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Ahlat M, Aydin C, Kaya S, Baysallar M. Identification of root canal microbiota profiles of periapical tissue diseases using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anaerobe 2023; 84:102791. [PMID: 37925063 DOI: 10.1016/j.anaerobe.2023.102791] [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: 05/08/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
OBJECTIVES The purpose of this study was to identify microorganisms isolated from various periapical tissue diseases using Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) and classify them via an unsupervised machine learning approach. METHODS A total of 150 patients with various apical conditions and teeth in need of endodontic retreatment were divided into five groups, including Retreatment, Acute Apical Abscess, Chronic Apical Abscess, Acute Apical Periodontitis, and Chronic Apical Periodontitis. Samples were collected from root canals using paper points after agitating with a #10 K file then microorganisms were identified using MALDI-TOF-MS. Data were analyzed using a hierarchical clustering method. Quadruple clusters and dendrograms were formed according to similarities and dissimilarities. RESULTS A total of 80 species were identified representative of six different phyla. The most similar microorganism species identified were: ''Enterococcus faecalis'' between 21 and 23-year-old female cases in Retreatment group; ''Lactobacillus rhamnosus'' between 20 and 18-year-old male cases in Symptomatic Apical Abscess cases; ''Lactobacillus paracasei'' between 26 and 40-year-old male cases in Asymptomatic Apical Abscess cases; ''Enterococcus faecalis'' between 48 and 50-year-old female cases in Symptomatic Apical Periodontitis cases; ''Lactobacillus rhamnosus'' between 48 and 60-year-old male cases in Asymptomatic Apical Periodontitis cases. CONCLUSIONS MALDI-TOF MS can be considered a fast and high-throughput screening technique for microbial species identification in endodontics. Thus, it will provide valuable data for future research designs regarding periapical tissue diseases. As the MALDI-TOF MS database expands and comprehensive data becomes available, the relationship between microbial profiles and disease progression will become increasingly apparent.
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Affiliation(s)
- Mete Ahlat
- University of Health Sciences, Gulhane Faculty of Dentistry, Department of Endodontics, Ankara, Turkey.
| | - Cumhur Aydin
- University of Health Sciences, Gulhane Faculty of Dentistry, Department of Endodontics, Ankara, Turkey.
| | - Sinem Kaya
- University of Health Sciences, Gulhane Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey.
| | - Mehmet Baysallar
- University of Health Sciences, Gulhane Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey.
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2
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Zhu Q, Luo J, Li HP, Ye W, Pan R, Shi KQ, Yang R, Xu H, Li H, Lee LP, Liu F. Robust Acute Pancreatitis Identification and Diagnosis: RAPIDx. ACS NANO 2023; 17:8564-8574. [PMID: 36988967 DOI: 10.1021/acsnano.3c00922] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The occurrence of acute pancreatitis (AP) is increasing significantly worldwide. However, current diagnostic methods of AP do not provide a clear clinical stratification of severity, and the prediction of complications in AP is still limited. Here, we present a robust AP identification and diagnosis (RAPIDx) method by the proteomic fingerprinting of intact nanoscale extracellular vesicles (EVs) from clinical samples. By tracking analysis of circulating biological nanoparticles released by cells (i.e., EVs) via bottom-up proteomics, we obtain close phenotype connections between EVs, cell types, and multiple tissues based on their specific proteomes and identify the serum amyloid A (SAA) proteins on EVs as potential biomarkers that are differentially expressed from AP patients significantly. We accomplish the quantitative analysis of EVs fingerprints using MALDI-TOF MS and find the SAA proteins (SAA1-1, desR-SAA1-2, SAA2, SAA1-2) with areas under the curve (AUCs) from 0.92 to 0.97, which allows us to detect AP within 30 min. We further realize that SAA1-1 and SAA2, combined with two protein peaks (5290.19, 14032.33 m/z), can achieve an AUC of 0.83 for classifying the severity of AP. The RAPIDx platform will facilitate timely diagnosis and treatment of AP before severity development and persistent organ failure and promote precision diagnostics and the early diagnosis of pancreatic cancer.
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Affiliation(s)
- Qingfu Zhu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jiaxin Luo
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Hui-Ping Li
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Wen Ye
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Reguang Pan
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Ke-Qing Shi
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Rui Yang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Hao Xu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Hengrui Li
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Luke P Lee
- Harvard Medical School, Department of Medicine, Brigham Women's Hospital, Boston, Massachusetts 02115, United States
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, California 94720, United States
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Korea
| | - Fei Liu
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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Saeed M, Koller G, Niazi S, Patel S, Mannocci F, Bruce K, Foschi F. Bacterial Contamination of Endodontic Materials before and after Clinical Storage. J Endod 2017; 43:1852-1856. [DOI: 10.1016/j.joen.2017.06.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/29/2017] [Accepted: 06/29/2017] [Indexed: 12/31/2022]
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4
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Kim S, Park J, Na J, Jung GY, Hwang J. Simultaneous Determination of Multiple microRNA Levels Utilizing Biotinylated Dideoxynucleotides and Mass Spectrometry. PLoS One 2016; 11:e0153201. [PMID: 27380276 PMCID: PMC4933350 DOI: 10.1371/journal.pone.0153201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/24/2016] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene translation and have been suggested as potent biomarkers in various disease states. In this study, we established an efficient method for simultaneous determination of multiple miRNA levels, employing the previously developed SPC-SBE (solid phase capture-single base extension) approach and MALDI-TOF mass spectrometry (MS). In this approach, we first perform reverse transcription of miRNAs extracted using stem-loop primers. Then the cDNA is co-amplified with competitors, synthetic oligonucleotides whose sequences precisely match cDNA except for one base, and the amplicons serve as templates for a multiplexed SBE reaction. Extension products are isolated using SPC and quantitatively analyzed with MALDI-TOF MS to determine multiple miRNA levels. Here we demonstrated concurrent analysis of four miRNA levels utilizing the approach. Furthermore, we showed the presented method significantly facilitated MS analysis of peak area ratio owing to SPC. The SPC process allowed effective removal of irrelevant reaction components prior to MS and promoted MS sample purification. Data obtained in this study was verified with RT-qPCR and agreement was shown on one order of magnitude scale, suggesting the SPC-SBE and MS approach has strong potential as a viable tool for high throughput miRNA analysis.
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Affiliation(s)
- Sobin Kim
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Korea
- * E-mail: (SK); (JH)
| | - Jungyun Park
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Jeongkyeong Na
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
- Department of Chemical Engineering, Pohang University of Sciences and Technology, Pohang, Gyeongbuk, Korea
| | - Jungwook Hwang
- Graduate School for Biomedical Science & Engineering, Hanyang University, Seoul, Korea
- Department of Medical Genetics, College of Medicine, Hanyang University, Seoul, Korea
- * E-mail: (SK); (JH)
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5
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Zhu J, Qiu C, Palla M, Nguyen T, Russo JJ, Ju J, Lin Q. A Microfluidic Device for Multiplex Single-Nucleotide Polymorphism Genotyping. RSC Adv 2014; 4:4269-4277. [PMID: 26594354 PMCID: PMC4651459 DOI: 10.1039/c3ra44091e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most abundant type of genetic variations; they provide the genetic fingerprint of individuals and are essential for genetic biomarker discoveries. Accurate detection of SNPs is of great significance for disease prevention, diagnosis and prognosis, and for prediction of drug response and clinical outcomes in patients. Nevertheless, conventional SNP genotyping methods are still limited by insufficient accuracy or labor-, time-, and resource-intensive procedures. Microfluidics has been increasingly utilized to improve efficiency; however, the currently available microfluidic genotyping systems still have shortcomings in accuracy, sensitivity, throughput and multiplexing capability. To address these challenges, we developed a multi-step SNP genotyping microfluidic device, which performs single-base extension of SNP specific primers and solid-phase purification of the extension products on a temperature-controlled chip. The products are ready for immediate detection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), providing identification of the alleles at the target loci. The integrated device enables efficient and automated operation, while maintaining the high accuracy and sensitivity provided by MS. The multiplex genotyping capability was validated by performing rapid, accurate and simultaneous detection of 4 loci on a synthetic template. The microfluidic device has the potential to perform automatic, accurate, quantitative and high-throughput assays covering a broad spectrum of applications in biological and clinical research, drug development and forensics.
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Affiliation(s)
- Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| | - Chunmei Qiu
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Mirkó Palla
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - ThaiHuu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| | - James J. Russo
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
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Zhu J, Palla M, Ronca S, Warpner R, Ju J, Lin Q. A MEMS-Based Approach to Single Nucleotide Polymorphism Genotyping. SENSORS AND ACTUATORS. A, PHYSICAL 2013; 195:175-182. [PMID: 24729659 PMCID: PMC3979494 DOI: 10.1016/j.sna.2012.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Genotyping of single nucleotide polymorphisms (SNPs) allows diagnosis of human genetic disorders associated with single base mutations. Conventional SNP genotyping methods are capable of providing either accurate or high-throughput detection, but are still labor-, time-, and resource-intensive. Microfluidics has been applied to SNP detection to provide fast, low-cost, and automated alternatives, although these applications are still limited by either accuracy or throughput issues. To address this challenge, we present a MEMS-based SNP genotyping approach that uses solid-phase-based reactions in a single microchamber on a temperature control chip. Polymerase chain reaction (PCR), allele specific single base extension (SBE), and desalting on microbeads are performed in the microchamber, which is coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the SBE product. Experimental results from genotyping of the SNP on exon 1 of the HBB gene, which causes sickle cell anemia, demonstrate the potential of the device for rapid, accurate, multiplexed and high-throughput detection of SNPs.
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Affiliation(s)
- Jing Zhu
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
| | - Mirkó Palla
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
- Department of Chemical Engineering, Columbia University,
New York, NY, USA
| | - Stefano Ronca
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
- Department of Mechanical and Industrial Engineering,
University of Brescia, Brescia, BS, Italy
| | - Ronald Warpner
- Department of Obstetrics and Gynecology, Columbia
University, New York, NY, USA
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University,
New York, NY, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University,
New York, NY, USA
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Qiu C, Kumar S, Guo J, Lu J, Shi S, Kalachikov SM, Russo JJ, Naini AB, Schon EA, Ju J. Mitochondrial single nucleotide polymorphism genotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using cleavable biotinylated dideoxynucleotides. Anal Biochem 2012; 427:202-10. [PMID: 22579594 DOI: 10.1016/j.ab.2012.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 04/19/2012] [Accepted: 05/02/2012] [Indexed: 10/28/2022]
Abstract
Characterization of mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) and mutations is crucial for disease diagnosis, which requires accurate and sensitive detection methods and quantification due to mitochondrial heteroplasmy. We report here the characterization of mutations for myoclonic epilepsy with ragged red fibers syndrome using chemically cleavable biotinylated dideoxynucleotides and a mass spectrometry (MS)-based solid phase capture (SPC) single base extension (SBE) assay. The method effectively eliminates unextended primers and primer dimers, and the presence of cleavable linkers between the base and biotin allows efficient desalting and release of the DNA products from solid phase for MS analysis. This approach is capable of high multiplexing, and the use of different length linkers for each of the purines and each of the pyrimidines permits better discrimination of the four bases by MS. Both homoplasmic and heteroplasmic genotypes were accurately determined on different mtDNA samples. The specificity of the method for mtDNA detection was validated by using mitochondrial DNA-negative cells. The sensitivity of the approach permitted detection of less than 5% mtDNA heteroplasmy levels. This indicates that the SPC-SBE approach based on chemically cleavable biotinylated dideoxynucleotides and MS enables rapid, accurate, and sensitive genotyping of mtDNA and has broad applications for genetic analysis.
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Affiliation(s)
- Chunmei Qiu
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
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8
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Qiu C, Kumar S, Guo J, Yu L, Guo W, Shi S, Russo JJ, Ju J. Design and synthesis of cleavable biotinylated dideoxynucleotides for DNA sequencing by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2012; 427:193-201. [PMID: 22543091 DOI: 10.1016/j.ab.2012.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Accepted: 04/17/2012] [Indexed: 01/03/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based methods have been widely explored for DNA sequencing. We report here the design, synthesis, and evaluation of a novel set of chemically cleavable biotinylated dideoxynucleotides, ddNTPs-N₃-biotin, for the DNA polymerase extension reaction and its application in DNA sequencing by mass spectrometry (MS). These nucleotide analogs have a biotin moiety attached to the 5 position of the pyrimidines (C and U) or the 7 position of the purines (A and G) via a chemically cleavable azido-based linker, with different length linker arms serving as mass tags that contribute to large mass differences among the nucleotides. We demonstrate that these modified nucleotides are efficiently incorporated by DNA polymerase, and the DNA strand bearing biotinylated nucleotides is captured by streptavidin-coated beads and efficiently released using tris(2-carboxyethyl)phosphine in aqueous solution, which is compatible with DNA and downstream procedures. We performed Sanger sequencing reactions using these nucleotides to generate DNA fragments for MALDI-TOF MS analysis. Both synthetic DNA and polymerase chain reaction (PCR) products were accurately decoded, and a read length of approximately 37 bases was achieved using these nucleotides in MS sequencing.
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Affiliation(s)
- Chunmei Qiu
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
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A multiplex MALDI-TOF MS approach facilitates genotyping of DNA from formalin-fixed paraffin-embedded tumour specimens. Pharmacogenet Genomics 2011; 20:598-604. [PMID: 20802378 DOI: 10.1097/fpc.0b013e32833deb16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The impact of single-nucleotide polymorphisms (SNPs) on tumour susceptibility and pathogenesis has gained enormous attention. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based genotyping facilitates the analysis of short DNA amplicons and is, therefore, a promising tool for the investigation of formalin-fixed paraffin-embedded (FFPE) tissue samples, particularly in targeted genotyping analysis. METHODS To examine the applicability of genotyping FFPE DNA with MALDI-TOF MS in multiplex reactions, we investigated five DNA samples extracted from FFPE tumour specimens from follicular lymphoma patients using different extraction methods (phenol-chloroform, commercial kit). Thirty-one SNPs from 25 genes, integrated in different-sized multiplex assays (7-plex, 10-plex, 14-plex, 24-plex), were analyzed. To investigate the reliability of genotyping tumour-derived DNA extracted from FFPE tissue, we examined 64 FFPE tumour specimens in comparison with matched germline DNA samples. RESULTS Call rates of 99.6 (274/275) and 93.5% (257/275) were observed for the DNA extracted with the phenol-chloroform approach or the commercial extraction kit, respectively. Increasing the number of SNPs per assay resulted in reduced genotyping call rates and genotyping quality, especially in the DNA samples isolated with the commercial extraction kit. When comparing the genotypes of DNA derived from germline and tumour (FFPE) specimens, a perfect concordance rate of 100% was detected. CONCLUSION Our data delineate that MALDI-TOF-based genotyping of FFPE DNA is reliable and reproducible even in multiplex reactions, enabling the retrospective investigation of FFPE study cohorts in future experiments.
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Duffield DS, Cai L, Kim S. Simultaneous determination of multiple mRNA levels utilizing MALDI-TOF mass spectrometry and biotinylated dideoxynucleotides. RNA (NEW YORK, N.Y.) 2010; 16:1285-1291. [PMID: 20410241 PMCID: PMC2874180 DOI: 10.1261/rna.1859810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 02/18/2010] [Indexed: 05/29/2023]
Abstract
Here we report an efficient method to simultaneously measure multiple mRNA levels utilizing mass spectrometry (MS) and molecular affinity isolation. In this approach, reverse transcription products of a group of mRNAs are subjected to competitive PCR with competitors and internal standards of known concentrations, and the PCR products are differentiated and quantified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS to determine the mRNA levels. The method provides high accuracy in quantitative MS analysis due to the facilitated purification of oligonucleotides by molecular affinity isolation. Additionally, owing to the molecular affinity isolation, only those oligonucleotides required for expression level determination are introduced into the mass spectrometer, while other irrelevant reaction components that could overlap with peaks of gene transcripts or competitors are removed prior to MS analysis. Thus the approach enhances the parallel analysis of multiple gene transcripts by MS. Utilizing the method we have simultaneously measured mRNA levels of four genes (Rho, Nrl, Hprt, and Lhx2) in mouse retinal tissue.
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Affiliation(s)
- Daniel Scott Duffield
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, USA
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Hong M, Zhou X, Li J, Tian Y, Zhu J. Nanoscale Architecture Dictates Detection Profile of Surface-Confined DNA by MALDI-TOF MS. Anal Chem 2009; 81:8839-45. [DOI: 10.1021/ac901815v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Min Hong
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Xin Zhou
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Jiping Li
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Yuan Tian
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Jin Zhu
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
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Sioud S, Genestie B, Jahouh F, Martin P, Banoub J. Gas-phase fragmentation study of biotin reagents using electrospray ionization tandem mass spectrometry on a quadrupole orthogonal time-of-flight hybrid instrument. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1941-1956. [PMID: 19496066 DOI: 10.1002/rcm.4091] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, we evaluated, by electrospray ionization mass spectrometry (ESI-MS) and collision-induced dissociation tandem mass spectrometry (CID-MS/MS) using a quadrupole orthogonal time-of-flight (QqToF)-MS/MS hybrid instrument, the gas-phase fragmentations of some commercially available biotinyl reagents. The biotin reagents used were: psoralen-BPE 1, p-diazobenzoyl biocytin (DBB) 2, photoreactive biotin 3, biotinyl-hexaethyleneglycol dimer 4, and the sulfo-SBED 5. The results showed that, during ESI-MS and CID-MS/MS analyses, the biotin reagents followed a similar gas-phase fragmentation pattern and the cleavages usually occurred at either end of the spacer arm of the biotin reagents. In general we have observed that the CID-MS/MS fragmentation routes of the five precursor protonated molecules obtained from the biotin linkers 1-5 afforded a series of product ions formed essentially by similar routes. The genesis and the structural identities of all the product ions obtained from the biotin linkers 1-5 have been assigned. All the exact mass assignments of the protonated molecules and the product ions were verified by conducting separate CID-MS/MS analysis of the deuterium-labelled precursor ions.
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Affiliation(s)
- Salim Sioud
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, A1B 3V6, Canada
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Cheok MH, Pottier N, Kager L, Evans WE. Pharmacogenetics in acute lymphoblastic leukemia. Semin Hematol 2009; 46:39-51. [PMID: 19100367 DOI: 10.1053/j.seminhematol.2008.09.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Progress in the treatment of acute lymphoblastic leukemia (ALL) in children has been remarkable, from a disease being lethal four decades ago to current cure rates exceeding 80%. This exemplary progress is largely due to the optimization of existing treatment modalities rather than the discovery of new antileukemic agents. However, despite these high cure rates, the annual number of children whose leukemia relapses after their initial therapy remains greater than that of new cases of most types of childhood cancers. The aim of pharmacogenetics is to develop strategies to personalize treatment and tailor therapy to individual patients, with the goal of optimizing efficacy and safety through better understanding of human genome variability and its influence on drug response. In this review, we summarize recent pharmacogenomic studies related to the treatment of pediatric ALL. These studies illustrate the promise of pharmacogenomics to further advance the treatment of human cancers, with childhood leukemia serving as a paradigm.
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Affiliation(s)
- Meyling H Cheok
- Jean-Pierre Aubert Research Center, INSERM U837, Genomics Core IRCL-IMPRT, Lille, France.
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14
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Fan C, Yu S, Wang C, Xing Y. A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:465-72. [PMID: 19020856 DOI: 10.1007/s00122-008-0913-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 10/09/2008] [Indexed: 05/21/2023]
Abstract
Comparative sequencing of GS3, the most important grain length (GL) QTL, has shown that differentiation of rice GL might be principally due to a single nucleotide polymorphism (SNP) between C and A in the second exon. A total of 180 varieties representing a wide range of rice germplasm were used for association analysis between C-A mutation and GL in order to confirm the potential causal mutation. A cleaved amplified polymorphic sequence (CAPS) marker, SF28, was developed based on the C-A polymorphism in the GS3 gene. A total of 142 varieties carried allele C with GL from 6.4 to 8.8 mm, while the remaining 38 varieties carried allele A with GL from 8.8 to 10.7 mm. Twenty-four unlinked SSR markers were selected to genotype 180 varieties for population structure analysis. Population structure was observed when the population was classified to three subpopulations. Average GL of either genotype A or genotype C within japonica among the three subpopulations had no significant difference from that in indica, respectively, although indica rice had longer grains on average than japonica in the 180 varieties. However, genotype C always had longer grain length on average than genotype A among three subpopulations. The mutation could explain 79.1, 66.4 and 34.7% of GL variation in the three subpopulations, respectively. These results clearly confirmed the mutation between C and A was highly associated with GL. The SF28 could be a functional marker for improvement of rice grain length.
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Affiliation(s)
- Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
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Abstract
Single nucleotide polymorphisms (SNPs) are the most frequently occurring genetic variation in the human genome, with the total number of SNPs reported in public SNP databases currently exceeding 9 million. SNPs are important markers in many studies that link sequence variations to phenotypic changes; such studies are expected to advance the understanding of human physiology and elucidate the molecular bases of diseases. For this reason, over the past several years a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis, yielding a large number of distinct approaches. This article presents a review of SNP genotyping techniques and examines their principles of genotype determination in terms of allele differentiation strategies and detection methods. Further, several current biomedical applications of SNP genotyping are discussed.
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Affiliation(s)
- Sobin Kim
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey 08854, USA.
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16
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Abstract
Over the past four decades, treatment of acute leukemia in children has made remarkable progress, from this disease being lethal to now achieving cure rates of 80% for acute lymphoblastic leukemia and 45% for acute myeloid leukemia. This progress is largely owed to the optimization of existing treatment modalities rather than the discovery of new agents. However, the annual number of patients with leukemia who experience relapse after initial therapy remains greater than that of new cases of most childhood cancers. The aim of pharmacogenetics is to develop strategies to personalize medications and tailor treatment regimens to individual patients, with the goal of enhancing efficacy and safety through better understanding of the person's genetic makeup. In this review, we summarize recent pharmacogenomic studies related to the treatment of pediatric acute leukemia. These include work using candidate-gene approaches, as well as genome-wide studies using haplotype mapping and gene expression profiling. These strategies illustrate the promise of pharmacogenomics to further advance the treatment of human cancers, with childhood leukemia serving as a paradigm.
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Affiliation(s)
- Meyling H Cheok
- St. Jude Children's Research Hospital, Department of Pharmaceutical Sciences, Memphis, TN 38105, USA.
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17
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Tost J, Gut IG. Genotyping single nucleotide polymorphisms by MALDI mass spectrometry in clinical applications. Clin Biochem 2005; 38:335-50. [PMID: 15766735 DOI: 10.1016/j.clinbiochem.2004.12.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Revised: 11/22/2004] [Accepted: 12/09/2004] [Indexed: 11/24/2022]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry has become one of the most powerful and widely applied technologies for SNP scoring and determination of allele frequencies in the post-genome sequencing era. Although different strategies for allele discrimination combined with MALDI were devised, in practice only primer extension methods are nowadays routinely used. This combination enables the rapid, quantitative, and direct detection of several genetic markers simultaneously in a broad variety of biological samples. In the field of molecular diagnostics, MALDI has been applied to the discovery of genetic markers, that are associated with a phenotype like a disease susceptibility or drug response, as well as an alternative means for diagnostic testing of a range of diseases for which the responsible mutations are already known. It is one of the first techniques with which whole genome scans based on single nucleotide polymorphisms were carried out. It is equally well suited for pathogen identification and the detection of emerging mutant strains as well as for the characterization of the genetic identity and quantitative trait loci mapping in farm animals. MALDI can also be used as a detection platform for a range of novel applications that are more demanding than standard SNP genotyping such as mutation/polymorphism discovery, molecular haplotyping, analysis of DNA methylation, and expression profiling. This review gives an introduction to the application of mass spectrometry for DNA analysis, and provides an overview of most studies using SNPs as genetic markers and MALDI mass spectrometric detection that are related to clinical applications and molecular diagnostics. Further, it aims to show specialized applications that might lead to diagnostic applications in the future. It does not speculate on whether this methodology will ever reach the diagnostic market.
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Affiliation(s)
- Jörg Tost
- Centre National de Génotypage, Bâtiment G2, 2 Rue Gaston Crémieux, CP 5721, 91057 Evry Cedex, France
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18
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Affiliation(s)
- Kazuhiko Nakatani
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8150, Japan.
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