of Catalysis and Organic Synthesis, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Xinjian Ji
- Laboratory of Therapeutic Proteins and Peptides, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Christian Heinis
- Laboratory of Therapeutic Proteins and Peptides, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
| | - Jerome Waser
- Laboratory of Catalysis and Organic Synthesis, Ecole Polytechnique Fédérale de Lausanne, EPFL, 1015, Lausanne, Switzerland
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Mansouri F, Ortiz D, Dyson PJ. Competitive binding studies of the nucleosomal histone targeting drug, [Ru(η 6-p-cymene)Cl 2(pta)] (RAPTA-C), with oligonucleotide-peptide mixtures. J Inorg Biochem 2023; 238:112043. [PMID: 36370502 DOI: 10.1016/j.jinorgbio.2022.112043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 11/07/2022]
Abstract
Protein crystallography and biochemical assays reveal that the organometallic drug, [Ru(η6-p-cymene)Cl2(pta)] (RAPTA-C), preferentially binds to nucleosomal histone proteins in chromatin. To better understand the binding mechanism we report here a mass spectrometric-based competitive binding study between a model peptide from the acidic patch region of the H2A histone protein (the region where RAPTA-C is known to bind) and an oligonucleotide. In contrast to the protein crystallography and biochemical assays, RAPTA-C preferentially binds to the oligonucleotide, confirming that steric factors, rather than electronic effects, primarily dictate binding of RAPTA-C to histone proteins within the nucleosome.
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Affiliation(s)
- Farangis Mansouri
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne CH-1015, Switzerland; Department of Chemistry Institute for Advanced Studies in Basic Sciences (IASBS), 444 Prof. Sobouti Blvd., Gava Zang, Zanjan 45137-66731, Iran
| | - Daniel Ortiz
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Paul J Dyson
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne CH-1015, Switzerland.
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Simultaneous mass spectrometry analysis of cisplatin with oligonucleotide-peptide mixtures: implications for the mechanism of action. J Biol Inorg Chem 2022; 27:239-248. [PMID: 35064831 PMCID: PMC8907109 DOI: 10.1007/s00775-022-01924-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/30/2021] [Indexed: 11/03/2022]
Abstract
AbstractAlthough genomic DNA is the primary target of anticancer platinum-based drugs, interactions with proteins also play a significant role in their overall activity. In this study, competitive binding of cisplatin with an oligonucleotide and two peptides corresponding to segments of H2A and H2B histone proteins was investigated by mass spectrometry. Following the determination of the cisplatin binding sites on the oligonucleotide and peptides by tandem mass spectrometry, competitive binding was studied and transfer of platinum fragments from the platinated peptides to the oligonucleotide explored. In conjunction with previous studies on the nucleosome, the results suggest that all four of the abundant histone proteins serve as a platinum drug reservoir in the cell nucleus, providing an adduct pool that can be ultimately transferred to the DNA.
Graphical abstract
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Tao J, Jia S, Wang M, Huang Z, Wang B, Zhang W, Wei Y, Li W, Jiang H, Du Z. Systematic Identification of Proteins Binding with Cisplatin in Blood by Affinity Chromatography and a Four-Dimensional Proteomic Method. J Proteome Res 2021; 20:4553-4565. [PMID: 34427088 DOI: 10.1021/acs.jproteome.1c00535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cisplatin is widely used for the treatment of various solid tumors. It is mainly administered by intravenous injection, and a substantial amount of the drug will bind to plasma proteins, a feature that is closely related to its pharmacokinetics, activity, toxicity, and side effects. However, due to the unique properties of platinum complexes and the complexity of the blood proteome, existing methods cannot systematically identify the binding proteome of cisplatin in blood. In this study, high-abundance protein separation and an ion mobility mass spectrometry-based 4D proteomic method were combined to systematically and comprehensively identify the binding proteins of cisplatin in blood. The characteristic isotope patterns of platinated peptides and a similarity algorithm were utilized to eliminate false-positive identification. Finally, 39 proteins were found to be platinated. Bioinformatics analysis showed that the identified proteins were mainly involved in the complement and coagulation cascade pathways. The binding ratio of some peptides with cisplatin was measured based on the area ratio of the free peptide using the parallel reaction monitoring method. This study provides a new method for systematically identifying binding proteins of metal drugs in blood, and the identified proteins might be helpful for understanding the toxicity of platinum anticancer drugs.
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Affiliation(s)
- Jianmei Tao
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Shuailong Jia
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430030, Hubei Province, PR China
| | - Meiqin Wang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Zhuobin Huang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Bo Wang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Wenwen Zhang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Yinyu Wei
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Wenzhuo Li
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Hongliang Jiang
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
| | - Zhifeng Du
- School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, Hubei Province, PR China
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Annunziata A, Liberti D, Bedini E, Cucciolito ME, Loreto D, Monti DM, Merlino A, Ruffo F. Square-Planar vs. Trigonal Bipyramidal Geometry in Pt(II) Complexes Containing Triazole-Based Glucose Ligands as Potential Anticancer Agents. Int J Mol Sci 2021; 22:ijms22168704. [PMID: 34445409 PMCID: PMC8395886 DOI: 10.3390/ijms22168704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022] Open
Abstract
This article describes the synthesis, characterization, and biological activity of novel square-planar cationic platinum(II) complexes containing glucoconjugated triazole ligands and a comparison with the results obtained from the corresponding five-coordinate complexes bearing the same triazole ligands. Stability in solution, reactivity with DNA and small molecules of the new compounds were evaluated by NMR, fluorescence, and UV–vis absorption spectroscopy, together with their cytotoxic action against pairs of immortalized and tumorigenic cell lines. The results show that the square-planar species exhibit greater stability than the corresponding five-coordinate ones. Furthermore, although the square-planar complexes are less cytotoxic than the latter ones, they exhibit a certain selectivity. These results simultaneously demonstrate that overall stability is a fundamental prerequisite for preserving the performance of the agents and that coordinative saturation constitutes a point in favor of their biological action.
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The Protein-Binding Behavior of Platinum Anticancer Drugs in Blood Revealed by Mass Spectrometry. Pharmaceuticals (Basel) 2021; 14:ph14020104. [PMID: 33572935 PMCID: PMC7911130 DOI: 10.3390/ph14020104] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Cisplatin and its analogues are widely used as chemotherapeutic agents in clinical practice. After being intravenously administrated, a substantial amount of platinum will bind with proteins in the blood. This binding is vital for the transport, distribution, and metabolism of drugs; however, toxicity can also occur from the irreversible binding between biologically active proteins and platinum drugs. Therefore, it is very important to study the protein-binding behavior of platinum drugs in blood. This review summarizes mass spectrometry-based strategies to identify and quantitate the proteins binding with platinum anticancer drugs in blood, such as offline high-performance liquid chromatography/inductively coupled plasma mass spectrometry (HPLC–ICP-MS) combined with electrospray ionization mass spectrometry (ESI-MS/MS) and multidimensional LC–ESI-MS/MS. The identification of in vivo targets in blood cannot be accomplished without first studying the protein-binding behavior of platinum drugs in vitro; therefore, relevant studies are also summarized. This knowledge will further our understanding of the pharmacokinetics and toxicity of platinum anticancer drugs, and it will be beneficial for the rational design of metal-based anticancer drugs.
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