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Rawat S, Subramaniam K, Subramanian SK, Subbarayan S, Dhanabalan S, Chidambaram SKM, Stalin B, Roy A, Nagaprasad N, Aruna M, Tesfaye JL, Badassa B, Krishnaraj R. Drug Repositioning Using Computer-aided Drug Design (CADD). Curr Pharm Biotechnol 2024; 25:301-312. [PMID: 37605405 DOI: 10.2174/1389201024666230821103601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/03/2023] [Accepted: 03/20/2023] [Indexed: 08/23/2023]
Abstract
Drug repositioning is a method of using authorized drugs for other unusually complex diseases. Compared to new drug development, this method is fast, low in cost, and effective. Through the use of outstanding bioinformatics tools, such as computer-aided drug design (CADD), computer strategies play a vital role in the re-transformation of drugs. The use of CADD's special strategy for target-based drug reuse is the most promising method, and its realization rate is high. In this review article, we have particularly focused on understanding the various technologies of CADD and the use of computer-aided drug design for target-based drug reuse, taking COVID-19 and cancer as examples. Finally, it is concluded that CADD technology is accelerating the development of repurposed drugs due to its many advantages, and there are many facts to prove that the new ligand-targeting strategy is a beneficial method and that it will gain momentum with the development of technology.
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Affiliation(s)
- Sona Rawat
- School of Life Sciences, Jaipur National University, Jaipur-302017, India
| | - Kanmani Subramaniam
- Department of Civil Engineering, KPR Institute of Engineering and Technology, Coimbatore-641407, Tamil Nadu, India
| | - Selva Kumar Subramanian
- Department of Sciences, Amrita School of Engineering, Coimbatore - 641112, Tamil Nadu, India
| | - Saravanan Subbarayan
- Department of Civil Engineering, National Institute of Technology, Trichy-620015, Tamil Nadu, India
| | - Subramanian Dhanabalan
- Department of Mechanical Engineering, M. Kumarasamy College of Engineering, Karur - 639113, Tamil Nadu, India
| | | | - Balasubramaniam Stalin
- Department of Mechanical Engineering, Anna University, Regional Campus Madurai, Madurai - 625 019, Tamil Nadu, India
| | - Arpita Roy
- Department of Biotechnology, School of Engineering & Technology, Sharda University, Greater Noida 201310, India
| | - Nagaraj Nagaprasad
- Department of Mechanical Engineering, ULTRA College of Engineering and Technology, Madurai - 625104, Tamilnadu, India
| | - Mahalingam Aruna
- College of Engineering and Computing, Al Ghurair University, Academic City, Dubai, UAE
| | - Jule Leta Tesfaye
- Dambi Dollo University, College of Natural and Computational Science, Department of Physics, Ethiopia
- Centre for Excellence-Indigenous Knowledge, Innovative Technology Transfer and Entrepreneurship, Dambi Dollo University, Dambi Dollo, Ethiopia
- Ministry of innovation and technology, Ethiopia
| | - Bayissa Badassa
- Department of Mechanical Engineering, Dambi Dollo University, Dambi Dollo, Ethiopia
| | - Ramaswamy Krishnaraj
- Centre for Excellence-Indigenous Knowledge, Innovative Technology Transfer and Entrepreneurship, Dambi Dollo University, Dambi Dollo, Ethiopia
- Ministry of innovation and technology, Ethiopia
- Department of Mechanical Engineering, Dambi Dollo University, Dambi Dollo, Ethiopia
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Saba L, Tagliagambe S. Quantitative medicine: Tracing the transition from holistic to reductionist approaches. A new "quantitative holism" is possible? J Public Health Res 2023; 12:22799036231182271. [PMID: 37361238 PMCID: PMC10286173 DOI: 10.1177/22799036231182271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
The practice of medicine has evolved significantly over time, from a more holistic to a reductionist or mechanistic approach. This paper briefly traces the history of medicine and the transition to quantitative medicine, which has enabled more personalized and targeted treatments, and improved understanding of the underlying biological mechanisms of disease. However, this shift has also presented some challenges and criticisms, including the danger of losing sight of the patient as a unique, whole individual. This paper explores the underlying principles and key contributions of quantitative medicine, as well as the context for its rise, including the development of new technologies and the influence of reductionist philosophies. The challenges and criticisms of this approach, and the need to balance reductionist and holistic approaches in order to achieve a comprehensive understanding of human health will be discussed. Ultimately, by integrating insights from philosophy, physics, and other fields, we may be able to develop new and innovative approaches that bridge the gap between reductionism and holism and improve patient outcomes with the new "quantitative holism."
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Affiliation(s)
- Luca Saba
- Luca Saba, University of Cagliari, SS 554 Monserrato, Cagliari 09124, Italy.
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From protein biomarkers to proteomics in dementia with Lewy Bodies. Ageing Res Rev 2023; 83:101771. [PMID: 36328346 DOI: 10.1016/j.arr.2022.101771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/15/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative dementia. Despite considerable research progress, there remain gaps in our understanding of the pathophysiology and there is no disease-modifying treatment. Proteomics is a powerful tool to elucidate complex biological pathways across heterogenous conditions. This review summarizes the widely used proteomic methods and presents evidence for protein dysregulation in the brain and peripheral tissues in DLB. Proteomics of post-mortem brain tissue shows that DLB shares common features with other dementias, such as synaptic dysfunction, but retains a unique protein signature. Promising diagnostic biomarkers are being identified in cerebrospinal fluid (CSF), blood, and peripheral tissues, such as serum Heart-type fatty acid binding protein. Research is needed to track these changes from the prodromal stage to established dementia, with standardized workflows to ensure replicability. Identifying novel protein targets in causative biological pathways could lead to the development of new targeted therapeutics or the stratification of participants for clinical trials.
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Omenn GS. Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years. Mol Cell Proteomics 2021; 20:100062. [PMID: 33640492 PMCID: PMC8058560 DOI: 10.1016/j.mcpro.2021.100062] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 02/08/2023] Open
Abstract
We celebrate the 10th anniversary of the launch of the HUPO Human Proteome Project (HPP) and its major milestone of confident detection of at least one protein from each of 90% of the predicted protein-coding genes, based on the output of the entire proteomics community. The Human Genome Project reached a similar decadal milestone 20 years ago. The HPP has engaged proteomics teams around the world, strongly influenced data-sharing, enhanced quality assurance, and issued stringent guidelines for claims of detecting previously "missing proteins." This invited perspective complements papers on "A High-Stringency Blueprint of the Human Proteome" and "The Human Proteome Reaches a Major Milestone" in special issues of Nature Communications and Journal of Proteome Research, respectively, released in conjunction with the October 2020 virtual HUPO Congress and its celebration of the 10th anniversary of the HUPO HPP.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan Medical School, Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, Ann Arbor, Michigan, USA.
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5
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Jiao Y, Preston S, Hofmann A, Taki A, Baell J, Chang BCH, Jabbar A, Gasser RB. A perspective on the discovery of selected compounds with anthelmintic activity against the barber's pole worm-Where to from here? ADVANCES IN PARASITOLOGY 2020; 108:1-45. [PMID: 32291083 DOI: 10.1016/bs.apar.2019.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Parasitic roundworms (nematodes) cause substantial morbidity and mortality in animals worldwide. Anthelmintic treatment is central to controlling these worms, but widespread resistance to most of the commercially available anthelmintics for veterinary and agricultural use is compromising control, such that there is an urgency to discover new and effective drugs. The purpose of this article is to review information on parasitic nematodes, the treatment and control of parasitic nematode infections and aspects of discovering new anthelmintics in the context of anthelmintic resistance problems, and then to discuss some progress that our group has made in identifying selected compounds with activity against nematodes. The focus of our recent work has been on discovering new chemical entities and known drugs with anthelmintic activities against Haemonchus contortus as well as other socioeconomically important parasitic nematodes for subsequent development. Using whole worm-based phenotypic assays, we have been screening compound collections obtained via product-development-partnerships and/or collaborators, and active compounds have been assessed for their potential as anthelmintic candidates. Following the screening of 15,333 chemicals from five distinct compound collections against H. contortus, we have discovered one new chemical entity (designated SN00797439), two human kinase inhibitors (SNS-032 and AG-1295), 14 tetrahydroquinoxaline analogues, one insecticide (tolfenpyrad) and two tolfenpyrad (pyrazole-5-carboxamide) derivatives (a-15 and a-17) with anthelmintic activity in vitro. Some of these 20 'hit' compounds have selectivity against H. contortus in vitro when compared to particular human cell lines. In our opinion, some of these compounds could represent starting points for 'lead' development. Accordingly, the next research steps to be pursued include: (i) chemical optimisation of representative chemicals via structure-activity relationship (SAR) evaluations; (ii) assessment of the breadth of spectrum of anthelmintic activity on a range of other parasitic nematodes, such as strongyloids, ascaridoids, enoplids and filarioids; (iii) detailed investigations of the absorption, distribution, metabolism, excretion and toxicity (ADMET) of optimised chemicals with broad nematocidal or nematostatic activity; and (iv) establishment of the modes of action of lead candidates.
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Affiliation(s)
- Yaqing Jiao
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Sarah Preston
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia; Faculty of Science and Technology, Federation University, Ballarat, VIC, Australia
| | - Andreas Hofmann
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Aya Taki
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Jonathan Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Bill C H Chang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Abdul Jabbar
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
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Paquet F, Bailey MR, Leggett RW, Etherington G, Blanchardon E, Smith T, Ratia G, Melo D, Fell TP, Berkovski V, Harrison JD. ICRP Publication 141: Occupational Intakes of Radionuclides: Part 4. Ann ICRP 2019; 48:9-501. [PMID: 31850780 DOI: 10.1177/0146645319834139] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The 2007 Recommendations (ICRP, 2007) introduced changes that affect the calculation of effective dose, and implied a revision of the dose coefficients for internal exposure, published previously in the Publication 30 series (ICRP, 1979a,b, 1980a, 1981, 1988) and Publication 68 (ICRP, 1994b). In addition, new data are now available that support an update of the radionuclide-specific information given in Publications 54 and 78 (ICRP, 1989a, 1997) for the design of monitoring programmes and retrospective assessment of occupational internal doses. Provision of new biokinetic models, dose coefficients, monitoring methods, and bioassay data was performed by Committee 2 and its task groups. A new series, the Occupational Intakes of Radionuclides (OIR) series, will replace the Publication 30 series and Publications 54, 68, and 78. OIR Part 1 (ICRP, 2015) describes the assessment of internal occupational exposure to radionuclides, biokinetic and dosimetric models, methods of individual and workplace monitoring, and general aspects of retrospective dose assessment. OIR Part 2 (ICRP, 2016), OIR Part 3 (ICRP, 2017), this current publication, and the final publication in the OIR series (OIR Part 5) provide data on individual elements and their radioisotopes, including information on chemical forms encountered in the workplace; a list of principal radioisotopes and their physical half-lives and decay modes; the parameter values of the reference biokinetic models; and data on monitoring techniques for the radioisotopes most commonly encountered in workplaces. Reviews of data on inhalation, ingestion, and systemic biokinetics are also provided for most of the elements. Dosimetric data provided in the printed publications of the OIR series include tables of committed effective dose per intake (Sv per Bq intake) for inhalation and ingestion, tables of committed effective dose per content (Sv per Bq measurement) for inhalation, and graphs of retention and excretion data per Bq intake for inhalation. These data are provided for all absorption types and for the most common isotope(s) of each element. The online electronic files that accompany the OIR series of publications contains a comprehensive set of committed effective and equivalent dose coefficients, committed effective dose per content functions, and reference bioassay functions. Data are provided for inhalation, ingestion, and direct input to blood. This fourth publication in the OIR series provides the above data for the following elements: lanthanum (La), cerium (Ce), praseodymium (Pr), neodymium (Nd), promethium (Pm), samarium (Sm), europium (Eu), gadolinium (Gd), terbium (Tb), dysprosium (Dy), holmium (Ho), erbium (Er), thulium (Tm), ytterbium (Yb), lutetium (Lu), actinium (Ac), protactinium (Pa), neptunium (Np), plutonium (Pu), americium (Am), curium (Cm), berkelium (Bk), californium (Cf), einsteinium (Es), and fermium (Fm).
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Orellana LH, Hatt JK, Iyer R, Chourey K, Hettich RL, Spain JC, Yang WH, Chee-Sanford JC, Sanford RA, Löffler FE, Konstantinidis KT. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. Sci Rep 2019; 9:17630. [PMID: 31772206 PMCID: PMC6879594 DOI: 10.1038/s41598-019-53679-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/14/2019] [Indexed: 01/29/2023] Open
Abstract
To what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3- g-1 dry soil d-1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3-) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.
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Affiliation(s)
- Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- Laboratorio de Enteropatogenos, Programa de Microbiología y Micología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ramsunder Iyer
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
| | - Karuna Chourey
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jim C Spain
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, Florida, USA
| | - Wendy H Yang
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joanne C Chee-Sanford
- U.S. Department of Agriculture, Agricultural Research Service, Urbana, Illinois, USA
| | - Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, Department of Microbiology, Department of Civil and Environmental Engineering, and Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Peters S, Hains PG, Lucas N, Robinson PJ, Tully B. A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs. J Proteome Res 2019; 18:1019-1031. [DOI: 10.1021/acs.jproteome.8b00709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sean Peters
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Peter G. Hains
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
- Cell Signalling Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Natasha Lucas
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Phillip J. Robinson
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Brett Tully
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
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Onco-omics Approaches and Applications in Clinical Trials for Cancer Patients. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1168:79-90. [DOI: 10.1007/978-3-030-24100-1_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Pathak RK, Baunthiyal M, Pandey D, Kumar A. Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities. 3 Biotech 2018; 8:454. [PMID: 30370195 PMCID: PMC6195494 DOI: 10.1007/s13205-018-1473-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
With the continuous increase in the population of developing countries and decline of natural resources, there is an urgent need to qualitatively and quantitatively augment crop productivity by using new tools and technologies for improvement of agriculturally important traits. The new scientific and technological omics-based approaches have enabled us to deal with several issues and challenges faced by modern agricultural system and provided us novel opportunities for ensuring food and nutritional security. Recent developments in sequencing techniques have made available huge amount of genomic and transcriptomic data on model and cultivated crop plants including Arabidopsis thaliana, Oryza sativa, Triticum aestivum etc. The sequencing data along with other data generated through several omics platforms have significantly influenced the disciplines of crop sciences. Gene discovery and expression profiling-based technologies are offering enormous opportunities to the scientific community which can now apply marker-assisted selection technology to assess and enhance diversity in their collected germplasm, introgress essential traits from new sources and investigate genes that control key traits of crop plants. Utilization of omics science and technologies for crop productivity, protection and management has recently been receiving a lot of attention; the majority of the efforts have been put into signifying the possible applications of various omics technologies in crop plant sciences. This article highlights the background of challenges and opportunities for augmentation of crop productivity through interventions of omics technologies in India.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Mamta Baunthiyal
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Present Address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
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Xu JW, Li YL, Zhang SJ, Yang WQ, Nie WT, Jiang HQ. Quantitative Serum Proteomic Analysis of Essential Hypertension Using iTRAQ Technique. BIOMED RESEARCH INTERNATIONAL 2017; 2017:6761549. [PMID: 29201909 PMCID: PMC5671681 DOI: 10.1155/2017/6761549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022]
Abstract
Essential hypertension (EH) is a risk factor for some severe diseases. This study aimed to screen out serum special proteins and seek interaction between them, which would provide new therapeutic targets and elucidate the comprehensive pathophysiological mechanism for EH. Patients with EH (Group A, n = 47) and healthy controls (HC) (Group B, n = 47) were recruited in this study. Serums from the two groups were analyzed with isobaric tags for relative and absolute quantitation coupled two-dimensional liquid chromatography followed by electrospray ionization-tandem mass spectrometry technique, while the candidate special proteins were verified with ELISA and western blot. A total of 404 proteins were identified, of which 30 proteins were upregulated (>1.2-fold, p < 0.05) and 81 proteins were downregulated (<0.833-fold, p < 0.05) compared with HC group. With GO, KEGG analysis, and literature retrieval, 4 proteins, cathepsin G, transforming growth factor beta-1, hyaluronidase-1, and kininogen-1, were found jointly involved in the renin-angiotensin-aldosterone system and kallikrein-kinin system. The profiles of these 4 candidate proteins were confirmed with ELISA and western blot. The concentration variation of these 4 proteins could better predict the occurrence and illustrate the pathophysiological mechanism of EH. And their discovery may help pave the way for exploring new therapies of EH.
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Affiliation(s)
- Jing-Wen Xu
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, Shandong Province, China
- Affiliated Hospital of Shandong Academy of Medical Sciences, 38 Shadowless Hill Road, Tianqiao District, Jinan, Shandong Province, China
| | - Yun-Lun Li
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, 16369 Jingshi Road, Lixia District, Jinan, Shandong Province, China
| | - Shi-Jun Zhang
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
| | - Wen-Qing Yang
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
| | - Wen-Ting Nie
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
| | - Hai-Qiang Jiang
- Shandong University of Traditional Chinese Medicine, 4655 Daxue Road, Changqing District, Jinan, Shandong Province, China
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Jin P, Wang K, Huang C, Nice EC. Mining the fecal proteome: from biomarkers to personalised medicine. Expert Rev Proteomics 2017; 14:445-459. [PMID: 28361558 DOI: 10.1080/14789450.2017.1314786] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance. Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current 'Proteomics Toolbox', explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform. Expert commentary: Integration of fecal proteomics with other proteomics and genomics strategies as well as bioinformatics is paving the way towards personalised medicine, which will bring with it improved global healthcare.
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Affiliation(s)
- Ping Jin
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Kui Wang
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Canhua Huang
- a Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology , the Affiliated Hospital of Hainan Medical College , Haikou , China.,b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Edouard C Nice
- b State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
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Identification of Tengfu Jiangya Tablet Target Biomarkers with Quantitative Proteomic Technique. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:7594805. [PMID: 28408942 PMCID: PMC5376940 DOI: 10.1155/2017/7594805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/08/2017] [Indexed: 12/21/2022]
Abstract
Tengfu Jiangya Tablet (TJT) is a well accepted antihypertension drug in China and its major active components were Uncaria total alkaloids and Semen Raphani soluble alkaloid. To further explore treatment effects mechanism of TJT on essential hypertension, a serum proteomic study was performed. Potential biomarkers were quantified in serum of hypertension individuals before and after taking TJT with isobaric tags for relative and absolute quantitation (iTRAQ) coupled two-dimensional liquid chromatography followed electrospray ionization-tandem mass spectrometry (2D LC-MS/MS) proteomics technique. Among 391 identified proteins with high confidence, 70 proteins were differentially expressed (fold variation criteria, >1.2 or <0.83) between two groups (39 upregulated and 31 downregulated). Combining with Gene Ontology annotation, KEGG pathway analysis, and literature retrieval, 5 proteins were chosen as key target biomarkers during TJT therapeutic process. And the alteration profiles of these 5 proteins were verified by ELISA and Western Blot. Proteins Kininogen 1 and Keratin 1 are members of Kallikrein system, while Myeloperoxidase, Serum Amyloid protein A, and Retinol binding protein 4 had been reported closely related to vascular endothelial injury. Our study discovered 5 target biomarkers of the compound Chinese medicine TJT. Secondly, this research initially revealed the antihypertension therapeutic mechanism of this drug from a brand-new aspect.
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Li YL, Zhang XY, Leng Y, Wu YL, Li J, Wu YX. Global protein expression analysis of molecular markers of DS-1-47, a component of implantation-promoting traditional chinese medicine. ACTA ACUST UNITED AC 2016; 36:910-915. [PMID: 27924510 DOI: 10.1007/s11596-016-1683-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/25/2016] [Indexed: 01/01/2023]
Abstract
This study investigated the molecular markers of DS-1-47, a component of an implantation- promoting traditional Chinese medicine consisting of Astragalus mongholicus, Atractylodes macrocephala, Scutellaria baicalensis and Dipsacales, in an attempt to clarify the molecular mechanism and action targets of DS-1-47. Controlled ovarian stimulation (COS) method was used to establish the implantation dysfunction models of mice. Animals were divided into normal pregnant group, COS model group and DS-1-47 group. Laser capture microdissection-double dimensional electrophoresis-mass spectrum (LCM-DE-MS) was used to analyze the uterine protein molecules that were possibly involved in the promotion of implantation. Twenty-three proteins in DS-1-47 group were significantly changed as compared to those in COS model group, with 7 proteins down-regulated and 16 proteins up-regulated. Except for some constituent proteins, the down-regulated proteins included collagen α-1 (VI) chain, keratin 7, keratin 14, myosin regulatory light chain 12B, myosin light polypeptide 9, heat shock protein β-7, and C-U-editing enzyme APOBEC-2; the up-regulated proteins included apolipoprotein A-I, calcium regulated protein-3, proliferating cell nuclear antigen, L-xylulose reductase, and calcium binding protein. These 23 proteins that were regulated by DS-1-47 represented a broad diversity of molecule functions. The down-regulated proteins were associated with stress and immune response, and those up-regulated proteins were related to proliferation. It was suggested that these proteins were important in regulating the uterine environment for the blastocyst implantation. By identification of DS-1-47 markers, proteomic analysis coupled with functional assays is demonstrated to be a promising approach to better understand the molecular mechanism of traditional Chinese medicine.
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Affiliation(s)
- Yan-Ling Li
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiao-Yan Zhang
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yu Leng
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yan-Li Wu
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jing Li
- Department of Emergency, Hubei General Hospital of Chinese People's Armed Police Forces, Wuhan, 430061, China.
| | - Yun-Xia Wu
- Department of Traditional Chinese Medicine, School of Pharmacy, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 2016. [PMID: 27887629 DOI: 10.1186/s13059–016–1103–0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
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Affiliation(s)
- Miten Jain
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Hugh E Olsen
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.
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Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 2016; 17:239. [PMID: 27887629 PMCID: PMC5124260 DOI: 10.1186/s13059-016-1103-0] [Citation(s) in RCA: 678] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
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Affiliation(s)
- Miten Jain
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Hugh E Olsen
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.
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Matthews H, Hanison J, Nirmalan N. "Omics"-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives. Proteomes 2016; 4:E28. [PMID: 28248238 PMCID: PMC5217350 DOI: 10.3390/proteomes4030028] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/01/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022] Open
Abstract
The pharmaceutical industry faces unsustainable program failure despite significant increases in investment. Dwindling discovery pipelines, rapidly expanding R&D budgets and increasing regulatory control, predict significant gaps in the future drug markets. The cumulative duration of discovery from concept to commercialisation is unacceptably lengthy, and adds to the deepening crisis. Existing animal models predicting clinical translations are simplistic, highly reductionist and, therefore, not fit for purpose. The catastrophic consequences of ever-increasing attrition rates are most likely to be felt in the developing world, where resistance acquisition by killer diseases like malaria, tuberculosis and HIV have paced far ahead of new drug discovery. The coming of age of Omics-based applications makes available a formidable technological resource to further expand our knowledge of the complexities of human disease. The standardisation, analysis and comprehensive collation of the "data-heavy" outputs of these sciences are indeed challenging. A renewed focus on increasing reproducibility by understanding inherent biological, methodological, technical and analytical variables is crucial if reliable and useful inferences with potential for translation are to be achieved. The individual Omics sciences-genomics, transcriptomics, proteomics and metabolomics-have the singular advantage of being complimentary for cross validation, and together could potentially enable a much-needed systems biology perspective of the perturbations underlying disease processes. If current adverse trends are to be reversed, it is imperative that a shift in the R&D focus from speed to quality is achieved. In this review, we discuss the potential implications of recent Omics-based advances for the drug development process.
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Affiliation(s)
- Holly Matthews
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College, London SW7 2AZ, UK.
| | - James Hanison
- Manchester Royal Infirmary, Oxford Road, Greater Manchester M13 9WL, UK.
| | - Niroshini Nirmalan
- Environment and Life Sciences, University of Salford, Greater Manchester M5 4WT, UK.
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Vrana M, Goodling A, Afkarian M, Prasad B. An Optimized Method for Protein Extraction from OCT-Embedded Human Kidney Tissue for Protein Quantification by LC-MS/MS Proteomics. ACTA ACUST UNITED AC 2016; 44:1692-6. [PMID: 27481856 DOI: 10.1124/dmd.116.071522] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/29/2016] [Indexed: 01/04/2023]
Abstract
The existing biobanks of remnant tissue from clinically indicated kidney biopsies are attractive potential reservoirs for quantification of clinically relevant human tissue proteins by quantitative proteomics. However, a significant caveat of this strategy is that the tissues are often preserved in optimal cutting temperature (OCT) medium. Although OCT is an effective method of preserving the morphologic and immunohistological characteristics of tissues for later study, it significantly impacts efforts to quantify protein expression by liquid chromatography-tandem mass spectrometry methods. We report here a simple, reproducible, and cost-effective procedure to extract proteins from OCT-embedded tissue samples. Briefly, the excess frozen OCT medium was scraped before thawing from the tissue specimens stored at -80°C for ∼3 months. The tissue samples were homogenized and diethyl ether/methanol extraction was performed to remove the remaining OCT medium. The recovered protein was denatured, reduced, and alkylated. The second step of protein extraction and desalting was performed by chloroform/methanol/water extraction of denatured proteins. The resultant protein pellet was trypsin-digested and the marker proteins of various kidney cellular compartments were quantified by targeted selective reaction monitoring proteomics. Upon comparison of peptide signals from OCT-embedded tissue and flash-frozen tissue from the same donors, both individual protein quantities, and their interindividual variabilities, were similar. Therefore, the approach reported here can be applied to clinical reservoirs of OCT-preserved kidney tissue to be used for quantitative proteomics studies of clinically relevant proteins expressed in different parts of the kidney (including drug transporters and metabolizing enzymes).
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Affiliation(s)
- Marc Vrana
- Department of Pharmaceutics (M.V., B.P.) and Kidney Research Institute and Division of Nephrology, Department of Medicine (A.G., M.A.), University of Washington, Seattle, Washington
| | - Anne Goodling
- Department of Pharmaceutics (M.V., B.P.) and Kidney Research Institute and Division of Nephrology, Department of Medicine (A.G., M.A.), University of Washington, Seattle, Washington
| | - Maryam Afkarian
- Department of Pharmaceutics (M.V., B.P.) and Kidney Research Institute and Division of Nephrology, Department of Medicine (A.G., M.A.), University of Washington, Seattle, Washington
| | - Bhagwat Prasad
- Department of Pharmaceutics (M.V., B.P.) and Kidney Research Institute and Division of Nephrology, Department of Medicine (A.G., M.A.), University of Washington, Seattle, Washington
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The omic approach to parasitic trematode research—a review of techniques and developments within the past 5 years. Parasitol Res 2016; 115:2523-43. [DOI: 10.1007/s00436-016-5079-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/26/2022]
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20
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Josić D, Andjelković U. The Role of Proteomics in Personalized Medicine. Per Med 2016. [DOI: 10.1007/978-3-319-39349-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kwasnik A, Tonry C, Ardle AM, Butt AQ, Inzitari R, Pennington SR. Proteomes, Their Compositions and Their Sources. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:3-21. [DOI: 10.1007/978-3-319-41448-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Ma H, Liu J, Ali MM, Mahmood MAI, Labanieh L, Lu M, Iqbal SM, Zhang Q, Zhao W, Wan Y. Nucleic acid aptamers in cancer research, diagnosis and therapy. Chem Soc Rev 2015; 44:1240-56. [PMID: 25561050 DOI: 10.1039/c4cs00357h] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligomers, identified from a random sequence pool, with the ability to form unique and versatile tertiary structures that bind to cognate molecules with superior specificity. Their small size, excellent chemical stability and low immunogenicity enable them to rival antibodies in cancer imaging and therapy applications. Their facile chemical synthesis, versatility in structural design and engineering, and the ability for site-specific modifications with functional moieties make aptamers excellent recognition motifs for cancer biomarker discovery and detection. Moreover, aptamers can be selected or engineered to regulate cancer protein functions, as well as to guide anti-cancer drug design or screening. This review summarizes their applications in cancer, including cancer biomarker discovery and detection, cancer imaging, cancer therapy, and anti-cancer drug discovery. Although relevant applications are relatively new, the significant progress achieved has demonstrated that aptamers can be promising players in cancer research.
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Affiliation(s)
- Haitao Ma
- The Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215006, China
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Perkins JR, Barrionuevo E, Ranea JA, Blanca M, Cornejo-Garcia JA. Systems biology approaches to enhance our understanding of drug hypersensitivity reactions. Clin Exp Allergy 2015; 44:1461-72. [PMID: 25040150 DOI: 10.1111/cea.12371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hypersensitivity drug reactions (HDRs) encompass a wide spectrum of unpredictable clinical entities. They represent an important health problem, affecting people of all ages, and lead to a large strain on the public health system. Here, we summarize experiments that use high-throughput genomics technologies to investigate HDRs. We also introduce the field of systems biology as a relatively recent discipline concerned with the integration and analysis of high-throughput data sets such as DNA microarrays and next-generation sequencing data. We describe previous studies that have applied systems biology techniques to related fields such as allergy and asthma. Finally, we present a number of potential applications of systems biology to the study of HDRs, in order to make the reader aware of the types of analyses that can be performed and the insights that can be gained through their application.
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Affiliation(s)
- J R Perkins
- Research Laboratory, IBIMA-Regional University Hospital of Malaga-UMA, Spain
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Tonry CL, Doherty D, O’Shea C, Morrissey B, Staunton L, Flatley B, Shannon A, Armstrong J, Pennington SR. Discovery and Longitudinal Evaluation of Candidate Protein Biomarkers for Disease Recurrence in Prostate Cancer. J Proteome Res 2015; 14:2769-83. [DOI: 10.1021/acs.jproteome.5b00041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Claire L. Tonry
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
| | - Darren Doherty
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
| | - Carmel O’Shea
- St. Luke’s Hospital, Rathgar, Dublin 6, Dublin, Ireland
| | - Brian Morrissey
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
| | - Lisa Staunton
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
| | - Brian Flatley
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
| | - Aoife Shannon
- St. Luke’s Hospital, Rathgar, Dublin 6, Dublin, Ireland
| | | | - Stephen R. Pennington
- Conway
Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
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Cantor DI, Nice EC, Baker MS. Recent findings from the human proteome project: opening the mass spectrometry toolbox to advance cancer diagnosis, surveillance and treatment. Expert Rev Proteomics 2015; 12:279-93. [DOI: 10.1586/14789450.2015.1040770] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Vachani A, Pass HI, Rom WN, Midthun DE, Edell ES, Laviolette M, Li XJ, Fong PY, Hunsucker SW, Hayward C, Mazzone PJ, Madtes DK, Miller YE, Walker MG, Shi J, Kearney P, Fang KC, Massion PP. Validation of a multiprotein plasma classifier to identify benign lung nodules. J Thorac Oncol 2015; 10:629-37. [PMID: 25590604 PMCID: PMC4382127 DOI: 10.1097/jto.0000000000000447] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Indeterminate pulmonary nodules (IPNs) lack clinical or radiographic features of benign etiologies and often undergo invasive procedures unnecessarily, suggesting potential roles for diagnostic adjuncts using molecular biomarkers. The primary objective was to validate a multivariate classifier that identifies likely benign lung nodules by assaying plasma protein expression levels, yielding a range of probability estimates based on high negative predictive values (NPVs) for patients with 8 to 30 mm IPNs. METHODS A retrospective, multicenter, case-control study was performed using multiple reaction monitoring mass spectrometry, a classifier comprising five diagnostic and six normalization proteins, and blinded analysis of an independent validation set of plasma samples. RESULTS The classifier achieved validation on 141 lung nodule-associated plasma samples based on predefined statistical goals to optimize sensitivity. Using a population based nonsmall-cell lung cancer prevalence estimate of 23% for 8 to 30 mm IPNs, the classifier identified likely benign lung nodules with 90% negative predictive value and 26% positive predictive value, as shown in our prior work, at 92% sensitivity and 20% specificity, with the lower bound of the classifier's performance at 70% sensitivity and 48% specificity. Classifier scores for the overall cohort were statistically independent of patient age, tobacco use, nodule size, and chronic obstructive pulmonary disease diagnosis. The classifier also demonstrated incremental diagnostic performance in combination with a four-parameter clinical model. CONCLUSIONS This proteomic classifier provides a range of probability estimates for the likelihood of a benign etiology that may serve as a noninvasive, diagnostic adjunct for clinical assessments of patients with IPNs.
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Affiliation(s)
- Anil Vachani
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Harvey I. Pass
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - William N. Rom
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - David E. Midthun
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Eric S. Edell
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Michel Laviolette
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Xiao-Jun Li
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Pui-Yee Fong
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Stephen W. Hunsucker
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Clive Hayward
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Peter J. Mazzone
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - David K. Madtes
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - York E. Miller
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Michael G. Walker
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Jing Shi
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Paul Kearney
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Kenneth C. Fang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
| | - Pierre P. Massion
- Division of Pulmonary, Allergy, and Critical Care Medicine, Penn Lung Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, New York; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine and Department of Environmental Medicine, New York University School of Medicine, New York University Langone Medical Center, New York, New York; Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota; Unité de Recherche en Pneumologie, Centre de Recherche de l’Hôpital Laval, Institut Universitaire de Cardiologie et de Pneumologie de l’Université Laval; Québec, Canada; Integrated Diagnostics, Seattle, Washington; Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Veterans Administration Eastern Colorado Healthcare System, University of Colorado Denver School of Medicine, Denver, Colorado; Statistics Consultant, Carlsbad, California; Thoracic Program, Vanderbilt-Ingram Comprehensive Cancer Center, Nashville, Tennessee; Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee
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Wang K, Huang C, Nice E. Recent advances in proteomics: towards the human proteome. Biomed Chromatogr 2015; 28:848-57. [PMID: 24861753 DOI: 10.1002/bmc.3157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
After the successful completion of the Human Genome project in 2003, the next major challenge was to understand when and where the encoded proteins were expressed, and to generate a map of the complex, interconnected pathways, networks and molecular systems (the human proteome) that, taken together, control the workings of all cells, tissues, organs and organisms. Proteomics will be fundamental for such studies. This review summarizes the key discoveries that laid down the foundations for proteomics as we now know it, and describes key recent technological advances that will undoubtedly contribute to achieving the initial goal of the Human Proteome Organization of identifying and characterizing at least one protein product and representative post-translational modifications, single amino acid polymorphisms and splice variant isoforms from the 20,300 human protein-coding genes within the next 10 years. Successful unraveling of the human proteome will undoubtedly improve our understanding of human biology at the cellular level and lay the foundations for improved diagnostic, prognostic, therapeutic and preventive medical outcomes as we enter the era of personalized medicine.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
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Boja ES, Kinsinger CR, Rodriguez H, Srinivas P. Integration of omics sciences to advance biology and medicine. Clin Proteomics 2014. [PMCID: PMC4274684 DOI: 10.1186/1559-0275-11-45] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In the past two decades, our ability to study cellular and molecular systems has been transformed through the development of omics sciences. While unlimited potential lies within massive omics datasets, the success of omics sciences to further our understanding of human disease and/or translating these findings to clinical utility remains elusive due to a number of factors. A significant limiting factor is the integration of different omics datasets (i.e., integromics) for extraction of biological and clinical insights. To this end, the National Cancer Institute (NCI) and the National Heart, Lung and Blood Institute (NHLBI) organized a joint workshop in June 2012 with the focus on integration issues related to multi-omics technologies that needed to be resolved in order to realize the full utility of integrating omics datasets by providing a glimpse into the disease as an integrated “system”. The overarching goals were to (1) identify challenges and roadblocks in omics integration, and (2) facilitate the full maturation of ‘integromics’ in biology and medicine. Participants reached a consensus on the most significant barriers for integrating omics sciences and provided recommendations on viable approaches to overcome each of these barriers within the areas of technology, bioinformatics and clinical medicine.
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Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS. Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan. Proteomics 2014; 14:975-88. [PMID: 24596128 DOI: 10.1002/pmic.201400041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/20/2014] [Indexed: 12/24/2022]
Abstract
At the 12th Annual HUPO World Congress of Proteomics in Japan, the Human Proteome Project (HPP) presented 16 scientific workshop sessions. Here we summarize highlights of ten workshops from the Biology and Disease-driven HPP (B/D-HPP) teams and three from the HPP Resource Pillars. Highlights of the three Chromosome-centric HPP sessions appeared in the many articles of the 2014 C-HPP special issue of the Journal of Proteome Research .
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Titz B, Elamin A, Martin F, Schneider T, Dijon S, Ivanov NV, Hoeng J, Peitsch MC. Proteomics for systems toxicology. Comput Struct Biotechnol J 2014; 11:73-90. [PMID: 25379146 PMCID: PMC4212285 DOI: 10.1016/j.csbj.2014.08.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology. Proteomic measurements are an integral component of this integrative strategy because protein alterations closely mirror biological effects, such as biological stress responses or global tissue alterations. Here, we provide an overview of the technical foundations and highlight select applications of proteomics for systems toxicology studies. With a focus on mass spectrometry-based proteomics, we summarize the experimental methods for quantitative proteomics and describe the computational approaches used to derive biological/mechanistic insights from these datasets. To illustrate how proteomics has been successfully employed to address mechanistic questions in toxicology, we summarized several case studies. Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework. We conclude that, owing to the critical importance of protein-level measurements and recent technological advances, proteomics will be an integral part of integrative systems toxicology approaches in the future.
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Li XJ, Hayward C, Fong PY, Dominguez M, Hunsucker SW, Lee LW, McLean M, Law S, Butler H, Schirm M, Gingras O, Lamontagne J, Allard R, Chelsky D, Price ND, Lam S, Massion PP, Pass H, Rom WN, Vachani A, Fang KC, Hood L, Kearney P. A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med 2014; 5:207ra142. [PMID: 24132637 DOI: 10.1126/scitranslmed.3007013] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Each year, millions of pulmonary nodules are discovered by computed tomography and subsequently biopsied. Because most of these nodules are benign, many patients undergo unnecessary and costly invasive procedures. We present a 13-protein blood-based classifier that differentiates malignant and benign nodules with high confidence, thereby providing a diagnostic tool to avoid invasive biopsy on benign nodules. Using a systems biology strategy, we identified 371 protein candidates and developed a multiple reaction monitoring (MRM) assay for each. The MRM assays were applied in a three-site discovery study (n = 143) on plasma samples from patients with benign and stage IA lung cancer matched for nodule size, age, gender, and clinical site, producing a 13-protein classifier. The classifier was validated on an independent set of plasma samples (n = 104), exhibiting a negative predictive value (NPV) of 90%. Validation performance on samples from a nondiscovery clinical site showed an NPV of 94%, indicating the general effectiveness of the classifier. A pathway analysis demonstrated that the classifier proteins are likely modulated by a few transcription regulators (NF2L2, AHR, MYC, and FOS) that are associated with lung cancer, lung inflammation, and oxidative stress networks. The classifier score was independent of patient nodule size, smoking history, and age, which are risk factors used for clinical management of pulmonary nodules. Thus, this molecular test provides a potential complementary tool to help physicians in lung cancer diagnosis.
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Affiliation(s)
- Xiao-jun Li
- Integrated Diagnostics, Seattle, WA 98109, USA
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Larina IM, Ivanisenko VA, Nikolaev EN, Grigorev AI. The Proteome of a Healthy Human during Physical Activity under Extreme Conditions. Acta Naturae 2014; 6:66-75. [PMID: 25349715 PMCID: PMC4207561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The review examines the new approaches in modern systems biology, in terms of their use for a deeper understanding of the physiological adaptation of a healthy human in extreme environments. Human physiology under extreme conditions of life, or environmental physiology, and systems biology are natural partners. The similarities and differences between the object and methods in systems biology, the OMICs (proteomics, transcriptomics, metabolomics) disciplines, and other related sciences have been studied. The latest data on environmental human physiology obtained using systems biology methods are discussed. The independent achievements of systems biology in studying the adaptation of a healthy human to physical activity, including human presence at high altitude, to the effects of hypoxia and oxidative stress have been noted. A reasonable conclusion is drawn that the application of the methods and approaches used in systems biology to study the molecular pattern of the adaptive mechanisms that develop in the human body during space flight can provide valuable fundamental knowledge and fill the picture of human metabolic pathways.
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Affiliation(s)
- I. M. Larina
- SSC RF Institute for Biomedical Problems, Russian Academy of Sciences, Khoroshevskoye shosse, 76a, 123007, Moscow, Russia
| | - V. A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Akad. Lavrentiev Ave., 10, 630090, Novosibirsk, Russia
| | - E. N. Nikolaev
- Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina Str., 4, 119334, Moscow, Russia
| | - A. I. Grigorev
- SSC RF Institute for Biomedical Problems, Russian Academy of Sciences, Khoroshevskoye shosse, 76a, 123007, Moscow, Russia
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Wang K, Huang C, Nice EC. Proteomics, genomics and transcriptomics: their emerging roles in the discovery and validation of colorectal cancer biomarkers. Expert Rev Proteomics 2014; 11:179-205. [PMID: 24611605 DOI: 10.1586/14789450.2014.894466] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Colorectal cancer (CRC) is the second most common cancer in females and the third in males. Since CRC is often diagnosed at an advanced stage when prognosis is poor, identification of biomarkers for early diagnosis is urgently required. Recent advances in proteomics, genomics and transcriptomics have facilitated high-throughput profiling of data generated from CRC-related genes and proteins, providing a window of information for biomarker discovery and validation. However, transfer of candidate biomarkers from bench to bedside remains a dilemma. In this review, we will discuss emerging proteomic technologies and highlight various sample types utilized for proteomics-based identification of CRC biomarkers. Moreover, recent breakthroughs in genomics and transcriptomics for the identification of CRC biomarkers, with particular emphasis on the merits of emerging methylomic and miRNAomic strategies, will be discussed. Integration of proteomics, genomics and transcriptomics will facilitate the discovery and validation of CRC biomarkers leading to the emergence of personalized medicine.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University , Chengdu, 610041 , P.R. China
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Ecological genomics of host behavior manipulation by parasites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:169-90. [PMID: 24277300 DOI: 10.1007/978-94-007-7347-9_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Among the vast array of niche exploitation strategies exhibited by millions of different species on Earth, parasitic lifestyles are characterized by extremely successful evolutionary outcomes. Some parasites even seem to have the ability to 'control' their host's behavior to fulfill their own vital needs. Research efforts in the past decades have focused on surveying the phylogenetic diversity and ecological nature of these host-parasite interactions, and trying to understand their evolutionary significance. However, to understand the proximal and ultimate causes of these behavioral alterations triggered by parasitic infections, the underlying molecular mechanisms governing them must be uncovered. Studies using ecological genomics approaches have identified key candidate molecules involved in host-parasite molecular cross-talk, but also molecules not expected to alter behavior. These studies have shown the importance of following up with functional analyses, using a comparative approach and including a time-series analysis. High-throughput methods surveying different levels of biological information, such as the transcriptome and the epigenome, suggest that specific biologically-relevant processes are affected by infection, that sex-specific effects at the level of behavior are recapitulated at the level of transcription, and that epigenetic control represents a key factor in managing life cycle stages of the parasite through temporal regulation of gene expression. Post-translational processes, such as protein-protein interactions (interactome) and post translational modifications (e.g. protein phosphorylation, phosphorylome), and processes modifying gene expression and translation, such as interactions with microRNAs (microRNAome), are examples of promising avenues to explore to obtain crucial insights into the proximal and ultimate causes of these fascinating and complex inter-specific interactions.
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Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS. Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. J Proteome Res 2013; 13:15-20. [PMID: 24364385 DOI: 10.1021/pr401144x] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One year ago the Human Proteome Project (HPP) leadership designated the baseline metrics for the Human Proteome Project to be based on neXtProt with a total of 13,664 proteins validated at protein evidence level 1 (PE1) by mass spectrometry, antibody-capture, Edman sequencing, or 3D structures. Corresponding chromosome-specific data were provided from PeptideAtlas, GPMdb, and Human Protein Atlas. This year, the neXtProt total is 15,646 and the other resources, which are inputs to neXtProt, have high-quality identifications and additional annotations for 14,012 in PeptideAtlas, 14,869 in GPMdb, and 10,976 in HPA. We propose to remove 638 genes from the denominator that are "uncertain" or "dubious" in Ensembl, UniProt/SwissProt, and neXtProt. That leaves 3844 "missing proteins", currently having no or inadequate documentation, to be found from a new denominator of 19,490 protein-coding genes. We present those tabulations and web links and discuss current strategies to find the missing proteins.
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Affiliation(s)
- Lydie Lane
- SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland
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Omenn GS. Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:866-73. [PMID: 24211518 DOI: 10.1016/j.bbapap.2013.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/17/2013] [Accepted: 10/31/2013] [Indexed: 12/24/2022]
Abstract
This article addresses three inter-related subjects: the development of the Human Plasma Proteome Peptide Atlas, the launch of the Human Proteome Project, and the emergence of alternative splice variant transcripts and proteins as important features of evolution and pathogenesis. The current Plasma Peptide Atlas provides evidence on which peptides have been detected for every protein confidently identified in plasma; there are links to their spectra and their estimated abundance, facilitating the planning of targeted proteomics for biomarker studies. The Human Proteome Project (HPP) combines a chromosome-centric C-HPP with a biology and disease-driven B/D-HPP, upon a foundation of mass spectrometry, antibody, and knowledgebase resource pillars. The HPP aims to identify the approximately 7000 "missing proteins" and to characterize all proteins and their many isoforms. Success will enable the larger research community to utilize newly-available peptides, spectra, informative MS transitions, and databases for targeted analyses of priority proteins for each organ and disease. Among the isoforms of proteins, splice variants have the special feature of greatly enlarging protein diversity without enlarging the genome; evidence is accumulating of striking differential expression of splice variants in cancers. In this era of RNA-sequencing and advanced mass spectrometry, it is no longer sufficient to speak simply of increased or decreased expression of genes or proteins without carefully examining the splice variants in the protein mixture produced from each multi-exon gene. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, MI, USA; Institute for Systems Biology, Seattle, WA, USA
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Omenn GS. The strategy, organization, and progress of the HUPO Human Proteome Project. J Proteomics 2013; 100:3-7. [PMID: 24145142 DOI: 10.1016/j.jprot.2013.10.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 02/04/2023]
Abstract
UNLABELLED The Human Proteome Project is a major, comprehensive initiative of the Human Proteome Organization. This global collaborative effort aims to identify and characterize at least one protein product and many PTM, SAP, and splice variant isoforms from the 20,300 human protein-coding genes. The deliverables are an extensive parts list and an array of technology platforms, reagents, spectral libraries, and linked knowledge bases that advance the field and facilitate the use of proteomics by a much wider community of life scientists. Such enablement will help address the Grand Challenge of using proteomics to bridge major gaps between evidence of genomic variation and diverse phenotypes. BIOLOGICAL SIGNIFICANCE The HUPO Human Proteome Project (HPP) has made an outstanding launch, including a special issue of the Journal of Proteome Research on the Chromosome-centric HPP with a total of 48 articles. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Gilbert S Omenn
- Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.
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Abstract
The Human Genome Project has transformed biology through its integrated big science approach to deciphering a reference human genome sequence along with the complete sequences of key model organisms. The project exemplifies the power, necessity and success of large, integrated, cross-disciplinary efforts - so-called 'big science' - directed towards complex major objectives. In this article, we discuss the ways in which this ambitious endeavor led to the development of novel technologies and analytical tools, and how it brought the expertise of engineers, computer scientists and mathematicians together with biologists. It established an open approach to data sharing and open-source software, thereby making the data resulting from the project accessible to all. The genome sequences of microbes, plants and animals have revolutionized many fields of science, including microbiology, virology, infectious disease and plant biology. Moreover, deeper knowledge of human sequence variation has begun to alter the practice of medicine. The Human Genome Project has inspired subsequent large-scale data acquisition initiatives such as the International HapMap Project, 1000 Genomes, and The Cancer Genome Atlas, as well as the recently announced Human Brain Project and the emerging Human Proteome Project.
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Affiliation(s)
- Leroy Hood
- Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA
| | - Lee Rowen
- Institute for Systems Biology, 401 Terry Ave N., Seattle, WA 98109, USA
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41
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Abstract
Perhaps paradoxically, we argue that the biological sciences are "data-limited". In contrast to the glut of DNA sequencing data available, high-throughput protein analysis is expensive and largely inaccessible. Hence, we posit that access to robust protein-level data is inadequate. Here, we use the framework of the formal engineering design process to both identify and understand the problems facing measurement science in the 21st century. In particular, discussion centers on the notable challenge of realizing protein analyses that are as effective (and transformative) as genomics tools. This Perspective looks through the lens of a case study on protein biomarker validation and verification, to highlight the importance of iterative design in realizing significant advances over currently available measurement capabilities in the candidate or targeted proteomics space. The Perspective follows a podium presentation given by the author at The 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences (μTAS 2012), specifically focusing on novel targeted proteomic measurement tools based in microfluidic design. The role of unmet needs identification, iteration in concept generation and development, and the existing gap in rapid prototyping tools for separations are all discussed.
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Affiliation(s)
- Amy E Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, California, United States.
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Omenn GS, Menon R, Zhang Y. Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. J Proteomics 2013; 90:28-37. [PMID: 23603631 DOI: 10.1016/j.jprot.2013.04.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/05/2013] [Accepted: 04/07/2013] [Indexed: 01/05/2023]
Abstract
Alternative splicing allows a single gene to generate multiple RNA transcripts which can be translated into functionally diverse protein isoforms. Current knowledge of splicing is derived mainly from RNA transcripts, with very little known about the expression level, 3D structures, and functional differences of the proteins. Splicing is a remarkable phenomenon of molecular and biological evolution. Studies which simply report up-regulation or down-regulation of protein or mRNA expression are confounded by the effects of mixtures of these isoforms. Besides understanding the net biological effects of the mixtures, we may be able to develop biomarker tests based on the observable differential expression of particular splice variants or combinations of splice variants in specific disease states. Here we review our work on differential expression of splice variant proteins in cancers and the feasibility of integrating proteomic analysis with structure-based conformational predictions of the differences between such isoforms.
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Affiliation(s)
- Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.
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Abstract
Studying complex biological systems in a holistic rather than a "one gene or one protein" at a time approach requires the concerted effort of scientists from a wide variety of disciplines. The Institute for Systems Biology (ISB) has seamlessly integrated these disparate fields to create a cross-disciplinary platform and culture in which "biology drives technology drives computation." To achieve this platform/culture, it has been necessary for cross-disciplinary ISB scientists to learn one another's languages and work together effectively in teams. The focus of this "systems" approach on disease has led to a discipline denoted systems medicine. The advent of technological breakthroughs in the fields of genomics, proteomics, and, indeed, the other "omics" is catalyzing striking advances in systems medicine that have and are transforming diagnostic and therapeutic strategies. Systems medicine has united genomics and genetics through family genomics to more readily identify disease genes. It has made blood a window into health and disease. It is leading to the stratification of diseases (division into discrete subtypes) for proper impedance match against drugs and the stratification of patients into subgroups that respond to environmental challenges in a similar manner (e.g. response to drugs, response to toxins, etc.). The convergence of patient-activated social networks, big data and their analytics, and systems medicine has led to a P4 medicine that is predictive, preventive, personalized, and participatory. Medicine will focus on each individual. It will become proactive in nature. It will increasingly focus on wellness rather than disease. For example, in 10 years each patient will be surrounded by a virtual cloud of billions of data points, and we will have the tools to reduce this enormous data dimensionality into simple hypotheses about how to optimize wellness and avoid disease for each individual. P4 medicine will be able to detect and treat perturbations in healthy individuals long before disease symptoms appear, thus optimizing the wellness of individuals and avoiding disease. P4 medicine will 1) improve health care, 2) reduce the cost of health care, and 3) stimulate innovation and new company creation. Health care is not the only subject that can benefit from such integrative, cross-disciplinary, and systems-driven platforms and cultures. Many other challenges plaguing our planet, such as energy, environment, nutrition, and agriculture can be transformed by using such an integrated and systems-driven approach.
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Affiliation(s)
- Leroy Hood
- To whom correspondence should be addressed. E-mail:
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Ivanov AR, Colangelo CM, Dufresne CP, Friedman DB, Lilley KS, Mechtler K, Phinney BS, Rose KL, Rudnick PA, Searle BC, Shaffer SA, Weintraub ST. Interlaboratory studies and initiatives developing standards for proteomics. Proteomics 2013; 13:904-9. [PMID: 23319436 DOI: 10.1002/pmic.201200532] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/18/2012] [Accepted: 12/19/2012] [Indexed: 01/02/2023]
Abstract
Proteomics is a rapidly transforming interdisciplinary field of research that embraces a diverse set of analytical approaches to tackle problems in fundamental and applied biology. This viewpoint article highlights the benefits of interlaboratory studies and standardization initiatives to enable investigators to address many of the challenges found in proteomics research. Among these initiatives, we discuss our efforts on a comprehensive performance standard for characterizing PTMs by MS that was recently developed by the Association of Biomolecular Resource Facilities (ABRF) Proteomics Standards Research Group (sPRG).
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Affiliation(s)
- Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS. The biology/disease-driven human proteome project (B/D-HPP): enabling protein research for the life sciences community. J Proteome Res 2012; 12:23-7. [PMID: 23259511 DOI: 10.1021/pr301151m] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The biology and disease oriented branch of the Human Proteome Project (B/D-HPP) was established by the Human Proteome Organization (HUPO) with the main goal of supporting the broad application of state-of the-art measurements of proteins and proteomes by life scientists studying the molecular mechanisms of biological processes and human disease. This will be accomplished through the generation of research and informational resources that will support the routine and definitive measurement of the process or disease relevant proteins. The B/D-HPP is highly complementary to the C-HPP and will provide datasets and biological characterization useful to the C-HPP teams. In this manuscript we describe the goals, the plans, and the current status of the of the B/D-HPP.
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Affiliation(s)
- Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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Hühmer AFR, Paulus A, Martin LB, Millis K, Agreste T, Saba J, Lill JR, Fischer SM, Dracup W, Lavery P. The Chromosome-Centric Human Proteome Project: A Call to Action. J Proteome Res 2012; 12:28-32. [DOI: 10.1021/pr300933p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Andreas F. R. Hühmer
- Thermo Fisher Scientific, Life Science
Mass Spectrometry, San Jose, California 95134, United States
| | - Aran Paulus
- Bio-Rad Laboratories, Life Science Group, San Jose, California 95126-2423, United States
| | - LeRoy B. Martin
- Waters Corporation, Beverly, Massachusetts 01915, United States
| | - Kevin Millis
- Cambridge Isotope Laboratories, Andover, Massachusetts 01810, United States
| | - Tasha Agreste
- Cambridge Isotope Laboratories, Andover, Massachusetts 01810, United States
| | - Julian Saba
- Thermo Fisher Scientific, Life Science
Mass Spectrometry, San Jose, California 95134, United States
| | - Jennie R. Lill
- Genentech Inc.,
1 DNA Way, South San Francisco, California 94080, United States
| | | | - William Dracup
- William Dracup, Nonlinear Dynamics Ltd., Keel House, Newcastle-upon-Tyne, NE1 2JE, England,
United Kingdom
| | - Paddy Lavery
- William Dracup, Nonlinear Dynamics Ltd., Keel House, Newcastle-upon-Tyne, NE1 2JE, England,
United Kingdom
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