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Cui H, You Y, Cheng GW, Lan Z, Zou KL, Mai QY, Han YH, Chen H, Zhao YY, Yu GT. Advanced materials and technologies for oral diseases. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2023; 24:2156257. [PMID: 36632346 PMCID: PMC9828859 DOI: 10.1080/14686996.2022.2156257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/15/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Oral disease, as a class of diseases with very high morbidity, brings great physical and mental damage to people worldwide. The increasing burden and strain on individuals and society make oral diseases an urgent global health problem. Since the treatment of almost all oral diseases relies on materials, the rapid development of advanced materials and technologies has also promoted innovations in the treatment methods and strategies of oral diseases. In this review, we systematically summarized the application strategies in advanced materials and technologies for oral diseases according to the etiology of the diseases and the comparison of new and old materials. Finally, the challenges and directions of future development for advanced materials and technologies in the treatment of oral diseases were refined. This review will guide the fundamental research and clinical translation of oral diseases for practitioners of oral medicine.
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Affiliation(s)
- Hao Cui
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Yan You
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Guo-Wang Cheng
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhou Lan
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Ke-Long Zou
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Qiu-Ying Mai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yan-Hua Han
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hao Chen
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Yu-Yue Zhao
- Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Guang-Tao Yu
- Stomatological Hospital, Southern Medical University, Guangzhou, China
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Dholariya S, Singh RD, Sonagra A, Yadav D, Vajaria BN, Parchwani D. Integrating Cutting-Edge Methods to Oral Cancer Screening, Analysis, and Prognosis. Crit Rev Oncog 2023; 28:11-44. [PMID: 37830214 DOI: 10.1615/critrevoncog.2023047772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Oral cancer (OC) has become a significant barrier to health worldwide due to its high morbidity and mortality rates. OC is among the most prevalent types of cancer that affect the head and neck region, and the overall survival rate at 5 years is still around 50%. Moreover, it is a multifactorial malignancy instigated by genetic and epigenetic variabilities, and molecular heterogeneity makes it a complex malignancy. Oral potentially malignant disorders (OPMDs) are often the first warning signs of OC, although it is challenging to predict which cases will develop into malignancies. Visual oral examination and histological examination are still the standard initial steps in diagnosing oral lesions; however, these approaches have limitations that might lead to late diagnosis of OC or missed diagnosis of OPMDs in high-risk individuals. The objective of this review is to present a comprehensive overview of the currently used novel techniques viz., liquid biopsy, next-generation sequencing (NGS), microarray, nanotechnology, lab-on-a-chip (LOC) or microfluidics, and artificial intelligence (AI) for the clinical diagnostics and management of this malignancy. The potential of these novel techniques in expanding OC diagnostics and clinical management is also reviewed.
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Affiliation(s)
- Sagar Dholariya
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Ragini D Singh
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | - Amit Sonagra
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
| | | | | | - Deepak Parchwani
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Rajkot, Gujarat, India
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Amran N, Abdul-Rahman PS. Differential proteome and functional analysis of NSCLC cell lines in response to Tualang honey treatment. JOURNAL OF ETHNOPHARMACOLOGY 2022; 293:115264. [PMID: 35398242 DOI: 10.1016/j.jep.2022.115264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/25/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Honey's therapeutic and nutrition effects have been discovered for centuries. Traditionally, it is applied as a health supplement as well as an alternative treatment for a variety of medical issues ranging from wound healing to anticancer therapy. Tualang honey (TH) is a natural sweet substance produced by Apis dorsata, naturally has a dark brown appearance from its high polyphenolic compounds. TH has been reported to show anticancer effects on various types of cancers including breast, oral, leukemia, cervical and lung cancer through several pathways. The detailed molecular mechanism of anticancer activity of TH as a chemopreventive and therapeutic agent is an interesting endeavor to understand. AIM OF THE STUDY Despite the anticancer effects of Tualang honey (TH) on various types of cancer have been widely reported, the exact molecular mechanism underlying its' anticancer action remains unpublished. Thus, this study aimed to investigate changes that occur on the proteome profile and the functional analysis of proteins with differential abundances within non-small cell lung cancer (NSCLC) cells that were treated with TH and discover the plausible molecular mechanism governing its' anticancer action. MATERIALS AND METHODS NSCLC cell lines (H23 and A549) were treated with 3.6% and 3.1% v/v of TH for 24 h, respectively. Protein extracts were obtained from control NSCLC cells and TH-treated NSCLC cells. Label-free quantitative proteomic analysis was subsequently performed in nanoACQUITY UPLC with quadrupole-time of flight (Q-TOF) Synapt G2 HDMS mass spectrometer system to identify and quantify proteins of TH-treated NSCLC cells. The gene ontology (GO) PANTHER classification system was performed to categorize the identified proteins based on their protein class, biological processes, and pathway. Meanwhile, the STRING functional protein association network database was used to analyze the functional protein-protein interaction and associated pathways of significantly different proteins of NSCLC cells. RESULTS A total of 634 and 554 proteins were identified from H23 and A549 cell lines where 88 differential proteins were upregulated and 103 were downregulated in TH-treated H23 cells, whilst 66 differential proteins were upregulated and 61 were downregulated in TH-treated A549 cells. Differently expressed proteins of NSCLC were observed to be associated with the cell cycle, apoptosis, and VEGFA-VEGFR signaling pathway. TH modulated these signaling pathways through downregulation of ELAVL1, H3F3A and PCNA proteins. Three potential protein markers were significantly downregulated in NSCLC cells such as HRAS, HSPB1, and TUBA1C when treated with TH. CONCLUSIONS Our findings suggested the anticancer activity of TH on NSCLC cells through modulation of pertinent cancer-related proteins that are associated with cell proliferation, apoptosis inhibition, and induction of angiogenesis.
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Affiliation(s)
- Nazirah Amran
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Puteri Shafinaz Abdul-Rahman
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia; University of Malaya Centre for Proteomics Research, UMCPR, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Pillai J, Chincholkar T, Dixit R, Pandey M. A systematic review of proteomic biomarkers in oral squamous cell cancer. World J Surg Oncol 2021; 19:315. [PMID: 34711249 PMCID: PMC8555221 DOI: 10.1186/s12957-021-02423-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/06/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Head and neck squamous cell cancer (HNSCC) is the most common cancer associated with chewing tobacco, in the world. As this is divided in to sites and subsites, it does not make it to top 10 cancers. The most common subsite is the oral cancer. At the time of diagnosis, more than 50% of patients with oral squamous cell cancers (OSCC) had advanced disease, indicating the lack of availability of early detection and risk assessment biomarkers. The new protein biomarker development and discovery will aid in early diagnosis and treatment which lead to targeted treatment and ultimately a good prognosis. METHODS This systematic review was performed as per PRISMA guidelines. All relevant studies assessing characteristics of oral cancer and proteomics were considered for analysis. Only human studies published in English were included, and abstracts, incomplete articles, and cell line or animal studies were excluded. RESULTS A total of 308 articles were found, of which 112 were found to be relevant after exclusion. The present review focuses on techniques of cancer proteomics and discovery of biomarkers using these techniques. The signature of protein expression may be used to predict drug response and clinical course of disease and could be used to individualize therapy with such knowledge. CONCLUSIONS Prospective use of these markers in the clinical setting will enable early detection, prediction of response to treatment, improvement in treatment selection, and early detection of tumor recurrence for disease monitoring. However, most of these markers for OSCC are yet to be validated.
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Affiliation(s)
| | | | - Ruhi Dixit
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Manoj Pandey
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221 005, India.
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Single-Cell Multiomics Analysis for Drug Discovery. Metabolites 2021; 11:metabo11110729. [PMID: 34822387 PMCID: PMC8623556 DOI: 10.3390/metabo11110729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 02/02/2023] Open
Abstract
Given the heterogeneity seen in cell populations within biological systems, analysis of single cells is necessary for studying mechanisms that cannot be identified on a bulk population level. There are significant variations in the biological and physiological function of cell populations due to the functional differences within, as well as between, single species as a result of the specific proteome, transcriptome, and metabolome that are unique to each individual cell. Single-cell analysis proves crucial in providing a comprehensive understanding of the biological and physiological properties underlying human health and disease. Omics technologies can help to examine proteins (proteomics), RNA molecules (transcriptomics), and the chemical processes involving metabolites (metabolomics) in cells, in addition to genomes. In this review, we discuss the value of multiomics in drug discovery and the importance of single-cell multiomics measurements. We will provide examples of the benefits of applying single-cell omics technologies in drug discovery and development. Moreover, we intend to show how multiomics offers the opportunity to understand the detailed events which produce or prevent disease, and ways in which the separate omics disciplines complement each other to build a broader, deeper knowledge base.
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Jawa Y, Yadav P, Gupta S, Mathan SV, Pandey J, Saxena AK, Kateriya S, Tiku AB, Mondal N, Bhattacharya J, Ahmad S, Chaturvedi R, Tyagi RK, Tandon V, Singh RP. Current Insights and Advancements in Head and Neck Cancer: Emerging Biomarkers and Therapeutics with Cues from Single Cell and 3D Model Omics Profiling. Front Oncol 2021; 11:676948. [PMID: 34490084 PMCID: PMC8418074 DOI: 10.3389/fonc.2021.676948] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022] Open
Abstract
Head and neck cancer (HNC) is among the ten leading malignancies worldwide, with India solely contributing one-third of global oral cancer cases. The current focus of all cutting-edge strategies against this global malignancy are directed towards the heterogeneous tumor microenvironment that obstructs most treatment blueprints. Subsequent to the portrayal of established information, the review details the application of single cell technology, organoids and spheroid technology in relevance to head and neck cancer and the tumor microenvironment acknowledging the resistance pattern of the heterogeneous cell population in HNC. Bioinformatic tools are used for study of differentially expressed genes and further omics data analysis. However, these tools have several challenges and limitations when analyzing single-cell gene expression data that are discussed briefly. The review further examines the omics of HNC, through comprehensive analyses of genomics, transcriptomics, proteomics, metabolomics, and epigenomics profiles. Patterns of alterations vary between patients, thus heterogeneity and molecular alterations between patients have driven the clinical significance of molecular targeted therapies. The analyses of potential molecular targets in HNC are discussed with connotation to the alteration of key pathways in HNC followed by a comprehensive study of protein kinases as novel drug targets including its ATPase and additional binding pockets, non-catalytic domains and single residues. We herein review, the therapeutic agents targeting the potential biomarkers in light of new molecular targeted therapies. In the final analysis, this review suggests that the development of improved target-specific personalized therapies can combat HNC's global plight.
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Affiliation(s)
- Yashika Jawa
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Pooja Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Shruti Gupta
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sivapar V. Mathan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jyoti Pandey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ajay K. Saxena
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Suneel Kateriya
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ashu B. Tiku
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Neelima Mondal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh K. Tyagi
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Vibha Tandon
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Rana P. Singh
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Sarbu M, Clemmer DE, Zamfir AD. Ion mobility mass spectrometry of human melanoma gangliosides. Biochimie 2020; 177:226-237. [DOI: 10.1016/j.biochi.2020.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 02/09/2023]
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Nassar SF, Raddassi K, Ubhi B, Doktorski J, Abulaban A. Precision Medicine: Steps along the Road to Combat Human Cancer. Cells 2020; 9:E2056. [PMID: 32916938 PMCID: PMC7563722 DOI: 10.3390/cells9092056] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 12/14/2022] Open
Abstract
The diagnosis and treatment of diseases such as cancer is becoming more accurate and specialized with the advent of precision medicine techniques, research and treatments. Reaching down to the cellular and even sub-cellular level, diagnostic tests can pinpoint specific, individual information from each patient, and guide providers to a more accurate plan of treatment. With this advanced knowledge, researchers and providers can better gauge the effectiveness of drugs, radiation, and other therapies, which is bound to lead to a more accurate, if not more positive, prognosis. As precision medicine becomes more established, new techniques, equipment, materials and testing methods will be required. Herein, we will examine the recent innovations in assays, devices and software, along with next generation sequencing in genomics diagnostics which are in use or are being developed for personalized medicine. So as to avoid duplication and produce the fullest possible benefit, all involved must be strongly encouraged to collaborate, across national borders, public and private sectors, science, medicine and academia alike. In this paper we will offer recommendations for tools, research and development, along with ideas for implementation. We plan to begin with discussion of the lessons learned to date, and the current research on pharmacogenomics. Given the steady stream of advances in imaging mass spectrometry and nanoLC-MS/MS, and use of genomic, proteomic and metabolomics biomarkers to distinguish healthy tissue from diseased cells, there is great potential to utilize pharmacogenomics to tailor a drug or drugs to a particular cohort of patients. Such efforts very well may bring increased hope for small groups of non-responders and those who have demonstrated adverse reactions to current treatments.
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Affiliation(s)
- Samuel F. Nassar
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, CT 06511, USA;
| | | | | | - Ahmad Abulaban
- Department of Neurology, Yale School of Medicine, New Haven, CT 06511, USA;
- Department of Medicine, King Saud Bin-Abdulaziz University, King Abdulaziz Medical City-National Guard Health Affairs, Riyadh 11426, Saudi Arabia
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Teclemariam ET, Pergande MR, Cologna SM. Considerations for mass spectrometry-based multi-omic analysis of clinical samples. Expert Rev Proteomics 2020; 17:99-107. [PMID: 31996049 DOI: 10.1080/14789450.2020.1724540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The role of mass spectrometry in biomolecule analysis has become paramount over the last several decades ranging in the analysis across model systems and human specimens. Accordingly, the presence of mass spectrometers in clinical laboratories has also expanded alongside the number of researchers investigating the protein, lipid, and metabolite composition of an array of biospecimens. With this increase in the number of omic investigations, it is important to consider the entire experimental strategy from sample collection and storage, data collection and analysis.Areas covered: In this short review, we outline considerations for working with clinical (e.g. human) specimens including blood, urine, and cerebrospinal fluid, with emphasis on sample handling, profiling composition, targeted measurements and relevance to disease. Discussions of integrated genomic or transcriptomic datasets are not included. A brief commentary is also provided regarding new technologies with clinical relevance.Expert opinion: The role of mass spectrometry to investigate clinically related specimens is on the rise and the ability to integrate multiple omics datasets from mass spectrometry measurements will be crucial to further understanding human health and disease.
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Affiliation(s)
- Esei T Teclemariam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.,Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, USA
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Relative quantitation of endogenous proteins by quadrupole-time of flight and tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1106-1107:11-18. [PMID: 30615973 DOI: 10.1016/j.jchromb.2018.12.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 11/23/2018] [Accepted: 12/16/2018] [Indexed: 01/17/2023]
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Chen XJ, Zhang XQ, Liu Q, Zhang J, Zhou G. Nanotechnology: a promising method for oral cancer detection and diagnosis. J Nanobiotechnology 2018; 16:52. [PMID: 29890977 PMCID: PMC5994839 DOI: 10.1186/s12951-018-0378-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/01/2018] [Indexed: 12/20/2022] Open
Abstract
Oral cancer is a common and aggressive cancer with high morbidity, mortality, and recurrence rate globally. Early detection is of utmost importance for cancer prevention and disease management. Currently, tissue biopsy remains the gold standard for oral cancer diagnosis, but it is invasive, which may cause patient discomfort. The application of traditional noninvasive methods-such as vital staining, exfoliative cytology, and molecular imaging-is limited by insufficient sensitivity and specificity. Thus, there is an urgent need for exploring noninvasive, highly sensitive, and specific diagnostic techniques. Nano detection systems are known as new emerging noninvasive strategies that bring the detection sensitivity of biomarkers to nano-scale. Moreover, compared to current imaging contrast agents, nanoparticles are more biocompatible, easier to synthesize, and able to target specific surface molecules. Nanoparticles generate localized surface plasmon resonances at near-infrared wavelengths, providing higher image contrast and resolution. Therefore, using nano-based techniques can help clinicians to detect and better monitor diseases during different phases of oral malignancy. Here, we review the progress of nanotechnology-based methods in oral cancer detection and diagnosis.
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Affiliation(s)
- Xiao-Jie Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, 430079 People’s Republic of China
| | - Xue-Qiong Zhang
- School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, Wuhan, 430070 People’s Republic of China
| | - Qi Liu
- Division of Pharmacoengineering and Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Jing Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, 430079 People’s Republic of China
- Department of Oral Medicine, School and Hospital of Stomatology, Wuhan University, Wuhan, 430079 People’s Republic of China
| | - Gang Zhou
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, 430079 People’s Republic of China
- Department of Oral Medicine, School and Hospital of Stomatology, Wuhan University, Wuhan, 430079 People’s Republic of China
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A dual-functional microfluidic chip for on-line detection of interleukin-8 based on rolling circle amplification. Biosens Bioelectron 2018; 102:652-660. [DOI: 10.1016/j.bios.2017.12.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/23/2017] [Accepted: 12/11/2017] [Indexed: 02/08/2023]
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Zhong Z, Mao S, Lin H, Lin JM, Lin J. Comparative proteomics of cancer stem cells in osteosarcoma using ultra-high-performance liquid chromatography and Orbitrap Fusion mass spectrometer. Talanta 2018; 178:362-368. [DOI: 10.1016/j.talanta.2017.09.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/13/2017] [Accepted: 09/17/2017] [Indexed: 01/04/2023]
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Lin L, Zheng J, Yu Q, Chen W, Xing J, Chen C, Tian R. High throughput and accurate serum proteome profiling by integrated sample preparation technology and single-run data independent mass spectrometry analysis. J Proteomics 2017; 174:9-16. [PMID: 29278786 DOI: 10.1016/j.jprot.2017.12.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/28/2017] [Accepted: 12/19/2017] [Indexed: 12/18/2022]
Abstract
Mass spectrometry (MS)-based serum proteome analysis is extremely challenging due to its high complexity and dynamic range of protein abundances. Developing high throughput and accurate serum proteomic profiling approach capable of analyzing large cohorts is urgently needed for biomarker discovery. Herein, we report a streamlined workflow for fast and accurate proteomic profiling from 1μL of blood serum. The workflow combined an integrated technique for highly sensitive and reproducible sample preparation and a new data-independent acquisition (DIA)-based MS method. Comparing with standard data dependent acquisition (DDA) approach, the optimized DIA method doubled the number of detected peptides and proteins with better reproducibility. Without protein immunodepletion and prefractionation, the single-run DIA analysis enables quantitative profiling of over 300 proteins with 50min gradient time. The quantified proteins span more than five orders of magnitude of abundance range and contain over 50 FDA-approved disease markers. The workflow allowed us to analyze 20 serum samples per day, with about 358 protein groups per sample being identified. A proof-of-concept study on renal cell carcinoma (RCC) serum samples confirmed the feasibility of the workflow for large scale serum proteomic profiling and disease-related biomarker discovery. BIOLOGICAL SIGNIFICANCE Blood serum or plasma is the predominant specimen for clinical proteomic studies while the analysis is extremely challenging for its high complexity. Many efforts had been made in the past for serum proteomics for maximizing protein identifications, whereas few have been concerned with throughput and reproducibility. Here, we establish a rapid, robust and high reproducible DIA-based workflow for streamlined serum proteomic profiling from 1μL serum. The workflow doesn't need protein depletion and pre-fractionation, while still being able to detect disease-relevant proteins accurately. The workflow is promising in clinical application, because the usage of small sample amounts makes blood testing much less invasive, the fully integrated sample preparation by the SISPROT technology greatly improve sample preparation throughput and reproducibility, and the scan feature of DIA method provides a way to convert nonrenewable clinical specimens into permanent digital proteome maps which could be easily reanalyzed.
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Affiliation(s)
- Lin Lin
- Materials Characterization & Preparation Center, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Jiaxin Zheng
- Department of Urology and Center of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Quan Yu
- Division of Advanced Manufacturing, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
| | - Wendong Chen
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jinchun Xing
- Department of Urology and Center of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Chenxi Chen
- Department of Urology and Center of Urology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China
| | - Ruijun Tian
- Department of Chemistry and Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China.
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Meyer JG, Schilling B. Clinical applications of quantitative proteomics using targeted and untargeted data-independent acquisition techniques. Expert Rev Proteomics 2017; 14:419-429. [PMID: 28436239 PMCID: PMC5671767 DOI: 10.1080/14789450.2017.1322904] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION While selected/multiple-reaction monitoring (SRM or MRM) is considered the gold standard for quantitative protein measurement, emerging data-independent acquisition (DIA) using high-resolution scans have opened a new dimension of high-throughput, comprehensive quantitative proteomics. These newer methodologies are particularly well suited for discovery of biomarker candidates from human disease samples, and for investigating and understanding human disease pathways. Areas covered: This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e.g., SWATH). Corresponding bioinformatics strategies, as well as application in biological and clinical studies are presented. Expert commentary: Nascent application of highly-multiplexed untargeted DIA, such as SWATH, for accurate protein quantification from clinically relevant and disease-related samples shows great potential to comprehensively investigate biomarker candidates and understand disease.
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Affiliation(s)
- Jesse G Meyer
- a Mass Spectrometry Core , Buck Institute for Research on Aging , Novato , CA , USA
| | - Birgit Schilling
- a Mass Spectrometry Core , Buck Institute for Research on Aging , Novato , CA , USA
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