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Abstract
There are probably no biological samples that did more to spur interest in proteomics than serum and plasma. The belief was that comparing the proteomes of these samples obtained from healthy and disease-affected individuals would lead to biomarkers that could be used to diagnose conditions such as cancer. While the continuing development of mass spectrometers with greater sensitivity and resolution has been invaluable, the invention of strategic strategies to separate circulatory proteins has been just as critical. Novel and creative separation techniques were required because serum and plasma probably have the greatest dynamic range of protein concentration of any biological sample. The concentrations of circulating proteins can range over twelve orders of magnitude, making it a challenge to identify low-abundance proteins where the bulk of the useful biomarkers are believed to exist. The major goals of this article are to (i) provide an historical perspective on the rapid development of serum and plasma proteomics; (ii) describe various separation techniques that have made obtaining an in-depth view of the proteome of these biological samples possible; and (iii) describe applications where serum and plasma proteomics have been employed to discover potential biomarkers for pathological conditions.
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Nielson CM, Jacobs JM, Orwoll ES. Proteomic studies of bone and skeletal health outcomes. Bone 2019; 126:18-26. [PMID: 30954730 PMCID: PMC7302501 DOI: 10.1016/j.bone.2019.03.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022]
Abstract
Proteins are an essential part of essentially all biological processes, and there is enormous variation in protein forms and concentrations that is not reflected in DNA or RNA. Recently there have been rapid advances in the ability to measure protein sequence, modification and concentration, particularly with methods based in mass spectrometry. Global measures of proteins in tissues or in the circulation provide a broad assessment of the proteome that can be extremely useful for discovery, and targeted proteomic measures can yield specific and sensitive assessments of specific peptides and proteins. While most proteomic measures are directed at the detection of consensus peptide sequences, mass spectrometry based proteomic methods also allow a detailed examination of the peptide sequence differences that result from genetic variants and that may have important effects on protein function. In evaluating proteomic data, a number of analytical considerations are important, including an understanding of missing data, the challenge of multiple testing and replication, and the use of rapidly evolving methods in systems biology. While proteomics has not yet had a major impact in skeletal research, interesting recent research has used these approaches in the study of bone cell biology and the discovery of biomarkers of skeletal disorders. Proteomics can be expected to have an increasing influence in the study of bone biology and pathophysiology.
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Affiliation(s)
| | - Jon M Jacobs
- Pacific Northwest National Laboratory, Richland, WA, USA
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Nice EC. Challenges for omics technologies in the implementation of personalized medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1505429] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
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Bao W, He F, Yu L, Gao J, Meng F, Ding Y, Zou H, Luo B. Complement cascade on severe traumatic brain injury patients at the chronic unconscious stage: implication for pathogenesis. Expert Rev Mol Diagn 2018; 18:761-766. [PMID: 29718755 DOI: 10.1080/14737159.2018.1471985] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Patients who awake from severely traumatic brain injury (TBI) may remain unconscious for many years. Although behavioral assessment and functional imaging are currently used as diagnostic tools, the molecular basis underlying chronic condition has yet to be explored. METHOD Plasma samples were obtained at 3 time points (1, 3 and 6 months) from 18 patients with chronic disorders of consciousness who survived severe TBI, and 6 healthy volunteers. A coupled isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics approach was used to screen differentially expressed proteins (DEPs) between patients and controls. Potential molecular mechanisms were further discussed through bioinformatics analyses. RESULT In total, 300 plasma proteins <1% false discovery rates were identified and 32 proteins were consistently altered between patients and controls. Biological pathway analysis revealed that the DEPs were predominantly involved in complement cascade. CONCLUSIONS This study discussed potential mechanisms of complement cascade underlying chronic stage in severe TBI.
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Affiliation(s)
- Wangxiao Bao
- a Department of Neurology, First Affiliated Hospital, Collaborative Innovation Center for Brain Science , Zhejiang University School of Medicine , Hangzhou , China
| | - Fangping He
- a Department of Neurology, First Affiliated Hospital, Collaborative Innovation Center for Brain Science , Zhejiang University School of Medicine , Hangzhou , China
| | - Lihua Yu
- b Department of Neurology , Zhejiang Provincial People's Hospital , Hangzhou , China.,e People's Hospital of Hangzhou Medical College , Hangzhou Zhejiang Province , China
| | - Jian Gao
- c Department of Rehabilitation , Hangzhou Hospital of Zhejiang CAPR , Hangzhou , China
| | - Fanxia Meng
- a Department of Neurology, First Affiliated Hospital, Collaborative Innovation Center for Brain Science , Zhejiang University School of Medicine , Hangzhou , China
| | - Yahui Ding
- d Department of Neurology, First Affiliated Hospital , Zhejiang Provincial People's Hospital , Hangzhou , China.,e People's Hospital of Hangzhou Medical College , Hangzhou Zhejiang Province , China
| | - Hai Zou
- d Department of Neurology, First Affiliated Hospital , Zhejiang Provincial People's Hospital , Hangzhou , China.,e People's Hospital of Hangzhou Medical College , Hangzhou Zhejiang Province , China
| | - Benyan Luo
- a Department of Neurology, First Affiliated Hospital, Collaborative Innovation Center for Brain Science , Zhejiang University School of Medicine , Hangzhou , China
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Chemonges S, Gupta R, Mills PC, Kopp SR, Sadowski P. Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serum. Proteome Sci 2017; 15:11. [PMID: 28615994 PMCID: PMC5466729 DOI: 10.1186/s12953-017-0119-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 06/02/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Unlike humans, there is currently no publicly available reference mass spectrometry-based circulating acellular proteome data for sheep, limiting the analysis and interpretation of a range of physiological changes and disease states. The objective of this study was to develop a robust and comprehensive method to characterise the circulating acellular proteome in ovine serum. METHODS Serum samples from healthy sheep were subjected to shotgun proteomic analysis using nano liquid chromatography nano electrospray ionisation tandem mass spectrometry (nanoLC-nanoESI-MS/MS) on a quadrupole time-of-flight instrument (TripleTOF® 5600+, SCIEX). Proteins were identified using ProteinPilot™ (SCIEX) and Mascot (Matrix Science) software based on a minimum of two unmodified highly scoring unique peptides per protein at a false discovery rate (FDR) of 1% software by searching a subset of the Universal Protein Resource Knowledgebase (UniProtKB) database (http://www.uniprot.org). PeptideShaker (CompOmics, VIB-UGent) searches were used to validate protein identifications from ProteinPilot™ and Mascot. RESULTS ProteinPilot™ and Mascot identified 245 and 379 protein groups (IDs), respectively, and PeptideShaker validated 133 protein IDs from the entire dataset. Since Mascot software is considered the industry standard and identified the most proteins, these were analysed using the Protein ANalysis THrough Evolutionary Relationships (PANTHER) classification tool revealing the association of 349 genes with 127 protein pathway hits. These data are available via ProteomeXchange with identifier PXD004989. CONCLUSIONS These results demonstrated for the first time the feasibility of characterising the ovine circulating acellular proteome using nanoLC-nanoESI-MS/MS. This peptide spectral data contributes to a protein library that can be used to identify a wide range of proteins in ovine serum.
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Affiliation(s)
- Saul Chemonges
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Rajesh Gupta
- Proteomics and Small Molecule Mass Spectrometry, Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
| | - Paul C. Mills
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Steven R. Kopp
- School of Veterinary Science, The University of Queensland, Gatton, Australia
| | - Pawel Sadowski
- Proteomics and Small Molecule Mass Spectrometry, Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
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Xu XF, Dai HP, Li YM, Xiao F, Wang C. Mass Spectrometry-based Proteomics in Acute Respiratory Distress Syndrome: A Powerful Modality for Pulmonary Precision Medicine. Chin Med J (Engl) 2017; 129:2357-64. [PMID: 27647196 PMCID: PMC5040023 DOI: 10.4103/0366-6999.190669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Objective: Acute respiratory distress syndrome (ARDS) is an acute and lethal clinical syndrome that is characterized by hypoxemic respiratory failure and diffuse alveolar inflammatory damage. This review aimed to search and discuss the mass spectrometry (MS)-based proteomic studies on different subsets of ARDS patients. Data Sources: Original research articles were collected from the PubMed database published in English up to December 2015. Study Selection: The literature search was done using the term “(acute lung injury OR acute respiratory distress syndrome) AND (proteomics OR proteome OR mass spectrum OR differential in-gel electrophoresis OR two-dimensional polyacrylamide gel electrophoresis)”. Related original research articles were included and were carefully analyzed. Results: Eight original proteomic researches on ARDS patients were found. The common proteomic modalities were two-dimensional (2D) high-performance liquid chromatography-based electronic spray ion-MS/MS and 2D-polyacrylamide gel electrophoresis/differential in-gel electrophoresis-based matrix-assisted laser desorption ionization-time of flight/MS. They compared the proteome between ARDS patients and normal controls and analyzed the dynamic changes of proteome at different ARDS stages or severity. The disturbed proteome in ARDS patients includes plasma acute-phase proteins, inflammatory/immune-associated proteins, and coagulation proteins. Conclusions: Although several previous studies have provided some useful information about the lung proteome in ARDS patients and gained several interesting disease-associated biomarkers, clinical proteomic studies in ARDS patients are still in the initial stage. An increased cooperation is still needed to establish a global and faithful database containing disease-specific proteome from the largest ARDS subsets.
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Affiliation(s)
- Xue-Feng Xu
- Department of Surgical Intensive Care Medicine, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029; National Clinical Research Centre for Respiratory Medicine, Beijing Hospital, Beijing 100730, China
| | - Hua-Ping Dai
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yan-Ming Li
- National Clinical Research Centre for Respiratory Medicine, Beijing Hospital, Beijing 100730, China
| | - Fei Xiao
- National Clinical Research Centre for Respiratory Medicine, Beijing Hospital, Beijing 100730, China
| | - Chen Wang
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing 100029, China
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Omenn GS, Lane L, Lundberg EK, Beavis RC, Overall CM, Deutsch EW. Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications. J Proteome Res 2016; 15:3951-3960. [PMID: 27487407 PMCID: PMC5129622 DOI: 10.1021/acs.jproteome.6b00511] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The HUPO Human Proteome Project (HPP) has two overall goals: (1) stepwise completion of the protein parts list-the draft human proteome including confidently identifying and characterizing at least one protein product from each protein-coding gene, with increasing emphasis on sequence variants, post-translational modifications (PTMs), and splice isoforms of those proteins; and (2) making proteomics an integrated counterpart to genomics throughout the biomedical and life sciences community. PeptideAtlas and GPMDB reanalyze all major human mass spectrometry data sets available through ProteomeXchange with standardized protocols and stringent quality filters; neXtProt curates and integrates mass spectrometry and other findings to present the most up to date authorative compendium of the human proteome. The HPP Guidelines for Mass Spectrometry Data Interpretation version 2.1 were applied to manuscripts submitted for this 2016 C-HPP-led special issue [ www.thehpp.org/guidelines ]. The Human Proteome presented as neXtProt version 2016-02 has 16,518 confident protein identifications (Protein Existence [PE] Level 1), up from 13,664 at 2012-12, 15,646 at 2013-09, and 16,491 at 2014-10. There are 485 proteins that would have been PE1 under the Guidelines v1.0 from 2012 but now have insufficient evidence due to the agreed-upon more stringent Guidelines v2.0 to reduce false positives. neXtProt and PeptideAtlas now both require two non-nested, uniquely mapping (proteotypic) peptides of at least 9 aa in length. There are 2,949 missing proteins (PE2+3+4) as the baseline for submissions for this fourth annual C-HPP special issue of Journal of Proteome Research. PeptideAtlas has 14,629 canonical (plus 1187 uncertain and 1755 redundant) entries. GPMDB has 16,190 EC4 entries, and the Human Protein Atlas has 10,475 entries with supportive evidence. neXtProt, PeptideAtlas, and GPMDB are rich resources of information about post-translational modifications (PTMs), single amino acid variants (SAAVSs), and splice isoforms. Meanwhile, the Biology- and Disease-driven (B/D)-HPP has created comprehensive SRM resources, generated popular protein lists to guide targeted proteomics assays for specific diseases, and launched an Early Career Researchers initiative.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Human Protein Science, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Emma K. Lundberg
- SciLifeLab Stockholm and School of Biotechnology, KTH, Karolinska Institutet Science Park, Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Ronald C. Beavis
- Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Christopher M. Overall
- Biochemistry and Molecular Biology, and Oral Biological and Medical Sciences University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, BC V6T 1Z3, Canada
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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Guo J, Cui Y, Yan Z, Luo Y, Zhang W, Deng S, Tang S, Zhang G, He QY, Wang T. Phosphoproteome Characterization of Human Colorectal Cancer SW620 Cell-Derived Exosomes and New Phosphosite Discovery for C-HPP. J Proteome Res 2016; 15:4060-4072. [PMID: 27470641 DOI: 10.1021/acs.jproteome.6b00391] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jiahui Guo
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yizhi Cui
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ziqi Yan
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yanzhang Luo
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Wanling Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Suyuan Deng
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shengquan Tang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Tong Wang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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Abstract
Non-small-cell lung cancer (NSCLC) is a heterogeneous disease with diverse pathological features. Clinical proteomics allows the discovery of molecular markers and new therapeutic targets for this most prevalent type of lung cancer. Some of them may be used to detect early lung cancer, while others may serve as predictive markers of resistance to different therapies. Therapeutic targets and prognostic markers in NSCLC have also been discovered. These proteomics biomarkers may help to pair the individual NSCLC patient with the best treatment option. Despite the fact that implementation of these biomarkers in the clinic appears to be scarce, the recently launched Precision Medicine Initiative may encourage their translation into clinical practice.
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Affiliation(s)
- William C S Cho
- a Department of Clinical Oncology , Queen Elizabeth Hospital , Kowloon , Hong Kong
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10
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Ebhardt HA, Root A, Sander C, Aebersold R. Applications of targeted proteomics in systems biology and translational medicine. Proteomics 2015; 15:3193-208. [PMID: 26097198 PMCID: PMC4758406 DOI: 10.1002/pmic.201500004] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/27/2015] [Accepted: 06/09/2015] [Indexed: 01/28/2023]
Abstract
Biological systems are composed of numerous components of which proteins are of particularly high functional significance. Network models are useful abstractions for studying these components in context. Network representations display molecules as nodes and their interactions as edges. Because they are difficult to directly measure, functional edges are frequently inferred from suitably structured datasets consisting of the accurate and consistent quantification of network nodes under a multitude of perturbed conditions. For the precise quantification of a finite list of proteins across a wide range of samples, targeted proteomics exemplified by selected/multiple reaction monitoring (SRM, MRM) mass spectrometry has proven useful and has been applied to a variety of questions in systems biology and clinical studies. Here, we survey the literature of studies using SRM-MS in systems biology and clinical proteomics. Systems biology studies frequently examine fundamental questions in network biology, whereas clinical studies frequently focus on biomarker discovery and validation in a variety of diseases including cardiovascular disease and cancer. Targeted proteomics promises to advance our understanding of biological networks and the phenotypic significance of specific network states and to advance biomarkers into clinical use.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Alex Root
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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11
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Yang L, Lian X, Zhang W, Guo J, Wang Q, Li Y, Chen Y, Yin X, Yang P, Lan F, He QY, Zhang G, Wang T. Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria. J Proteome Res 2015. [DOI: 10.1021/acs.jproteome.5b00480] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lijuan Yang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xinlei Lian
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wanling Zhang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jie Guo
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing Wang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yang Chen
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xingfeng Yin
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | | | | | - Qing-Yu He
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
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12
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Chen Y, Li Y, Zhong J, Zhang J, Chen Z, Yang L, Cao X, He QY, Zhang G, Wang T. Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins. J Proteome Res 2015; 14:3693-709. [DOI: 10.1021/pr501103r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yang Chen
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jiayong Zhong
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhipeng Chen
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lijuan Yang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xin Cao
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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13
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Omenn GS, Guan Y, Menon R. A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. J Proteomics 2014; 107:103-12. [PMID: 24802673 DOI: 10.1016/j.jprot.2014.04.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/09/2014] [Accepted: 04/10/2014] [Indexed: 02/07/2023]
Abstract
Combined RNA-Seq and proteomics analyses reveal striking differential expression of splice isoforms of key proteins in important cancer pathways and networks. Even between primary tumor cell lines from histologically similar inflammatory breast cancers, we find striking differences in hormone receptor-negative cell lines that are ERBB2 (Her2/neu)-amplified versus ERBB1 (EGFR) over-expressed with low ERBB2 activity. We have related these findings to protein-protein interaction networks, signaling and metabolic pathways, and methods for predicting functional variants among multiple alternative isoforms. Understanding the upstream ligands and regulators and the downstream pathways and interaction networks for ERBB receptors is certain to be important for explanation and prediction of the variable levels of expression and therapeutic responses of ERBB+tumors in the breast and in other organ sites. Alternative splicing is a remarkable evolutionary development that increases protein diversity from multi-exonic genes without requiring expansion of the genome. It is no longer sufficient to report the up- or down-expression of genes and proteins without dissecting the complexity due to alternative splicing. This article is part of a Special Issue entitled: 20Years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini , Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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Affiliation(s)
- Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
| | - Yuanfang Guan
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
| | - Rajasree Menon
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
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