1
|
Zhou Z, Zhang R, Zhou A, Lv J, Chen S, Zou H, Zhang G, Lin T, Wang Z, Zhang Y, Weng S, Han X, Liu Z. Proteomics appending a complementary dimension to precision oncotherapy. Comput Struct Biotechnol J 2024; 23:1725-1739. [PMID: 38689716 PMCID: PMC11058087 DOI: 10.1016/j.csbj.2024.04.044] [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: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Recent advances in high-throughput proteomic profiling technologies have facilitated the precise quantification of numerous proteins across multiple specimens concurrently. Researchers have the opportunity to comprehensively analyze the molecular signatures in plentiful medical specimens or disease pattern cell lines. Along with advances in data analysis and integration, proteomics data could be efficiently consolidated and employed to recognize precise elementary molecular mechanisms and decode individual biomarkers, guiding the precision treatment of tumors. Herein, we review a broad array of proteomics technologies and the progress and methods for the integration of proteomics data and further discuss how to better merge proteomics in precision medicine and clinical settings.
Collapse
Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Ruiqi Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
2
|
McCabe MC, Gejji V, Barnebey A, Siuzdak G, Hoang LT, Pham T, Larson KY, Saviola AJ, Yannone SM, Hansen KC. From volcanoes to the bench: Advantages of novel hyperthermoacidic archaeal proteases for proteomics workflows. J Proteomics 2023; 289:104992. [PMID: 37634627 DOI: 10.1016/j.jprot.2023.104992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023]
Abstract
Here we introduce hyperthermoacidic archaeal proteases (HTA-Proteases©) isolated from organisms that thrive in nearly boiling acidic volcanic springs and investigate their use for bottom-up proteomic experiments. We find that HTA-Proteases have novel cleavage specificities, show no autolysis, function in dilute formic acid, and store at ambient temperature for years. HTA-Proteases function optimally at 70-90 °C and pH of 2-4 with rapid digestion kinetics. The extreme HTA-Protease reaction conditions actively denature sample proteins, obviate the use of chaotropes, are largely independent of reduction and alkylation, and allow for a one-step/five-minute sample preparation protocol without sample manipulation, dilution, or additional cleanup. We find that brief one-step HTA-Protease protocols significantly increase proteome and protein sequence coverage with datasets orthogonal to trypsin. Importantly, HTA-Protease digests markedly increase coverage and identifications for ribonucleoproteins, histones, and mitochondrial membrane proteins as compared to tryptic digests alone. In addition to increased coverage in these classes, HTA-Proteases and simplified one-step protocols are expected to reduce technical variability and advance the fields of clinical and high-throughput proteomics. This work reveals significant utility of heretofore unavailable HTA-Proteases for proteomic workflows. We discuss some of the potential for these remarkable enzymes to empower new proteomics methods, approaches, and biological insights. SIGNIFICANCE: Here we introduce new capabilities for bottom-up proteomics applications with hyperthermoacidic archaeal proteases (HTA-Proteases©). HTA-Proteases have novel cleavage specificity, require no chaotropes, and allow simple one-step/five-minute sample preparations that promise to reduce variability between samples and laboratories. HTA-Proteases generate unique sets of observable peptides that are non-overlapping with tryptic peptides and significantly increase sequence coverage and available peptide targets relative to trypsin alone. HTA-Proteases show some bias for the detection and coverage of nucleic acid-binding proteins and membrane proteins relative to trypsin. These new ultra-stable enzymes function optimally in nearly boiling acidic conditions, show no autolysis, and do not require aliquoting as they are stable for years at ambient temperatures. Used independently or in conjunction with tryptic digests, HTA-Proteases offer increased proteome coverage, unique peptide targets, and brief one-step protocols amenable to automation, rapid turnaround, and high-throughput approaches.
Collapse
Affiliation(s)
- Maxwell C McCabe
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Varun Gejji
- Cinder Biological, Inc., 1933 Davis Street, STE 208, San Leandro, CA 94577, USA
| | - Adam Barnebey
- Cinder Biological, Inc., 1933 Davis Street, STE 208, San Leandro, CA 94577, USA
| | - Gary Siuzdak
- Departments of Chemistry, Molecular, and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Linh Truc Hoang
- Departments of Chemistry, Molecular, and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Truc Pham
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Keira Y Larson
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Steven M Yannone
- Cinder Biological, Inc., 1933 Davis Street, STE 208, San Leandro, CA 94577, USA.
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA.
| |
Collapse
|
3
|
Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
|
4
|
Walls D, Cooney G, Loughran ST. A Synopsis of Proteins and Their Purification. Methods Mol Biol 2023; 2699:1-14. [PMID: 37646990 DOI: 10.1007/978-1-0716-3362-5_1] [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] [Indexed: 09/01/2023]
Abstract
The goal of protein purification is to separate a specific protein from all other biomolecules. Classical chromatographic procedures have been designed to exploit particular distinguishing features of individual target proteins, such as size, shape, physicochemical properties, and binding affinity. Advances in molecular biology and bioinformatics have positively contributed at every level to the challenge of purifying individual proteins and more recently have led to the development of high-throughput proteomic platforms. In this chapter, a synopsis of advancements in the field of protein chromatography is presented, with reference to the principal tools and resources that are available to assist with protein purification strategies.
Collapse
Affiliation(s)
- Dermot Walls
- School of Biotechnology , Dublin City University, Dublin, Ireland
| | - Gary Cooney
- School of Biotechnology , Dublin City University, Dublin, Ireland
| | - Sinéad T Loughran
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Ireland.
| |
Collapse
|
5
|
Cui M, Cheng C, Zhang L. High-throughput proteomics: a methodological mini-review. J Transl Med 2022; 102:1170-1181. [PMID: 36775443 PMCID: PMC9362039 DOI: 10.1038/s41374-022-00830-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 11/15/2022] Open
Abstract
Proteomics plays a vital role in biomedical research in the post-genomic era. With the technological revolution and emerging computational and statistic models, proteomic methodology has evolved rapidly in the past decade and shed light on solving complicated biomedical problems. Here, we summarize scientific research and clinical practice of existing and emerging high-throughput proteomics approaches, including mass spectrometry, protein pathway array, next-generation tissue microarrays, single-cell proteomics, single-molecule proteomics, Luminex, Simoa and Olink Proteomics. We also discuss important computational methods and statistical algorithms that can maximize the mining of proteomic data with clinical and/or other 'omics data. Various principles and precautions are provided for better utilization of these tools. In summary, the advances in high-throughput proteomics will not only help better understand the molecular mechanisms of pathogenesis, but also to identify the signature signaling networks of specific diseases. Thus, modern proteomics have a range of potential applications in basic research, prognostic oncology, precision medicine, and drug discovery.
Collapse
Affiliation(s)
- Miao Cui
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Mount Sinai West, New York, NY, USA
| | - Chao Cheng
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Lanjing Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA. .,Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA. .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA. .,Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA.
| |
Collapse
|
6
|
Proteomics and Schizophrenia: The Evolution of a Great Partnership. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1400:129-138. [DOI: 10.1007/978-3-030-97182-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
7
|
Antunes ASLM, de Almeida V, Crunfli F, Carregari VC, Martins-de-Souza D. Proteomics for Target Identification in Psychiatric and Neurodegenerative Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1286:251-264. [PMID: 33725358 DOI: 10.1007/978-3-030-55035-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Psychiatric and neurodegenerative disorders such as schizophrenia (SCZ), Parkinson's disease (PD), and Alzheimer's disease (AD) continue to grow around the world with a high impact on health, social, and economic outcomes for the patient and society. Despite efforts, the etiology and pathophysiology of these disorders remain unclear. Omics technologies have contributed to the understanding of the molecular mechanisms that underlie these complex disorders and have suggested novel potential targets for treatment and diagnostics. Here, we have highlighted the unique and common pathways shared between SCZ, PD, and AD and highlight the main proteomic findings over the last 5 years using in vitro models, postmortem brain samples, and cerebrospinal fluid (CSF) or blood of patients. These studies have identified possible therapeutic targets and disease biomarkers. Further studies including target validation, the use of large sample sizes, and the integration of omics findings with bioinformatics tools are required to provide a better comprehension of pharmacological targets.
Collapse
Affiliation(s)
- André S L M Antunes
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
| | - Valéria de Almeida
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Fernanda Crunfli
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Victor C Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria, Conselho Nacional de Desenvolvimento Científico e Tecnológico, São Paulo, Brazil
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Parkes GM, Niranjan M. Uncovering extensive post-translation regulation during human cell cycle progression by integrative multi-'omics analysis. BMC Bioinformatics 2019; 20:536. [PMID: 31664894 PMCID: PMC6820968 DOI: 10.1186/s12859-019-3150-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/04/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Analysis of high-throughput multi-'omics interactions across the hierarchy of expression has wide interest in making inferences with regard to biological function and biomarker discovery. Expression levels across different scales are determined by robust synthesis, regulation and degradation processes, and hence transcript (mRNA) measurements made by microarray/RNA-Seq only show modest correlation with corresponding protein levels. RESULTS In this work we are interested in quantitative modelling of correlation across such gene products. Building on recent work, we develop computational models spanning transcript, translation and protein levels at different stages of the H. sapiens cell cycle. We enhance this analysis by incorporating 25+ sequence-derived features which are likely determinants of cellular protein concentration and quantitatively select for relevant features, producing a vast dataset with thousands of genes. We reveal insights into the complex interplay between expression levels across time, using machine learning methods to highlight outliers with respect to such models as proteins associated with post-translationally regulated modes of action. CONCLUSIONS We uncover quantitative separation between modified and degraded proteins that have roles in cell cycle regulation, chromatin remodelling and protein catabolism according to Gene Ontology; and highlight the opportunities for providing biological insights in future model systems.
Collapse
Affiliation(s)
- Gregory M Parkes
- University of Southampton, University Road, Southampton, SO17 1BJ, UK.
| | - Mahesan Niranjan
- University of Southampton, University Road, Southampton, SO17 1BJ, UK
| |
Collapse
|
10
|
Panner Selvam MK, Agarwal A. Sperm and Seminal Plasma Proteomics: Molecular Changes Associated with Varicocele-Mediated Male Infertility. World J Mens Health 2019; 38:472-483. [PMID: 31385477 PMCID: PMC7502311 DOI: 10.5534/wjmh.190018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/03/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Male infertility is a rising problem and the etiology at the molecular level is unclear. Use of omics has provided an insight into the underlying cellular changes in the spermatozoa of infertile men. Proteomics is one the promising omics techniques for biomarker screening that can provide complete information on molecular processes associated with male infertility. Varicocele is a pressing issue in the field of male infertility and the search for an appropriate diagnostic and therapeutic biomarker is still ongoing. In this review, we discuss the reports on proteomic profiles of sperm and seminal plasma in male infertility and provide an in-depth insight into varicocele studies associated with male infertility.
Collapse
Affiliation(s)
| | - Ashok Agarwal
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA.
| |
Collapse
|
11
|
Proteomic Investigations of Autism Spectrum Disorder: Past Findings, Current Challenges, and Future Prospects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:235-252. [DOI: 10.1007/978-3-030-05542-4_12] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
12
|
Personalised Medicine: The Odyssey from Hope to Practice. J Pers Med 2018; 8:jpm8040031. [PMID: 30248964 PMCID: PMC6313378 DOI: 10.3390/jpm8040031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 01/08/2023] Open
Abstract
In this endeavour, inspired by the Odyssey, we aim to embark with the reader on a journey on a ship from Troy to Ithaca, coursing through the history of the momentous events and achievements that paved the way for personalised medicine. We will set sail amidst important genetic discoveries, beginning with the discovery of the first human genome, and voyage through the projects that contributed to the progress of pharmacogenomic studies. Concurrently, we will propose methods to overcome the obstacles that are slowing the potential full implementation of accumulated knowledge into everyday practice. This journey aims to reflect on the frontiers of current genetic knowledge and the practical use of this knowledge in preventive, diagnostic and pharmacogenomic approaches to directly impact the socio-economic aspects of public health.
Collapse
|
13
|
Cho Y, Ross RS. A mini review: Proteomics approaches to understand disused vs. exercised human skeletal muscle. Physiol Genomics 2018; 50:746-757. [PMID: 29958080 DOI: 10.1152/physiolgenomics.00043.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Immobilization, bed rest, or denervation leads to muscle disuse and subsequent skeletal muscle atrophy. Muscle atrophy can also occur as a component of various chronic diseases such as cancer, AIDS, sepsis, diabetes, and chronic heart failure or as a direct result of genetic muscle disorders. In addition to this atrophic loss of muscle mass, metabolic deregulation of muscle also occurs. In contrast, physical exercise plays a beneficial role in counteracting disuse-induced atrophy by increasing muscle mass and strength. Along with this, exercise can also reduce mitochondrial dysfunction and metabolic deregulation. Still, while exercise causes valuable metabolic and functional adaptations in skeletal muscle, the mechanisms and effectors that lead to these changes such as increased mitochondria content or enhanced protein synthesis are not fully understood. Therefore, mechanistic insights may ultimately provide novel ways to treat disuse induced atrophy and metabolic deregulation. Mass spectrometry (MS)-based proteomics offers enormous promise for investigating the molecular mechanisms underlying disuse and exercise-induced changes in skeletal muscle. This review will focus on initial findings uncovered by using proteomics approaches with human skeletal muscle specimens and discuss their potential for the future study.
Collapse
Affiliation(s)
- Yoshitake Cho
- Division of Cardiology, Department of Medicine, University of California San Diego , La Jolla, California
| | - Robert S Ross
- Division of Cardiology, Department of Medicine, University of California San Diego , La Jolla, California.,Cardiology Section, Department of Medicine, Veterans Administration Healthcare , San Diego, California
| |
Collapse
|
14
|
Zhang C, Ding W, Liu Y, Hu Z, Zhu D, Wang X, Yu L, Wang L, Shen H, Zhang W, Ren C, Li K, Weng D, Deng W, Ma D, Wang H. Proteomics-based identification of VDAC1 as a tumor promoter in cervical carcinoma. Oncotarget 2018; 7:52317-52328. [PMID: 27419626 PMCID: PMC5239554 DOI: 10.18632/oncotarget.10562] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 06/12/2016] [Indexed: 02/05/2023] Open
Abstract
We used oxidative isotope-coded affinity tags (OxICAT) to investigate the global redox status of proteins in human papillomavirus (HPV)-related cervical cancer cells, in order to identify a potential target for gene therapy. Voltage-dependent anion channel 1 (VDAC1) was found to be highly oxidized in HPV-positive cervical cancer cells. VDAC1 expression correlated significantly with the invasion of cervical cancer, the grade of cervical intraepithelial neoplasia (CIN) and the expression of HPV16 E7 in CIN. Knockdown of VDAC1 in cell lines increased the rate of apoptosis, while overexpression of the VDAC1 (respectively) partly reversed the effect. Thus, VDAC1 may promote the malignant progression of HPV-related disease, and treatments designed to suppress VDAC1 could prevent the progression of HPV-induced cervical disease.
Collapse
Affiliation(s)
- Changlin Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.,Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, Guangdong 510060, China
| | - Wencheng Ding
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yuan Liu
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan 610041, China
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Da Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Xiaoli Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Lan Yu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Liming Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hui Shen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Weican Zhang
- Department of Obstetrics and Gynecology, Hebei Medical University, Shijiazhuang, Hebei 050017, China
| | - Ci Ren
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Kezhen Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Danhui Weng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Wuguo Deng
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, Guangdong 510060, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Hui Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| |
Collapse
|
15
|
Update on the proteomics of male infertility: A systematic review. Arab J Urol 2017; 16:103-112. [PMID: 29713541 PMCID: PMC5922221 DOI: 10.1016/j.aju.2017.11.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 11/17/2017] [Accepted: 11/19/2017] [Indexed: 02/07/2023] Open
Abstract
Objective To assess the role of differentially expressed proteins as a resource for potential biomarker identification of infertility, as male infertility is of rising concern in reproductive medicine and evidence pertaining to its aetiology at a molecular level particularly proteomic as spermatozoa lack transcription and translation. Proteomics is considered as a major field in molecular biology to validate the target proteins in a pathophysiological state. Differential expression analysis of sperm proteins in infertile men and bioinformatics analysis offer information about their involvement in biological pathways. Materials and methods Literature search was performed on PubMed, Medline, and Science Direct databases using the keywords ‘sperm proteomics’ and ‘male infertility’. We also reviewed the relevant cross references of retrieved articles and included them in the review process. Articles written in any language other than English were excluded. Results Of 575 articles identified, preliminary screening for relevant studies eliminated 293 articles. At the next level of selection, from 282 studies only 80 articles related to male infertility condition met the selection criteria and were included in this review. Conclusion In this molecular era, sperm proteomics has created a platform for enhanced understanding of male reproductive physiology as a potential tool for identification of novel protein biomarkers related to sperm function in infertile men. Therefore, it is believed that proteomic biomarkers can overcome the gaps in information from conventional semen analysis that are of limited clinical utility.
Collapse
|
16
|
Szoko N, McShane AJ, Natowicz MR. Proteomic explorations of autism spectrum disorder. Autism Res 2017; 10:1460-1469. [DOI: 10.1002/aur.1803] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/30/2017] [Accepted: 04/01/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Nicholas Szoko
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic; Cleveland OH
| | - Adam J. McShane
- Pathology & Laboratory Medicine Institute, Cleveland Clinic; Cleveland OH
| | - Marvin R. Natowicz
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic; Cleveland OH
- Pathology & Laboratory Medicine Institute, Cleveland Clinic; Cleveland OH
- Genomic Medicine, Neurology and Pediatrics Institutes, Cleveland Clinic; Cleveland OH
| |
Collapse
|
17
|
A Synopsis of Proteins and Their Purification. Methods Mol Biol 2016. [PMID: 27730545 DOI: 10.1007/978-1-4939-6412-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The isolation of a given protein, free of all other biomolecules, is the primary objective of any protein purification scheme. Classical chromatographic procedures have been designed to exploit particular distinguishing features of individual target proteins, such as size, physicochemical properties, and binding affinity. Advances in molecular biology and bioinformatics have positively contributed at every level to the challenge of purifying individual proteins and more recently have led to the development of high-throughput proteomic platforms. Here, a synopsis of developments in the field of protein chromatography is given, with reference to the principal tools and resources that are available to assist with protein purification processes.
Collapse
|
18
|
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.
Collapse
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.
| |
Collapse
|
19
|
Dowling P, Moran B, McAuley E, Meleady P, Henry M, Clynes M, McMenamin M, Leonard N, Monks M, Wynne B, Ormond P, Larkin A. Quantitative label-free mass spectrometry analysis of formalin-fixed, paraffin-embedded tissue representing the invasive cutaneous malignant melanoma proteome. Oncol Lett 2016; 12:3296-3304. [PMID: 27899996 PMCID: PMC5103945 DOI: 10.3892/ol.2016.5101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/15/2016] [Indexed: 12/22/2022] Open
Abstract
Understanding the events at a protein level that govern the progression from melanoma in situ to invasive melanoma are important areas of current research to be developed. Recent advances in the analysis of formalin-fixed, paraffin-embedded tissue by proteomics, particularly using the filter-aided sample preparation protocol, has opened up the possibility of studying vast archives of clinical material and associated medical records. In the present study, quantitative protein profiling was performed using tandem mass spectrometry, and the proteome differences between melanoma in situ and invasive melanoma were compared. Biological pathway analyses revealed several signalling pathways differing between melanoma in situ and invasive melanoma, including metabolic pathways and the phosphoinositide 3-kinase-Akt signalling pathway. Selected proteins of interest (14–3-3ε and fatty acid synthase) were subsequently investigated using immunohistochemical analysis of tissue microarrays. Identifying the key proteins that play significant roles in the establishment of a more invasive phenotype in melanoma may ultimately aid diagnosis and treatment decisions.
Collapse
Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Republic of Ireland
| | - Benvon Moran
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Republic of Ireland; Department of Dermatology, St. James's Hospital, Trinity College Dublin, Dublin 8, Republic of Ireland
| | - Edel McAuley
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Republic of Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Republic of Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Republic of Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Republic of Ireland
| | - Mairin McMenamin
- Department of Dermatology, St. James's Hospital, Trinity College Dublin, Dublin 8, Republic of Ireland
| | - Niamh Leonard
- Department of Dermatology, St. James's Hospital, Trinity College Dublin, Dublin 8, Republic of Ireland
| | - Mary Monks
- Department of Dermatology, St. James's Hospital, Trinity College Dublin, Dublin 8, Republic of Ireland
| | - Bairbre Wynne
- Department of Dermatology, St. James's Hospital, Trinity College Dublin, Dublin 8, Republic of Ireland
| | - Patrick Ormond
- Department of Dermatology, St. James's Hospital, Trinity College Dublin, Dublin 8, Republic of Ireland
| | - Annemarie Larkin
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Republic of Ireland
| |
Collapse
|
20
|
da Costa JP, Carvalhais V, Ferreira R, Amado F, Vilanova M, Cerca N, Vitorino R. Proteome signatures—how are they obtained and what do they teach us? Appl Microbiol Biotechnol 2015. [DOI: 10.1007/s00253-015-6795-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
21
|
Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS. Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project. J Proteome Res 2015; 14:3415-31. [DOI: 10.1021/pr5013009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Péter Horvatovich
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Emma K. Lundberg
- Science
for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, 128 Academia Road Sec. 2, Taipei 115, Taiwan
| | - Fuchu He
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Edouard C. Nice
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Robert J. Goode
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Simon Yu
- Department
of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Shoba Ranganathan
- Department
of Chemistry and Biomolecular Sciences and ARC Centre of Excellence
in Bioinformatics, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Mark S. Baker
- Australian
School of Advanced Medicine, Macquarie University, Sydney, NSW 2109, Australia
| | - Gilberto B. Domont
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Erika Velasquez
- Proteomics Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Av Athos da Silveira Ramos 149, CT-A542, 21941-909 Rio de Janeriro, Rj, Brazil
| | - Dong Li
- The State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Haidian District, Beijing 100850, China
| | - Siqi Liu
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
- BGI Shenzhen, Beishan Road, Yantian District, Shenzhen, 518083, China
| | - Quanhui Wang
- Beijing Institute of Genomics and BGI Shenzhen, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein
Research of Guangdong
Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Rajasree Menon
- Department of Computational Medicine & Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Yuanfang Guan
- Departments of Computational Medicine & Bioinformatics and Computer Sciences, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Fernando J. Corrales
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Victor Segura
- ProteoRed-ISCIII,
Biomolecular and Bioinformatics Resources Platform (PRB2), Spanish
Consortium of C-HPP (Chr-16), CIMA, University of Navarra, 31008 Pamplona, Spain
- Chr16 SpHPP Consortium, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - J. Ignacio Casal
- Department
of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas (CIB-CSIC), 28040 Madrid, Spain
| | | | - Juan P. Albar
- Centro Nacional de Biotecnologia (CNB-CSIC), Cantoblanco, 28049 Madrid, Spain
| | - Manuel Fuentes
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Maria Gonzalez-Gonzalez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Paula Diez
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Rosa M. Degano
- Cancer
Research Center. Proteomics Unit and General Service of Cytometry,
Department of Medicine, University of Salmanca-CSIC, IBSAL, Campus Miguel de Unamuno
s/n, 37007 Salamanca, Spain
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics
Centre, Vancouver Island
Technology Park, #3101−4464 Markham Street, Victoria, British Columbia V8Z 7X8, Canada
| | - Andrea Urbani
- Proteomics
and Metabonomic, Laboratory, Fondazione Santa Lucia, Rome, Italy
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | - Alessio Soggiu
- Department
of Veterinary Science and Public Health (DIVET), University of Milano, via Celoria 10, 20133 Milano, Italy
| | - Tadashi Yamamoto
- Institute
of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | | | | | - Andrey Lisitsa
- Orechovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Cheryl F. Lichti
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Ekaterina Mostovenko
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - Roger A. Kroes
- Falk Center for Molecular Therapeutics, Department of Biomedical Engineering, Northwestern University, 1801 Maple Ave., Suite 4300, Evanston, Illinois 60201, United States
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Ákos Végvári
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Thomas E. Fehniger
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan
1, 9713 AV Groningen, The Netherlands
| | - Juan Antonio Vizcaíno
- European Molecular
Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, CB10 1SD, Hinxton, Cambridge, United Kingdom
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109, United States
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Department
of Human Protein Science, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Carol L. Nilsson
- Department
of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, Texas 77555-0617, United States
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Department of Biomedical Engineering, Lund University, BMC D13, 221 84 Lund, Sweden
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics and School of Public Health, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Seul-Ki Jeong
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Jong-Sun Lim
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - Young-Ki Paik
- Departments of Integrated Omics for Biomedical Science & Biochemistry, College of Life Science and Technology, Yonsei Proteome Research Center, Yonsei University, Seoul, 120-749, Korea
| | - William S. Hancock
- The
Barnett Institute of Chemical and Biological Analysis, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| |
Collapse
|
22
|
Jiang J, Wang K, Nice EC, Zhang T, Huang C. High-throughput screening of cellular redox sensors using modern redox proteomics approaches. Expert Rev Proteomics 2015; 12:543-55. [PMID: 26184698 DOI: 10.1586/14789450.2015.1069189] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cancer cells are characterized by higher levels of intracellular reactive oxygen species (ROS) due to metabolic aberrations. ROS are widely accepted as second messengers triggering pivotal signaling pathways involved in the process of cell metabolism, cell cycle, apoptosis, and autophagy. However, the underlying cellular mechanisms remain largely unknown. Recently, accumulating evidence has demonstrated that ROS initiate redox signaling through direct oxidative modification of the cysteines of key redox-sensitive proteins (termed redox sensors). Uncovering the functional changes underlying redox regulation of redox sensors is urgently required, and the role of different redox sensors in distinct disease states still remains to be identified. To assist this, redox proteomics has been developed for the high-throughput screening of redox sensors, which will benefit the development of novel therapeutic strategies for cancer treatment. Highlighted here are recent advances in redox proteomics approaches and their applications in identifying redox sensors involved in tumor development.
Collapse
Affiliation(s)
- Jingwen Jiang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China.,b 2 Hainan Medical University, Haikou, 571199, PR China
| | - Kui Wang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Edouard C Nice
- c 3 Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Tao Zhang
- d 4 School of Biomedical Sciences, Chengdu Medical College, Chengdu 610500, PR China
| | - Canhua Huang
- a 1 State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China.,b 2 Hainan Medical University, Haikou, 571199, PR China
| |
Collapse
|
23
|
Mahboob S, Mohamedali A, Ahn SB, Schulz-Knappe P, Nice E, Baker MS. Is isolation of comprehensive human plasma peptidomes an achievable quest? J Proteomics 2015; 127:300-9. [PMID: 25979773 DOI: 10.1016/j.jprot.2015.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/06/2015] [Accepted: 05/09/2015] [Indexed: 01/12/2023]
Abstract
The low molecular weight (LMW; <10kDa)* plasma peptidome has been considered a source of useful diagnostic biomarkers and potentially therapeutic molecules, as it contains many cytokines, peptide hormones, endogenous peptide products and potentially bioactive fragments derived from the parent proteome. The small size of the peptides allows them almost unrestricted vascular and interstitial access, and hence distribution across blood-brain barriers, tumour and other vascular permeability barriers. Therefore, the peptidome may carry specific signatures or fingerprints of an individual's health, wellbeing or disease status. This occurs primarily because of the advantage the peptidome has in being readily accessible in human blood and/or other biofluids. However, the co-expression of highly abundant proteins (>10kDa) and other factors present inherently in human plasma make direct analysis of the blood peptidome one of the most challenging tasks faced in contemporary analytical biochemistry. A comprehensive compendium of extraction and fractionation tools has been collected concerning the isolation and micromanipulation of peptides. However, the search for a reliable, accurate and reproducible single or combinatorial separation process for capturing and analysing the plasma peptidome remains a challenge. This review outlines current techniques used for the separation and detection of plasma peptides and suggests potential avenues for future investigation. This article is part of a Special Issue entitled: HUPO 2014.
Collapse
Affiliation(s)
- S Mahboob
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | - A Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, NSW 2109, Australia
| | - S B Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | | | - E Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - M S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia.
| |
Collapse
|
24
|
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]
|