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Pralea IE, Moldovan RC, Țigu AB, Ionescu C, Iuga CA. Mass Spectrometry-Based Omics for the Characterization of Triple-Negative Breast Cancer Bio-Signature. J Pers Med 2020; 10:jpm10040277. [PMID: 33322818 PMCID: PMC7768464 DOI: 10.3390/jpm10040277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Triple-negative breast cancer (TNBC) represents an unmet medical need due to a high rate of metastatic occurrence and poor overall survival, pathology aggressiveness, heterogeneous clinical behavior and limited cytotoxic chemotherapy options available because of the absence of targetable receptors. The current standard of care in TNBC is represented by chemotherapy and surgery associated with low overall survival and high relapse rates. Hopes of overcoming current limited and unspecific approaches of TNBC therapy lie in studying the metabolic rewiring of these types of breast cancer, thus understanding the mechanisms involved in the occurrence and progression of the disease. Due to its heterogeneity, a clinically relevant sub-classification of this type of breast cancer based on biomarker panels is greatly needed in order to guide treatment decisions. Mass spectrometry-based omics may provide very useful tools to address the current needs of targetable biomarker discovery and validation. The present review aims to provide a comprehensive view of the current clinical diagnosis and therapy of TNBC highlighting the need for a new approach. Therefore, this paper offers a detailed mass spectrometry-based snapshot of TNBC metabolic adjustment, emphasizing a complex network of variables governing the diverse and aggressive clinical behavior of TNBC.
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Affiliation(s)
- Ioana-Ecaterina Pralea
- Department of Proteomics and Metabolomics, Research Center for Advanced Medicine–MedFuture, “Iuliu Hațieganu” University of Medicine and Pharmacy, Louis Pasteur Street 4-6, 400349 Cluj-Napoca, Romania; (I.-E.P.); (R.-C.M.)
| | - Radu-Cristian Moldovan
- Department of Proteomics and Metabolomics, Research Center for Advanced Medicine–MedFuture, “Iuliu Hațieganu” University of Medicine and Pharmacy, Louis Pasteur Street 4-6, 400349 Cluj-Napoca, Romania; (I.-E.P.); (R.-C.M.)
| | - Adrian-Bogdan Țigu
- Department of Translational Medicine, Research Center for Advanced Medicine–MedFuture, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania;
| | - Corina Ionescu
- Department of Pharmaceutical Biochemistry and Clinical Laboratory, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania;
| | - Cristina-Adela Iuga
- Department of Proteomics and Metabolomics, Research Center for Advanced Medicine–MedFuture, “Iuliu Hațieganu” University of Medicine and Pharmacy, Louis Pasteur Street 4-6, 400349 Cluj-Napoca, Romania; (I.-E.P.); (R.-C.M.)
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, Louis Pasteur Street 6, 400349 Cluj-Napoca, Romania
- Correspondence:
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Neumann EK, Djambazova KV, Caprioli RM, Spraggins JM. Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2401-2415. [PMID: 32886506 PMCID: PMC9278956 DOI: 10.1021/jasms.0c00232] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Imaging mass spectrometry has become a mature molecular mapping technology that is used for molecular discovery in many medical and biological systems. While powerful by itself, imaging mass spectrometry can be complemented by the addition of other orthogonal, chemically informative imaging technologies to maximize the information gained from a single experiment and enable deeper understanding of biological processes. Within this review, we describe MALDI, SIMS, and DESI imaging mass spectrometric technologies and how these have been integrated with other analytical modalities such as microscopy, transcriptomics, spectroscopy, and electrochemistry in a field termed multimodal imaging. We explore the future of this field and discuss forthcoming developments that will bring new insights to help unravel the molecular complexities of biological systems, from single cells to functional tissue structures and organs.
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Affiliation(s)
- Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Katerina V Djambazova
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
| | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
- Department of Medicine, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, 607 Light Hall, Nashville, Tennessee 37205, United States
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue S #9160, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, Tennessee 37235, United States
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53
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Giordano S, Takeda S, Donadon M, Saiki H, Brunelli L, Pastorelli R, Cimino M, Soldani C, Franceschini B, Di Tommaso L, Lleo A, Yoshimura K, Nakajima H, Torzilli G, Davoli E. Rapid automated diagnosis of primary hepatic tumour by mass spectrometry and artificial intelligence. Liver Int 2020; 40:3117-3124. [PMID: 32662575 PMCID: PMC7754124 DOI: 10.1111/liv.14604] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/17/2020] [Accepted: 07/09/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Complete surgical resection with negative margin is one of the pillars in treatment of liver tumours. However, current techniques for intra-operative assessment of tumour resection margins are time-consuming and empirical. Mass spectrometry (MS) combined with artificial intelligence (AI) is useful for classifying tissues and provides valuable prognostic information. The aim of this study was to develop a MS-based system for rapid and objective liver cancer identification and classification. METHODS A large dataset derived from 222 patients with hepatocellular carcinoma (HCC, 117 tumours and 105 non-tumours) and 96 patients with mass-forming cholangiocarcinoma (MFCCC, 50 tumours and 46 non-tumours) were analysed by Probe Electrospray Ionization (PESI) MS. AI by means of support vector machine (SVM) and random forest (RF) algorithms was employed. For each classifier, sensitivity, specificity and accuracy were calculated. RESULTS The overall diagnostic accuracy exceeded 94% in both the AI algorithms. For identification of HCC vs non-tumour tissue, RF was the best, with 98.2% accuracy, 97.4% sensitivity and 99% specificity. For MFCCC vs non-tumour tissue, both algorithms gave 99.0% accuracy, 98% sensitivity and 100% specificity. CONCLUSIONS The herein reported MS-based system, combined with AI, permits liver cancer identification with high accuracy. Its bench-top size, minimal sample preparation and short working time are the main advantages. From diagnostics to therapeutics, it has the potential to influence the decision-making process in real-time with the ultimate aim of improving cancer patient cure.
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Affiliation(s)
- Silvia Giordano
- Mass Spectrometry LaboratoryEnvironmental Health Sciences DepartmentIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly,Present address:
Shimadzu Italia SrlMilanItaly
| | - Sen Takeda
- Department of Anatomy and Cell BiologyUniversity of Yamanashi Faculty of MedicineChuoJapan
| | - Matteo Donadon
- Department of Hepatobiliary and General SurgeryHumanitas UniversityHumanitas Clinical and Research Center – IRCCSMilanItaly,Laboratory of Hepatobiliary ImmunopathologyHumanitas Clinical and Research Center – IRCCSMilanItaly
| | | | - Laura Brunelli
- Mass Spectrometry LaboratoryEnvironmental Health Sciences DepartmentIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Roberta Pastorelli
- Mass Spectrometry LaboratoryEnvironmental Health Sciences DepartmentIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Matteo Cimino
- Department of Hepatobiliary and General SurgeryHumanitas UniversityHumanitas Clinical and Research Center – IRCCSMilanItaly,Laboratory of Hepatobiliary ImmunopathologyHumanitas Clinical and Research Center – IRCCSMilanItaly
| | - Cristiana Soldani
- Department of Hepatobiliary and General SurgeryHumanitas UniversityHumanitas Clinical and Research Center – IRCCSMilanItaly
| | - Barbara Franceschini
- Department of Hepatobiliary and General SurgeryHumanitas UniversityHumanitas Clinical and Research Center – IRCCSMilanItaly
| | - Luca Di Tommaso
- Department of PathologyHumanitas UniversityHumanitas Clinical and Research Center – IRCCSMilanItaly
| | - Ana Lleo
- Laboratory of Hepatobiliary ImmunopathologyHumanitas Clinical and Research Center – IRCCSMilanItaly,Department of Internal MedicineHumanitas UniversityHumanitas Clinical and Research Center – IRCCSMilanItaly
| | - Kentaro Yoshimura
- Department of Anatomy and Cell BiologyUniversity of Yamanashi Faculty of MedicineChuoJapan
| | | | - Guido Torzilli
- Department of Hepatobiliary and General SurgeryHumanitas UniversityHumanitas Clinical and Research Center – IRCCSMilanItaly,Laboratory of Hepatobiliary ImmunopathologyHumanitas Clinical and Research Center – IRCCSMilanItaly
| | - Enrico Davoli
- Mass Spectrometry LaboratoryEnvironmental Health Sciences DepartmentIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
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54
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Keating MF, Zhang J, Feider CL, Retailleau S, Reid R, Antaris A, Hart B, Tan G, Milner TE, Miller K, Eberlin LS. Integrating the MasSpec Pen to the da Vinci Surgical System for In Vivo Tissue Analysis during a Robotic Assisted Porcine Surgery. Anal Chem 2020; 92:11535-11542. [PMID: 32786489 DOI: 10.1021/acs.analchem.0c02037] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Minimally invasive robotic-assisted surgeries have been increasingly used as a first-line of treatment for patients undergoing oncologic surgeries. In-situ tissue identification is critical to guide tissue resection and assist decision-making. Traditional intraoperative histopathologic analysis of frozen tissue sections can be time-consuming and present logistical challenges which interrupt surgical workflows. We report the development and implementation of a laparoscopic, drop-in version of the MasSpec Pen device integrated into the da Vinci Xi Surgical system for in vivo tissue analysis in a robotic-assisted porcine surgery. We evaluated the performance of the drop-in MasSpec Pen during surgery by introducing the device into the animal upper gastrointestinal system and performing in vivo analyses of the stomach and liver, including charred and bloody tissues after electrocauterization. The molecular profiles obtained included ions tentatively identified as metabolites and lipids typically observed with MasSpec Pen analysis, without causing observable tissue damage. Statistical classifiers built to distinguish porcine liver and stomach tissues using the in vivo data yielded an overall tissue identification accuracy of 98% (n = 53 analyses). The results provide evidence that the drop-in MasSpec Pen developed can be used to acquire mass spectra in vivo during a robotic-assisted surgery and might be used as an in vivo tissue assessment tool to help guide surgical resections and streamline surgical workflows.
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Affiliation(s)
- Michael F Keating
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78751, United States
| | - Jialing Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78751, United States
| | - Clara L Feider
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78751, United States
| | | | - Robert Reid
- Intuitive Surgical, Sunnyvale, California 94086, United States
| | | | - Bradley Hart
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Gina Tan
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Thomas E Milner
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78751, United States
| | - Kyle Miller
- Intuitive Surgical, Sunnyvale, California 94086, United States
| | - Livia S Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78751, United States
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55
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Vijayalakshmi K, Shankar V, Bain RM, Nolley R, Sonn GA, Kao CS, Zhao H, Tibshirani R, Zare RN, Brooks JD. Identification of diagnostic metabolic signatures in clear cell renal cell carcinoma using mass spectrometry imaging. Int J Cancer 2020; 147:256-265. [PMID: 31863456 PMCID: PMC8571954 DOI: 10.1002/ijc.32843] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/14/2019] [Accepted: 12/09/2019] [Indexed: 12/31/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common and lethal subtype of kidney cancer. Intraoperative frozen section (IFS) analysis is used to confirm the diagnosis during partial nephrectomy. However, surgical margin evaluation using IFS analysis is time consuming and unreliable, leading to relatively low utilization. In our study, we demonstrated the use of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) as a molecular diagnostic and prognostic tool for ccRCC. DESI-MSI was conducted on fresh-frozen 23 normal tumor paired nephrectomy specimens of ccRCC. An independent validation cohort of 17 normal tumor pairs was analyzed. DESI-MSI provides two-dimensional molecular images of tissues with mass spectra representing small metabolites, fatty acids and lipids. These tissues were subjected to histopathologic evaluation. A set of metabolites that distinguish ccRCC from normal kidney were identified by performing least absolute shrinkage and selection operator (Lasso) and log-ratio Lasso analysis. Lasso analysis with leave-one-patient-out cross-validation selected 57 peaks from over 27,000 metabolic features across 37,608 pixels obtained using DESI-MSI of ccRCC and normal tissues. Baseline Lasso of metabolites predicted the class of each tissue to be normal or cancerous tissue with an accuracy of 94 and 76%, respectively. Combining the baseline Lasso with the ratio of glucose to arachidonic acid could potentially reduce scan time and improve accuracy to identify normal (82%) and ccRCC (88%) tissue. DESI-MSI allows rapid detection of metabolites associated with normal and ccRCC with high accuracy. As this technology advances, it could be used for rapid intraoperative assessment of surgical margin status.
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Affiliation(s)
| | - Vishnu Shankar
- Department of Biomedical Data Science, and Statistics, Stanford University, Stanford, California 94305 USA
| | - Ryan M. Bain
- Department of Chemistry, Stanford University, Stanford, California 94305 USA
- Present address: Dow Chemical Co. Midland, Michigan 48674 USA
| | - Rosalie Nolley
- Department of Urology, Stanford University, Stanford, California 94305 USA
| | - Geoffrey A. Sonn
- Department of Urology, Stanford University, Stanford, California 94305 USA
| | - Chia-Sui Kao
- Department of Pathology, Stanford University, Stanford, California 94305 USA
| | - Hongjuan Zhao
- Department of Urology, Stanford University, Stanford, California 94305 USA
| | - Robert Tibshirani
- Department of Biomedical Data Science, and Statistics, Stanford University, Stanford, California 94305 USA
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, California 94305 USA
| | - James D. Brooks
- Department of Urology, Stanford University, Stanford, California 94305 USA
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56
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The intelligent knife (iKnife) and its intraoperative diagnostic advantage for the treatment of cervical disease. Proc Natl Acad Sci U S A 2020; 117:7338-7346. [PMID: 32179675 PMCID: PMC7132269 DOI: 10.1073/pnas.1916960117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clearance of surgical margins in early cervical cancer prevents the need for adjuvant chemoradiation and associated morbidity and allows fertility preservation. Clearance of disease is also crucial in the surgical management of local recurrence of cervical tumors with exenterative surgery. In this study intelligent knife technology was able to discriminate healthy from abnormal lesions on the cervix with high accuracy, highlighting the potential to improve intraoperative management of women treated surgically for cervical cancer and, as a result, patient outcomes. While pilot experiments in vivo are encouraging, accuracy remains to be validated in larger patient cohorts. Future studies could also explore whether this technology could be used for management of cervical preinvasive disease. Clearance of surgical margins in cervical cancer prevents the need for adjuvant chemoradiation and allows fertility preservation. In this study, we determined the capacity of the rapid evaporative ionization mass spectrometry (REIMS), also known as intelligent knife (iKnife), to discriminate between healthy, preinvasive, and invasive cervical tissue. Cervical tissue samples were collected from women with healthy, human papilloma virus (HPV) ± cervical intraepithelial neoplasia (CIN), or cervical cancer. A handheld diathermy device generated surgical aerosol, which was transferred into a mass spectrometer for subsequent chemical analysis. Combination of principal component and linear discriminant analysis and least absolute shrinkage and selection operator was employed to study the spectral differences between groups. Significance of discriminatory m/z features was tested using univariate statistics and tandem MS performed to elucidate the structure of the significant peaks allowing separation of the two classes. We analyzed 87 samples (normal = 16, HPV ± CIN = 50, cancer = 21 patients). The iKnife discriminated with 100% accuracy normal (100%) vs. HPV ± CIN (100%) vs. cancer (100%) when compared to histology as the gold standard. When comparing normal vs. cancer samples, the accuracy was 100% with a sensitivity of 100% (95% CI 83.9 to 100) and specificity 100% (79.4 to 100). Univariate analysis revealed significant MS peaks in the cancer-to-normal separation belonging to various classes of complex lipids. The iKnife discriminates healthy from premalignant and invasive cervical lesions with high accuracy and can improve oncological outcomes and fertility preservation of women treated surgically for cervical cancer. Larger in vivo research cohorts are required to validate these findings.
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57
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Hale OJ, Cooper HJ. In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates. Biochem Soc Trans 2020; 48:317-326. [PMID: 32010951 PMCID: PMC7054757 DOI: 10.1042/bst20190793] [Citation(s) in RCA: 5] [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: 11/18/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 12/15/2022]
Abstract
Advances in sample preparation, ion sources and mass spectrometer technology have enabled the detection and characterisation of intact proteins. The challenges associated include an appropriately soft ionisation event, efficient transmission and detection of the often delicate macromolecules. Ambient ion sources, in particular, offer a wealth of strategies for analysis of proteins from solution environments, and directly from biological substrates. The last two decades have seen rapid development in this area. Innovations include liquid extraction surface analysis, desorption electrospray ionisation and nanospray desorption electrospray ionisation. Similarly, developments in native mass spectrometry allow protein-protein and protein-ligand complexes to be ionised and analysed. Identification and characterisation of these large ions involves a suite of hyphenated mass spectrometry techniques, often including the coupling of ion mobility spectrometry and fragmentation techniques. The latter include collision, electron and photon-induced methods, each with their own characteristics and benefits for intact protein identification. In this review, recent developments for in situ protein analysis are explored, with a focus on ion sources and tandem mass spectrometry techniques used for identification.
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Affiliation(s)
- Oliver J. Hale
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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58
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Swiner DJ, Jackson S, Burris BJ, Badu-Tawiah AK. Applications of Mass Spectrometry for Clinical Diagnostics: The Influence of Turnaround Time. Anal Chem 2020; 92:183-202. [PMID: 31671262 PMCID: PMC7896279 DOI: 10.1021/acs.analchem.9b04901] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This critical review discusses how the need for reduced clinical turnaround times has influenced chemical instrumentation. We focus on the development of modern mass spectrometry (MS) and its application in clinical diagnosis. With increased functionality that takes advantage of novel front-end modifications and computational capabilities, MS can now be used for non-traditional clinical analyses, including applications in clinical microbiology for bacteria differentiation and in surgical operation rooms. We summarize here recent developments in the field that have enabled such capabilities, which include miniaturization for point-of-care testing, direct complex mixture analysis via ambient ionization, chemical imaging and profiling, and systems integration.
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Affiliation(s)
- Devin J. Swiner
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Sierra Jackson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Benjamin J. Burris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
| | - Abraham K. Badu-Tawiah
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
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59
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Misra BB, Misra A. The chemical exposome of type 2 diabetes mellitus: Opportunities and challenges in the omics era. Diabetes Metab Syndr 2020; 14:23-38. [PMID: 31838434 DOI: 10.1016/j.dsx.2019.12.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a global silent killer, with > 450 million affected adults worldwide. A diverse array of non-modifiable risk factors such as family history, age (> 45 yrs), race/ethnicity, genetics, and history of gestational diabetes and modifiable risk factors such as physical inactivity, high body fat, body weight, high blood pressure, and high cholesterol for progression of prediabetes to T2DM. Given, that the modern world human population is constantly exposed to multiple stressors in the form of physical (i.e., sound, weather etc.) and chemical environment (i.e., diet, pollutants etc.), industrialization, and modernization has led to form a basis for exposomal correlation with T2DM incidence. Over the past decade, there have been emerging reports on association of levels of persistent organic pollutants (POPs), phthalates, antibiotics, drugs, air pollution, pesticides, and heavy metals with T2DM. In this review, we discuss the well known chemical exposome that has been associated with T2DM; the tools and approaches to capture this chemical exposome, and future opportunities and challenges in this exciting area of research. We further provide a window of thoughts, whether omics technologies can help fill in the gaps to help provide high throughput exposomics datasets in an unbiased manner to help understand T2DM pathophysiology in the context of industrialization, drastic lifestyle changes, urbanization, and pollution. We also discuss and provide guidelines/call to action for future exposomics studies investigating the association of T2DM with exposomes in the context of both epidemiological and experimental approaches.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, 27157, NC, USA
| | - Anoop Misra
- Diabetes Foundation (India), Safdarjung Development Area, New Delhi, India; Fortis C-DOC Centre of Excellence for Diabetes, Metabolic Diseases and Endocrinology, Chirag Enclave, Nehru Place, New Delhi, India.
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60
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Kuo TH, Dutkiewicz EP, Pei J, Hsu CC. Ambient Ionization Mass Spectrometry Today and Tomorrow: Embracing Challenges and Opportunities. Anal Chem 2019; 92:2353-2363. [DOI: 10.1021/acs.analchem.9b05454] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ting-Hao Kuo
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Ewelina P. Dutkiewicz
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Jiying Pei
- School of Marine Sciences, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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61
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Wang J, Han X. Analytical challenges of shotgun lipidomics at different resolution of measurements. Trends Analyt Chem 2019; 121:115697. [PMID: 32713986 PMCID: PMC7382544 DOI: 10.1016/j.trac.2019.115697] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The essence of shotgun lipidomics is to maintain consistency of the chemical environment of lipid samples during mass spectrometry acquisition. This strategy is suitable for large-scale quantitative analysis. This strategy also allows sufficient time to collect data to improve the signal-to-noise ratio. The initial approach of shotgun lipidomics was the electrospray ionization (ESI)-based direct infusion mass spectrometry strategy. With development of mass spectrometry for small molecules, shotgun lipidomics methods have been extended to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and ambient mass spectrometry, including MS imaging methods. Furthermore, the object of analysis has extended from organ and body fluid levels to tissue and cell levels with technological developments. In this article, we summarize the status and technical challenges of shotgun lipidomics at different resolution of measurements from the mass spectrometry perspective.
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Affiliation(s)
- Jianing Wang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
- Department of Medicine – Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
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Holzlechner M, Eugenin E, Prideaux B. Mass spectrometry imaging to detect lipid biomarkers and disease signatures in cancer. Cancer Rep (Hoboken) 2019; 2:e1229. [PMID: 32729258 PMCID: PMC7941519 DOI: 10.1002/cnr2.1229] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 11/04/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Current methods to identify, classify, and predict tumor behavior mostly rely on histology, immunohistochemistry, and molecular determinants. However, better predictive markers are required for tumor diagnosis and evaluation. Due, in part, to recent technological advancements, metabolomics and lipid biomarkers have become a promising area in cancer research. Therefore, there is a necessity for novel and complementary techniques to identify and visualize these molecular markers within tumors and surrounding tissue. RECENT FINDINGS Since its introduction, mass spectrometry imaging (MSI) has proven to be a powerful tool for mapping analytes in biological tissues. By adding the label-free specificity of mass spectrometry to the detailed spatial information of traditional histology, hundreds of lipids can be imaged simultaneously within a tumor. MSI provides highly detailed lipid maps for comparing intra-tumor, tumor margin, and healthy regions to identify biomarkers, patterns of disease, and potential therapeutic targets. In this manuscript, recent advancement in sample preparation and MSI technologies are discussed with special emphasis on cancer lipid research to identify tumor biomarkers. CONCLUSION MSI offers a unique approach for biomolecular characterization of tumor tissues and provides valuable complementary information to histology for lipid biomarker discovery and tumor classification in clinical and research cancer applications.
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Affiliation(s)
- Matthias Holzlechner
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| | - Eliseo Eugenin
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
| | - Brendan Prideaux
- Department of Neuroscience, Cell Biology, and AnatomyThe University of Texas Medical Branch at Galveston (UTMB)GalvestonTexas
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Ogrinc N, Saudemont P, Balog J, Robin YM, Gimeno JP, Pascal Q, Tierny D, Takats Z, Salzet M, Fournier I. Water-assisted laser desorption/ionization mass spectrometry for minimally invasive in vivo and real-time surface analysis using SpiderMass. Nat Protoc 2019; 14:3162-3182. [PMID: 31597965 DOI: 10.1038/s41596-019-0217-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 06/14/2019] [Indexed: 11/09/2022]
Abstract
Rapid, sensitive, precise and accurate analysis of samples in their native in vivo environment is critical to better decipher physiological and physiopathological mechanisms. SpiderMass is an ambient mass spectrometry (MS) system designed for mobile in vivo and real-time surface analyses of biological tissues. The system uses a fibered laser, which is tuned to excite the most intense vibrational band of water, resulting in a process termed water-assisted laser desorption/ionization (WALDI). The water molecules act as an endogenous matrix in a matrix-assisted laser desorption ionization (MALDI)-like scenario, leading to the desorption/ionization of biomolecules (lipids, metabolites and proteins). The ejected material is transferred to the mass spectrometer through an atmospheric interface and a transfer line that is several meters long. Here, we formulate a three-stage procedure that includes (i) a laser system setup coupled to a Waters Q-TOF or Thermo Fisher Q Exactive mass analyzer, (ii) analysis of specimens and (iii) data processing. We also describe the optimal setup for the analysis of cell cultures, fresh-frozen tissue sections and in vivo experiments on skin. With proper optimization, the system can be used for a variety of different targets and applications. The entire procedure takes 1-2 d for complex samples.
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Affiliation(s)
- Nina Ogrinc
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
| | - Philippe Saudemont
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
- SATT-Nord, Immeuble Central Gare, Lille, France
| | - Julia Balog
- Department of Surgery and Cancer, St Mary's Hospital, Imperial College London, London, UK
| | - Yves-Marie Robin
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
- Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, Lille, France
| | - Jean-Pascal Gimeno
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
| | - Quentin Pascal
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
- OCR (Oncovet Clinical Research), Eurasanté, Loos, France
| | - Dominique Tierny
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
- OCR (Oncovet Clinical Research), Eurasanté, Loos, France
| | - Zoltan Takats
- Department of Surgery and Cancer, St Mary's Hospital, Imperial College London, London, UK
| | - Michel Salzet
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France.
| | - Isabelle Fournier
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France.
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64
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Zhao X, Zhang W, Zhang D, Liu X, Cao W, Chen Q, Ouyang Z, Xia Y. A lipidomic workflow capable of resolving sn- and C[double bond, length as m-dash]C location isomers of phosphatidylcholines. Chem Sci 2019; 10:10740-10748. [PMID: 32153749 PMCID: PMC7020929 DOI: 10.1039/c9sc03521d] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/04/2019] [Indexed: 01/01/2023] Open
Abstract
As a major class of mammalian lipids, phosphatidylcholines (PCs) often contain mixtures of structural isomers, resulting from different lipogenesis pathways. Profiling PCs at the isomer level, however, remains challenging in lipidomic settings, especially for characterizing the positions of fatty acyls on the glycerol backbone (sn-positions) and the locations of carbon-carbon double bonds (C[double bond, length as m-dash]Cs) in unsaturated acyl chains. In this work, we have developed a workflow for profiling PCs down to sn- and C[double bond, length as m-dash]C locations at high coverage and sensitivity. This capability is enabled by radical-directed fragmentation, forming sn-1 specific fragment ions upon collision-induced dissociation (CID) of bicarbonate anion adducts of PCs ([M + HCO3]-) inside a mass spectrometer. This new tandem mass spectrometry (MS/MS) method can be simply incorporated into liquid chromatography by employing ammonium bicarbonate in the mobile phase without any instrument modification needed. It is also compatible with the online Paternò-Büchì reaction and subsequent MS/MS for the assignment of C[double bond, length as m-dash]C locations in sn-1 fatty acyl chains of unsaturated PCs. The analytical performance of the workflow is manifested by identification of 82 distinct PC molecular species from the polar extract of bovine liver, including quantification of 19 pairs of sn-isomers. Finally, we demonstrate that five pairs of PC sn-isomers show significant compositional changes in tissue samples of human breast cancer relative to controls, suggesting a potential for monitoring PC sn-isomers for biomedical applications.
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Affiliation(s)
- Xue Zhao
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological , Department of Chemistry , Tsinghua University , Beijing 100084 , China .
| | - Wenpeng Zhang
- Department of Chemistry , Purdue University , West Lafayette , IN 47907 , USA
| | - Donghui Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments , Department of Precision Instrument , Tsinghua University , Beijing , 100084 , China
| | - Xinwei Liu
- State Key Laboratory of Precision Measurement Technology and Instruments , Department of Precision Instrument , Tsinghua University , Beijing , 100084 , China
| | - Wenbo Cao
- State Key Laboratory of Precision Measurement Technology and Instruments , Department of Precision Instrument , Tsinghua University , Beijing , 100084 , China
| | - Qinhua Chen
- Affiliated Dongfeng Hospital , Hubei University of Medicine , Shiyan , Hubei Province 442000 , China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments , Department of Precision Instrument , Tsinghua University , Beijing , 100084 , China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological , Department of Chemistry , Tsinghua University , Beijing 100084 , China .
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65
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Sukhikh G, Chagovets V, Wang X, Rodionov V, Kometova V, Tokareva A, Kononikhin A, Starodubtseva N, Chingin K, Chen H, Frankevich V. Combination of Low-Temperature Electrosurgical Unit and Extractive Electrospray Ionization Mass Spectrometry for Molecular Profiling and Classification of Tissues. Molecules 2019; 24:molecules24162957. [PMID: 31443190 PMCID: PMC6720730 DOI: 10.3390/molecules24162957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 11/17/2022] Open
Abstract
Real-time molecular navigation of tissue surgeries is an important goal at present. Combination of electrosurgical units and mass spectrometry (MS) to perform accurate molecular visualization of biological tissues has been pursued by many research groups. Determination of molecular tissue composition at a particular location by surgical smoke analysis is now of increasing interest for clinical use. However, molecular analysis of surgical smoke is commonly lacking molecular specificity and is associated with significant carbonization and chemical contamination, which are mainly related to the high temperature of smoke at which many molecules become unstable. Unlike traditional electrosurgical tools, low-temperature electrosurgical units allow tissue dissection without substantial heating. Here, we show that low-temperature electrosurgical units can be used for desorption of molecules from biological tissues without thermal degradation. The use of extractive electrospray ionization technique for the ionization of desorbed molecules allowed us to obtain mass spectra of healthy and pathological tissues with high degree of differentiation. Overall, the data indicate that the described approach has potential for intraoperative use.
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Affiliation(s)
- Gennady Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov of the Ministry of Healthcare of Russian Federation, Moscow 117997, Russia
- Department of Obstetrics, Gynecology, Perinatology and Reproductology, First Moscow State Medical University named after I.M. Sechenov, Moscow 119991, Russia
| | - Vitaliy Chagovets
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov of the Ministry of Healthcare of Russian Federation, Moscow 117997, Russia
| | - Xinchen Wang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China
| | - Valeriy Rodionov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov of the Ministry of Healthcare of Russian Federation, Moscow 117997, Russia
| | - Vlada Kometova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov of the Ministry of Healthcare of Russian Federation, Moscow 117997, Russia
| | - Alisa Tokareva
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Alexey Kononikhin
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov of the Ministry of Healthcare of Russian Federation, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Natalia Starodubtseva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov of the Ministry of Healthcare of Russian Federation, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China
| | - Huanwen Chen
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China
| | - Vladimir Frankevich
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I.Kulakov of the Ministry of Healthcare of Russian Federation, Moscow 117997, Russia.
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66
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Greaves RF, Bernardini S, Ferrari M, Fortina P, Gouget B, Gruson D, Lang T, Loh TP, Morris HA, Park JY, Roessler M, Yin P, Kricka LJ. Key questions about the future of laboratory medicine in the next decade of the 21st century: A report from the IFCC-Emerging Technologies Division. Clin Chim Acta 2019; 495:570-589. [DOI: 10.1016/j.cca.2019.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 12/21/2022]
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