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Recent progress in mass spectrometry proteomics for biomedical research. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1093-1113. [DOI: 10.1007/s11427-017-9175-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022]
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Dimitrakopoulos L, Prassas I, Diamandis EP, Charames GS. Onco-proteogenomics: Multi-omics level data integration for accurate phenotype prediction. Crit Rev Clin Lab Sci 2017; 54:414-432. [DOI: 10.1080/10408363.2017.1384446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Lampros Dimitrakopoulos
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Ioannis Prassas
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON, Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - George S. Charames
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Joseph and Wolf Lebovic Health Complex, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
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Menschaert G, David F. Proteogenomics from a bioinformatics angle: A growing field. MASS SPECTROMETRY REVIEWS 2017; 36:584-599. [PMID: 26670565 PMCID: PMC6101030 DOI: 10.1002/mas.21483] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/01/2015] [Indexed: 05/16/2023]
Abstract
Proteogenomics is a research area that combines areas as proteomics and genomics in a multi-omics setup using both mass spectrometry and high-throughput sequencing technologies. Currently, the main goals of the field are to aid genome annotation or to unravel the proteome complexity. Mass spectrometry based identifications of matching or homologues peptides can further refine gene models. Also, the identification of novel proteoforms is also made possible based on detection of novel translation initiation sites (cognate or near-cognate), novel transcript isoforms, sequence variation or novel (small) open reading frames in intergenic or un-translated genic regions by analyzing high-throughput sequencing data from RNAseq or ribosome profiling experiments. Other proteogenomics studies using a combination of proteomics and genomics techniques focus on antibody sequencing, the identification of immunogenic peptides or venom peptides. Over the years, a growing amount of bioinformatics tools and databases became available to help streamlining these cross-omics studies. Some of these solutions only help in specific steps of the proteogenomics studies, e.g. building custom sequence databases (based on next generation sequencing output) for mass spectrometry fragmentation spectrum matching. Over the last few years a handful integrative tools also became available that can execute complete proteogenomics analyses. Some of these are presented as stand-alone solutions, whereas others are implemented in a web-based framework such as Galaxy. In this review we aimed at sketching a comprehensive overview of all the bioinformatics solutions that are available for this growing research area. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:584-599, 2017.
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Affiliation(s)
- Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics, Department of
Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience
Engineering, Ghent University, Ghent, Belgium
- To whom correspondence should be addressed. Tel:
+32 9 264 99 22; Fax: +32 9 264 6220;
| | - Fenyö David
- Center for Health Informatics and Bioinformatics and Department of
Biochemistry and Molecular Pharmacology, New York University School of Medicine, New
York, New York, USA
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Dimitrakopoulos L, Prassas I, Berns EMJJ, Foekens JA, Diamandis EP, Charames GS. Variant peptide detection utilizing mass spectrometry: laying the foundations for proteogenomic identification and validation. Clin Chem Lab Med 2017; 55:1291-1304. [PMID: 28157690 DOI: 10.1515/cclm-2016-0947] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/07/2016] [Indexed: 01/29/2023]
Abstract
BACKGROUND Proteogenomics is an emerging field at the intersection of genomics and proteomics. Many variant peptides corresponding to single nucleotide variations (SNVs) are associated with specific diseases. The aim of this study was to demonstrate the feasibility of proteogenomic-based variant peptide detection in disease models and clinical specimens. METHODS We sought to detect p53 single amino acid variant (SAAV) peptides in breast cancer tumor samples that have been previously subjected to sequencing analysis. Initially, two cancer cell lines having a cellular tumor antigen p53 (TP53) mutation and one wild type for TP53 were analyzed by selected reaction monitoring (SRM) assays as controls. One pool of wild type and one pool of mutated for TP53 cytosolic extracts were assayed with a shotgun proteogenomic workflow. Furthermore, 18 individual samples having a mutation in TP53 were assayed by SRM. RESULTS Two mutant p53 peptides were successfully detected in two cancer cell lines as expected from their DNA sequence. Wild type p53 peptides were detected in both cytosolic pools, however, none of the mutant p53 peptides were identified. Mutations at the protein level were detected in two cytosolic extracts and whole tumor lysates from the same patients by SRM analysis. Six thousand and six hundred and twenty eight non-redundant proteins were identified in the two cytosolic pools, thus greatly improving a previously reported cytosolic proteome. CONCLUSIONS In the current study we show the great potential of using proteogenomics for the direct identification of cancer-associated mutations in clinical samples and we discuss current limitations and future perspectives.
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55
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Zhu FY, Chen MX, Ye NH, Shi L, Ma KL, Yang JF, Cao YY, Zhang Y, Yoshida T, Fernie AR, Fan GY, Wen B, Zhou R, Liu TY, Fan T, Gao B, Zhang D, Hao GF, Xiao S, Liu YG, Zhang J. Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:518-533. [PMID: 28407323 DOI: 10.1111/tpj.13571] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 05/19/2023]
Abstract
In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.
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Affiliation(s)
- Fu-Yuan Zhu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Mo-Xian Chen
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Neng-Hui Ye
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
| | - Lu Shi
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Jing-Fang Yang
- College of Chemistry, Central China Normal University, Wuhan, China
| | - Yun-Ying Cao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Takuya Yoshida
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | | | - Bo Wen
- BGI-Shenzhen, Shenzhen, China
| | | | - Tie-Yuan Liu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tao Fan
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Bei Gao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Di Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ge-Fei Hao
- College of Chemistry, Central China Normal University, Wuhan, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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Hernandez-Valladares M, Vaudel M, Selheim F, Berven F, Bruserud Ø. Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers. Expert Rev Proteomics 2017; 14:649-663. [DOI: 10.1080/14789450.2017.1352474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Frode Selheim
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Frode Berven
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Øystein Bruserud
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
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Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines. Genome Med 2017; 9:62. [PMID: 28716134 PMCID: PMC5514513 DOI: 10.1186/s13073-017-0454-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/22/2017] [Indexed: 02/07/2023] Open
Abstract
Background Onco-proteogenomics aims to understand how changes in a cancer’s genome influences its proteome. One challenge in integrating these molecular data is the identification of aberrant protein products from mass-spectrometry (MS) datasets, as traditional proteomic analyses only identify proteins from a reference sequence database. Methods We established proteomic workflows to detect peptide variants within MS datasets. We used a combination of publicly available population variants (dbSNP and UniProt) and somatic variations in cancer (COSMIC) along with sample-specific genomic and transcriptomic data to examine proteome variation within and across 59 cancer cell-lines. Results We developed a set of recommendations for the detection of variants using three search algorithms, a split target-decoy approach for FDR estimation, and multiple post-search filters. We examined 7.3 million unique variant tryptic peptides not found within any reference proteome and identified 4771 mutations corresponding to somatic and germline deviations from reference proteomes in 2200 genes among the NCI60 cell-line proteomes. Conclusions We discuss in detail the technical and computational challenges in identifying variant peptides by MS and show that uncovering these variants allows the identification of druggable mutations within important cancer genes. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0454-9) contains supplementary material, which is available to authorized users.
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Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics 2017; 16:959-981. [PMID: 28456751 DOI: 10.1074/mcp.mr117.000024] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 12/20/2022] Open
Abstract
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e. the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease. Many methods and tools have been developed or adapted to enable an array of integrative proteogenomic approaches and in this article, we systematically classify published methods and tools into four major categories, (1) Sequence-centric proteogenomics; (2) Analysis of proteogenomic relationships; (3) Integrative modeling of proteogenomic data; and (4) Data sharing and visualization. We provide a comprehensive review of methods and available tools in each category and highlight their typical applications.
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Affiliation(s)
- Kelly V Ruggles
- From the ‡Department of Medicine, New York University School of Medicine, New York, New York 10016
| | - Karsten Krug
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Xiaojing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Karl R Clauser
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Jing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Samuel H Payne
- **Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - David Fenyö
- ‡‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016; .,§§Institute for Systems Genetics, New York University School of Medicine, New York, New York 10016
| | - Bing Zhang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030; .,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - D R Mani
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
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Otte KA, Schlötterer C. Polymorphism-aware protein databases - a prerequisite for an unbiased proteomic analysis of natural populations. Mol Ecol Resour 2017; 17:1148-1155. [DOI: 10.1111/1755-0998.12656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 01/12/2017] [Accepted: 01/20/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Kathrin A. Otte
- Institut für Populationsgenetik; Vetmeduni Vienna; Veterinärplatz 1 1210 Vienna Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik; Vetmeduni Vienna; Veterinärplatz 1 1210 Vienna Austria
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60
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Murray HC, Dun MD, Verrills NM. Harnessing the power of proteomics for identification of oncogenic, druggable signalling pathways in cancer. Expert Opin Drug Discov 2017; 12:431-447. [PMID: 28286965 DOI: 10.1080/17460441.2017.1304377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Genomic and transcriptomic profiling of tumours has revolutionised our understanding of cancer. However, the majority of tumours possess multiple mutations, and determining which oncogene, or even which pathway, to target is difficult. Proteomics is emerging as a powerful approach to identify the functionally important pathways driving these cancers, and how they can be targeted therapeutically. Areas covered: The authors provide a technical overview of mass spectrometry based approaches for proteomic profiling, and review the current and emerging strategies available for the identification of dysregulated networks, pathways, and drug targets in cancer cells, with a key focus on the ability to profile cancer kinomes. The potential applications of mass spectrometry in the clinic are also highlighted. Expert opinion: The addition of proteomic information to genomic platforms - 'proteogenomics' - is providing unparalleled insight in cancer cell biology. Application of improved mass spectrometry technology and methodology, in particular the ability to analyse post-translational modifications (the PTMome), is providing a more complete picture of the dysregulated networks in cancer, and uncovering novel therapeutic targets. While the application of proteomics to discovery research will continue to rise, improved workflow standardisation and reproducibility is required before mass spectrometry can enter routine clinical use.
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Affiliation(s)
- Heather C Murray
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
| | - Matthew D Dun
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
| | - Nicole M Verrills
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
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61
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Fu S, Liu X, Luo M, Xie K, Nice EC, Zhang H, Huang C. Proteogenomic studies on cancer drug resistance: towards biomarker discovery and target identification. Expert Rev Proteomics 2017; 14:351-362. [PMID: 28276747 DOI: 10.1080/14789450.2017.1299006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment. Areas covered: In this review, we will present recent advances in proteogenomic investigations of cancer drug resistance with an emphasis on integrative proteogenomic pipelines and the biomarker discovery which contributes to achieving the goal of using precision/personalized medicine for cancer treatment. Expert commentary: The discovery and comprehensive understanding of potential biomarkers help identify the cohort of patients who may benefit from particular treatments, and will assist real-time clinical decision-making to maximize therapeutic efficacy and minimize adverse effects. With the development of MS-based proteomics and NGS-based sequencing, a growing number of proteogenomic tools are being developed specifically to investigate cancer drug resistance.
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Affiliation(s)
- Shuyue Fu
- a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Xiang Liu
- b Department of Pathology , Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital , Chengdu , P.R. China
| | - Maochao Luo
- c West China School of Public Health, Sichuan University , Chengdu , P.R.China
| | - Ke Xie
- d Department of Oncology , Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital , Chengdu , P.R. China
| | - Edouard C Nice
- e Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- f School of Medicine , Yangtze University , P. R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center , West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
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62
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Tan Z, Nie S, McDermott SP, Wicha MS, Lubman DM. Single Amino Acid Variant Profiles of Subpopulations in the MCF-7 Breast Cancer Cell Line. J Proteome Res 2017; 16:842-851. [PMID: 28076950 DOI: 10.1021/acs.jproteome.6b00824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cancers are initiated and developed from a small population of stem-like cells termed cancer stem cells (CSCs). There is heterogeneity among this CSC population that leads to multiple subpopulations with their own distinct biological features and protein expression. The protein expression and function may be impacted by amino acid variants that can occur largely due to single nucleotide changes. We have thus performed proteomic analysis of breast CSC subpopulations by mass spectrometry to study the presence of single amino acid variants (SAAVs) and their relation to breast cancer. We have used CSC markers to isolate pure breast CSC subpopulation fractions (ALDH+ and CD44+/CD24- cell populations) and the mature luminal cells (CD49f-EpCAM+) from the MCF-7 breast cancer cell line. By searching the Swiss-CanSAAVs database, 374 unique SAAVs were identified in total, where 27 are cancer-related SAAVs. 135 unique SAAVs were found in the CSC population compared with the mature luminal cells. The distribution of SAAVs detected in MCF-7 cells was compared with those predicted from the Swiss-CanSAAVs database, where we found distinct differences in the numbers of SAAVs detected relative to that expected from the Swiss-CanSAAVs database for several of the amino acids.
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Affiliation(s)
- Zhijing Tan
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Song Nie
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States.,Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, Washington 99352, United States
| | - Sean P McDermott
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan , Ann Arbor, Michigan 48109, United States.,Comprehensive Cancer Center, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Max S Wicha
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan , Ann Arbor, Michigan 48109, United States.,Comprehensive Cancer Center, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan , Ann Arbor, Michigan 48109, United States
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Qin J, Yan B, Hu Y, Wang P, Wang J. Applications of integrative OMICs approaches to gene regulation studies. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0085-y] [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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64
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Bhat AR, Gupta MK, Krithivasan P, Dhas K, Nair J, Reddy RB, Sudheendra HV, Chavan S, Vardhan H, Darsi S, Balakrishnan L, Katragadda S, Kekatpure V, Suresh A, Tata P, Panda B, Kuriakose MA, Sirdeshmukh R. Sample preparation method considerations for integrated transcriptomic and proteomic analysis of tumors. Proteomics Clin Appl 2016; 11. [PMID: 27801551 DOI: 10.1002/prca.201600100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/16/2016] [Accepted: 10/26/2016] [Indexed: 01/09/2023]
Affiliation(s)
| | - Manoj Kumar Gupta
- Institute of Bioinformatics; International Tech Park; Bangalore India
- Manipal University; Madhav Nagar; Manipal India
| | - Priya Krithivasan
- Ganit Labs, Bio-IT Centre; Institute of Bioinformatics and Applied Biotechnology; Bangalore India
| | - Kunal Dhas
- Ganit Labs, Bio-IT Centre; Institute of Bioinformatics and Applied Biotechnology; Bangalore India
| | - Jayalakshmi Nair
- Ganit Labs, Bio-IT Centre; Institute of Bioinformatics and Applied Biotechnology; Bangalore India
| | - Ram Bhupal Reddy
- Head and Neck Oncology; Mazumdar Shaw Medical Centre; Narayana Health; Bangalore India
- Mazumdar Shaw Center for Translational Research; Mazumdar Shaw Medical Foundation; Narayana Health; Bangalore India
| | | | - Sandip Chavan
- Institute of Bioinformatics; International Tech Park; Bangalore India
| | - Harsha Vardhan
- Head and Neck Oncology; Mazumdar Shaw Medical Centre; Narayana Health; Bangalore India
- Mazumdar Shaw Center for Translational Research; Mazumdar Shaw Medical Foundation; Narayana Health; Bangalore India
| | - Sujatha Darsi
- Head and Neck Oncology; Mazumdar Shaw Medical Centre; Narayana Health; Bangalore India
| | | | | | - Vikram Kekatpure
- Head and Neck Oncology; Mazumdar Shaw Medical Centre; Narayana Health; Bangalore India
| | - Amritha Suresh
- Head and Neck Oncology; Mazumdar Shaw Medical Centre; Narayana Health; Bangalore India
- Mazumdar Shaw Center for Translational Research; Mazumdar Shaw Medical Foundation; Narayana Health; Bangalore India
| | | | - Binay Panda
- Ganit Labs, Bio-IT Centre; Institute of Bioinformatics and Applied Biotechnology; Bangalore India
| | - Moni A. Kuriakose
- Head and Neck Oncology; Mazumdar Shaw Medical Centre; Narayana Health; Bangalore India
- Mazumdar Shaw Center for Translational Research; Mazumdar Shaw Medical Foundation; Narayana Health; Bangalore India
| | - Ravi Sirdeshmukh
- Institute of Bioinformatics; International Tech Park; Bangalore India
- Mazumdar Shaw Center for Translational Research; Mazumdar Shaw Medical Foundation; Narayana Health; Bangalore India
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Broodman I, Lindemans J, van Sten J, Bischoff R, Luider T. Serum Protein Markers for the Early Detection of Lung Cancer: A Focus on Autoantibodies. J Proteome Res 2016; 16:3-13. [DOI: 10.1021/acs.jproteome.6b00559] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | | | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University of Groningen, Antonius
Deusinglaan 1, 9713 AV Groningen, The Netherlands
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66
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Proteomic analysis and translational perspective of hepatocellular carcinoma: Identification of diagnostic protein biomarkers by an onco-proteogenomics approach. Kaohsiung J Med Sci 2016; 32:535-544. [DOI: 10.1016/j.kjms.2016.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 02/07/2023] Open
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67
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Caron E, Kowalewski DJ, Chiek Koh C, Sturm T, Schuster H, Aebersold R. Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry. Mol Cell Proteomics 2016; 14:3105-17. [PMID: 26628741 DOI: 10.1074/mcp.o115.052431] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field.
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Affiliation(s)
- Etienne Caron
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland;
| | - Daniel J Kowalewski
- §Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ching Chiek Koh
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Theo Sturm
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Heiko Schuster
- §Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Ruedi Aebersold
- From the ‡Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; ¶Faculty of Science, University of Zurich, Zurich, Switzerland
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68
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Yeom J, Kabir MH, Lim B, Ahn HS, Kim SY, Lee C. A proteogenomic approach for protein-level evidence of genomic variants in cancer cells. Sci Rep 2016; 6:35305. [PMID: 27734975 PMCID: PMC5062161 DOI: 10.1038/srep35305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 09/27/2016] [Indexed: 11/20/2022] Open
Abstract
Variations in protein coding sequence may sometimes play important roles in cancer development. However, since variants may not express into proteins due to various cellular quality control systems, it is important to get protein-level evidence of the genomic variations. We present a proteogenomic strategy getting protein-level evidence of genomic variants, which we call sequential targeted LC-MS/MS based on prediction of peptide pI and Retention time (STaLPIR). Our approach shows improved peptide identification, and has the potential for the unbiased analysis of variant sequence as well as corresponding reference sequence. Integrated analysis of DNA, mRNA and protein suggests that protein expression level of the nonsynonymous variant is regulated either before or after translation, according to influence of the variant on protein function. In conclusion, our data provides an excellent approach getting direct evidence for the expression of variant protein forms from genome sequence data.
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Affiliation(s)
- Jeonghun Yeom
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Department of Biological Chemistry, Korea University of Science and Technology, Daejeon 34113 Republic of Korea
| | - Mohammad Humayun Kabir
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Byungho Lim
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Hee-Sung Ahn
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Department of Biological Chemistry, Korea University of Science and Technology, Daejeon 34113 Republic of Korea
| | - Seon-Young Kim
- Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Department of Biological Chemistry, Korea University of Science and Technology, Daejeon 34113 Republic of Korea
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69
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Tentori AM, Yamauchi KA, Herr AE. Detection of Isoforms Differing by a Single Charge Unit in Individual Cells. Angew Chem Int Ed Engl 2016; 55:12431-5. [PMID: 27595864 PMCID: PMC5201312 DOI: 10.1002/anie.201606039] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 11/10/2022]
Abstract
To measure protein isoforms in individual mammalian cells, we report single-cell resolution isoelectric focusing (scIEF) and high-selectivity immunoprobing. Microfluidic design and photoactivatable materials establish the tunable pH gradients required by IEF and precisely control the transport and handling of each 17-pL cell lysate during analysis. The scIEF assay resolves protein isoforms with resolution down to a single-charge unit, including both endogenous cytoplasmic and nuclear proteins from individual mammalian cells.
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Affiliation(s)
- Augusto M Tentori
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin A Yamauchi
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Amy E Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA.
- Department of Bioengineering, UC Berkeley, 308B Stanley Hall, Berkeley, CA, 94720, USA.
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70
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Tentori AM, Yamauchi KA, Herr AE. Detection of Isoforms Differing by a Single Charge Unit in Individual Cells. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Augusto M. Tentori
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA USA
| | - Kevin A. Yamauchi
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
| | - Amy E. Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
- Department of Bioengineering UC Berkeley 308B Stanley Hall Berkeley CA 94720 USA
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71
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Oh S, Kim HS. Emerging power of proteomics for delineation of intrinsic tumor subtypes and resistance mechanisms to anti-cancer therapies. Expert Rev Proteomics 2016; 13:929-939. [PMID: 27599289 DOI: 10.1080/14789450.2016.1233063] [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] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Despite extreme genetic heterogeneity, tumors often show similar alterations in the expression, stability, and activation of proteins important in oncogenic signaling pathways. Thus, classifying tumor samples according to shared proteomic features may help facilitate the identification of cancer subtypes predictive of therapeutic responses and prognostic for patient outcomes. Meanwhile, understanding mechanisms of intrinsic and acquired resistance to anti-cancer therapies at the protein level may prove crucial to devising reversal strategies. Areas covered: Herein, we review recent advances in quantitative proteomic technology and their applications in studies to identify intrinsic tumor subtypes of various tumors, to illuminate mechanistic aspects of pharmacological and oncogenic adaptations, and to highlight interaction targets for anti-cancer compounds and cancer-addicted proteins. Expert commentary: Quantitative proteomic technologies are being successfully employed to classify tumor samples into distinct intrinsic subtypes, to improve existing DNA/RNA based classification methods, and to evaluate the activation status of key signaling pathways.
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Affiliation(s)
- Sejin Oh
- a Brain Korea 21 Project for Medical Science, Severance Biomedical Science Institute , Yonsei University College of Medicine , Seoul , Korea
| | - Hyun Seok Kim
- a Brain Korea 21 Project for Medical Science, Severance Biomedical Science Institute , Yonsei University College of Medicine , Seoul , Korea
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72
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Sajjad W, Rafiq M, Ali B, Hayat M, Zada S, Sajjad W, Kumar T. Proteogenomics: New Emerging Technology. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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73
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Kim Y, Jeon J, Mejia S, Yao CQ, Ignatchenko V, Nyalwidhe JO, Gramolini AO, Lance RS, Troyer DA, Drake RR, Boutros PC, Semmes OJ, Kislinger T. Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer. Nat Commun 2016; 7:11906. [PMID: 27350604 PMCID: PMC4931234 DOI: 10.1038/ncomms11906] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 05/11/2016] [Indexed: 01/27/2023] Open
Abstract
Biomarkers are rapidly gaining importance in personalized medicine. Although numerous molecular signatures have been developed over the past decade, there is a lack of overlap and many biomarkers fail to validate in independent patient cohorts and hence are not useful for clinical application. For these reasons, identification of novel and robust biomarkers remains a formidable challenge. We combine targeted proteomics with computational biology to discover robust proteomic signatures for prostate cancer. Quantitative proteomics conducted in expressed prostatic secretions from men with extraprostatic and organ-confined prostate cancers identified 133 differentially expressed proteins. Using synthetic peptides, we evaluate them by targeted proteomics in a 74-patient cohort of expressed prostatic secretions in urine. We quantify a panel of 34 candidates in an independent 207-patient cohort. We apply machine-learning approaches to develop clinical predictive models for prostate cancer diagnosis and prognosis. Our results demonstrate that computationally guided proteomics can discover highly accurate non-invasive biomarkers. Proteomic technologies are capable of identifying thousands of proteins in biological samples, but biomarker applications are lagging. Here the authors use Multiple Reaction Monitoring Mass Spectrometry to delineate peptide signatures that accurately distinguish between defined prostate cancer patient risk groups.
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Affiliation(s)
- Yunee Kim
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Jouhyun Jeon
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 0A3
| | - Salvador Mejia
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Cindy Q Yao
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7.,Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 0A3
| | - Vladimir Ignatchenko
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5G 1L7
| | - Julius O Nyalwidhe
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, USA.,Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507-1627, USA
| | - Anthony O Gramolini
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Raymond S Lance
- Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507-1627, USA.,Department of Urology, Eastern Virginia Medical School, Norfolk, Virginia 23462, USA
| | - Dean A Troyer
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, USA.,Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507-1627, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7.,Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 0A3.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - O John Semmes
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23507, USA.,Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23507-1627, USA
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5G 1L7
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74
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Kuznetsova KG, Trufanov PV, Moysa AA, Pyatnitskiy MA, Zgoda VG, Gorshkov MV, Moshkovskii SA. Threonine versus isothreonine in synthetic peptides analyzed by high-resolution liquid chromatography/tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:1323-1331. [PMID: 27173114 DOI: 10.1002/rcm.7566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/15/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
RATIONALE One of the problems in proteogenomic research aimed at identification of variant peptides is the presence of peptides with amino acid isomers of different origin in the analyzed samples. Among the most challenging examples are peptides with threonine and isothreonine (homoserine) in their sequences. Indeed, the latter residue may appear in vitro as a methionine substitution during sample preparation for shotgun proteome analysis. Yet, this substitution of Met to isoThr is not encoded genetically and should be unambiguously distinguished from, e.g., point mutations in proteins that result in Met conversion to Thr. METHODS In this work we compared tandem mass (MS/MS) spectra produced by an Orbitrap mass spectrometer of Thr- and isoThr-containing tryptic peptides and found a distinctive feature in their collisionally activated fragmentation patterns. RESULTS Up to 84% of MS/MS spectra for peptides containing isoThr residues have been positively specified. We also studied the differences in retention times for peptides containing Thr isoforms that can be further used for their distinction. CONCLUSIONS Threonine can be distinguished from isothreonine by its retention time and HCD fragmentation pattern, specifically relative intensity of the bn - product ion, which can be further used in proteomic research. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Pavel V Trufanov
- Institute of Biomedical Chemistry, Moscow, Russia
- Moscow State University, Biological Faculty, Moscow, Russia
| | - Alexander A Moysa
- Institute of Biomedical Chemistry, Moscow, Russia
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Mikhail V Gorshkov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Sergei A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Medical University, Moscow, Russia
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75
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Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:521-45. [PMID: 27049631 PMCID: PMC4991544 DOI: 10.1146/annurev-anchem-071015-041722] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Mass spectrometry-based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.
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Affiliation(s)
- Gloria M Sheynkman
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706;
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76
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Trecate G, Sinues PML, Orlandi R. Noninvasive strategies for breast cancer early detection. Future Oncol 2016; 12:1395-411. [DOI: 10.2217/fon-2015-0071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Breast cancer screening and presurgical diagnosis are currently based on mammography, ultrasound and more sensitive imaging technologies; however, noninvasive biomarkers represent both a challenge and an opportunity for early detection of cancer. An extensive number of potential breast cancer biomarkers have been discovered by microarray hybridization or sequencing of circulating DNA, noncoding RNA and blood cell RNA; multiplex analysis of immune-related molecules and mass spectrometry-based approaches for high-throughput detection of protein, endogenous peptides, circulating and volatile metabolites. However, their medical relevance and their translation to clinics remain to be exploited. Once they will be fully validated, cancer biomarkers, used in combination with the current and emerging imaging technologies, represent an avenue to a personalized breast cancer diagnosis.
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Affiliation(s)
- Giovanna Trecate
- Department of Imaging Diagnosis & Radiotherapy, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Rosaria Orlandi
- Molecular Targeting Unit, Department of Experimental Oncology & Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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77
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Basu B, Basu S. Correlating and Combining Genomic and Proteomic Assessment with In Vivo Molecular Functional Imaging: Will This Be the Future Roadmap for Personalized Cancer Management? Cancer Biother Radiopharm 2016; 31:75-84. [DOI: 10.1089/cbr.2015.1922] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sandip Basu
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Mumbai, India
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78
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Locard-Paulet M, Pible O, Gonzalez de Peredo A, Alpha-Bazin B, Almunia C, Burlet-Schiltz O, Armengaud J. Clinical implications of recent advances in proteogenomics. Expert Rev Proteomics 2016; 13:185-99. [DOI: 10.1586/14789450.2016.1132169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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79
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Bartram MP, Habbig S, Pahmeyer C, Höhne M, Weber LT, Thiele H, Altmüller J, Kottoor N, Wenzel A, Krueger M, Schermer B, Benzing T, Rinschen MM, Beck BB. Three-layered proteomic characterization of a novel ACTN4 mutation unravels its pathogenic potential in FSGS. Hum Mol Genet 2016; 25:1152-64. [PMID: 26740551 DOI: 10.1093/hmg/ddv638] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 12/31/2015] [Indexed: 01/09/2023] Open
Abstract
Genetic diseases constitute the most important cause for end-stage renal disease in children and adolescents. Mutations in the ACTN4 gene, encoding the actin-binding protein α-actinin-4, are a rare cause of autosomal dominant familial focal segmental glomerulosclerosis (FSGS). Here, we report the identification of a novel, disease-causing ACTN4 mutation (p.G195D, de novo) in a sporadic case of childhood FSGS using next generation sequencing. Proteome analysis by quantitative mass spectrometry (MS) of patient-derived urinary epithelial cells indicated that ACTN4 levels were significantly decreased when compared with healthy controls. By resolving the peptide bearing the mutated residue, we could proof that the mutant protein is less abundant when compared with the wild-type protein. Further analyses revealed that the decreased stability of p.G195D is associated with increased ubiquitylation in the vicinity of the mutation site. We next defined the ACTN4 interactome, which was predominantly composed of cytoskeletal modulators and LIM domain-containing proteins. Interestingly, this entire group of proteins, including several highly specific ACTN4 interactors, was globally decreased in the patient-derived cells. Taken together, these data suggest a mechanistic link between ACTN4 instability and proteome perturbations of the ACTN4 interactome. Our findings advance the understanding of dominant effects exerted by ACTN4 mutations in FSGS. This study illustrates the potential of genomics and complementary, high-resolution proteomics analyses to study the pathogenicity of rare gene variants.
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Affiliation(s)
- Malte P Bartram
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Sandra Habbig
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Department of Pediatrics
| | - Caroline Pahmeyer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Martin Höhne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | | | | | | | | | | | - Marcus Krueger
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
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80
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Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames. Nat Commun 2016; 7:10238. [PMID: 26728094 PMCID: PMC4728431 DOI: 10.1038/ncomms10238] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 11/16/2015] [Indexed: 12/21/2022] Open
Abstract
In view of recent reports documenting pervasive translation outside of canonical protein-coding sequences, we wished to determine the proportion of major histocompatibility complex (MHC) class I-associated peptides (MAPs) derived from non-canonical reading frames. Here we perform proteogenomic analyses of MAPs eluted from human B cells using high-throughput mass spectrometry to probe the six-frame translation of the B-cell transcriptome. We report that ∼10% of MAPs originate from allegedly noncoding genomic sequences or exonic out-of-frame translation. The biogenesis and properties of these ‘cryptic MAPs' differ from those of conventional MAPs. Cryptic MAPs come from very short proteins with atypical C termini, and are coded by transcripts bearing long 3′UTRs enriched in destabilizing elements. Relative to conventional MAPs, cryptic MAPs display different MHC class I-binding preferences and harbour more genomic polymorphisms, some of which are immunogenic. Cryptic MAPs increase the complexity of the MAP repertoire and enhance the scope of CD8 T-cell immunosurveillance. Cryptic translation of the 'non-coding' genome is increasingly recognised, however its biological significance remains unclear. Laumont et al. employ proteogenomic techniques to map the human immunoproteome, and find that approximately 10% of MHC class I-associated peptides are cryptic.
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81
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Proteogenomic Analysis of Single Amino Acid Polymorphisms in Cancer Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 926:93-113. [PMID: 27686808 DOI: 10.1007/978-3-319-42316-6_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The integration of genomics and proteomics has led to the emergence of proteogenomics, a field of research successfully applied to the characterization of cancer samples. The diagnosis, prognosis and response to therapy of cancer patients will largely benefit from the identification of mutations present in their genome. The current state of the art of high throughput experiments for genome-wide detection of somatic mutations in cancer samples has allowed the development of projects such as the TCGA, in which hundreds of cancer genomes have been sequenced. This huge amount of data can be used to generate protein sequence databases in which each entry corresponds to a mutated peptide associated with certain cancer types. In this chapter, we describe a bioinformatics workflow for creating these databases and detecting mutated peptides in cancer samples from proteomic shotgun experiments. The performance of the proposed method has been evaluated using publicly available datasets from four cancer cell lines.
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82
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Proteogenomic Tools and Approaches to Explore Protein Coding Landscapes of Eukaryotic Genomes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 926:1-10. [DOI: 10.1007/978-3-319-42316-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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83
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Vaudel M, Barsnes H, Ræder H, Berven FS. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 926:65-75. [DOI: 10.1007/978-3-319-42316-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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84
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Wang X, Slebos RJC, Chambers MC, Tabb DL, Liebler DC, Zhang B. proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data. Mol Cell Proteomics 2015; 15:1164-75. [PMID: 26657539 PMCID: PMC4813696 DOI: 10.1074/mcp.m115.052860] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Indexed: 01/13/2023] Open
Abstract
To facilitate genome-based representation and analysis of proteomics data, we developed a new bioinformatics framework, proBAMsuite, in which a central component is the protein BAM (proBAM) file format for organizing peptide spectrum matches (PSMs)1 within the context of the genome. proBAMsuite also includes two R packages, proBAMr and proBAMtools, for generating and analyzing proBAM files, respectively. Applying proBAMsuite to three recently published proteomics datasets, we demonstrated its utility in facilitating efficient genome-based sharing, interpretation, and integration of proteomics data. First, the interpretation of proteomics data is significantly enhanced with the rich genomic annotation information. Second, PSMs can be easily reannotated using user-specified gene annotation schemes and assembled into both protein and gene identifications. Third, using the genome as a common reference, proBAMsuite facilitates seamless proteomics and proteogenomics data integration. Finally, proBAM files can be readily visualized in genome browsers and thus bring proteomics data analysis to a general audience beyond the proteomics community. Results from this study establish proBAMsuite as a useful bioinformatics framework for proteomics and proteogenomics research.
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Affiliation(s)
| | - Robbert J C Slebos
- §Department of Biochemistry, ¶Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232
| | | | - David L Tabb
- From the ‡Department of Biomedical Informatics, §Department of Biochemistry
| | - Daniel C Liebler
- From the ‡Department of Biomedical Informatics, §Department of Biochemistry, ¶Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232
| | - Bing Zhang
- From the ‡Department of Biomedical Informatics, ‖Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232;
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85
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Xu S, Zhou R, Ren Z, Zhou B, Lin Z, Hou G, Deng Y, Zi J, Lin L, Wang Q, Liu X, Xu X, Wen B, Liu S. Appraisal of the Missing Proteins Based on the mRNAs Bound to Ribosomes. J Proteome Res 2015; 14:4976-84. [PMID: 26500078 DOI: 10.1021/acs.jproteome.5b00476] [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] [Indexed: 11/30/2022]
Abstract
Considering the technical limitations of mass spectrometry in protein identification, the mRNAs bound to ribosomes (RNC-mRNA) are assumed to reflect the mRNAs participating in the translational process. The RNC-mRNA data are reasoned to be useful for appraising the missing proteins. A set of the multiomics data including free-mRNAs, RNC-mRNAs, and proteomes was acquired from three liver cancer cell lines. On the basis of the missing proteins in neXtProt (release 2014-09-19), the bioinformatics analysis was carried out in three phases: (1) finding how many neXtProt missing proteins have or do not have RNA-seq and/or MS/MS evidence, (2) analyzing specific physicochemical and biological properties of the missing proteins that lack both RNA-seq and MS/MS evidence, and (3) analyzing the combined properties of these missing proteins. Total of 1501 missing proteins were found by neither RNC-mRNA nor MS/MS in the three liver cancer cell lines. For these missing proteins, some are expected higher hydrophobicity, unsuitable detection, or sensory functions as properties at the protein level, while some are predicted to have nonexpressing chromatin structures on the corresponding gene level. With further integrated analysis, we could attribute 93% of them (1391/1501) to these causal factors, which result in the expression products scarcely detected by RNA-seq or MS/MS.
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Affiliation(s)
- Shaohang Xu
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Ruo Zhou
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Zhe Ren
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Baojin Zhou
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Zhilong Lin
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Guixue Hou
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , BeiChen West Road, Beijing 100101, China
| | - Yamei Deng
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , BeiChen West Road, Beijing 100101, China
| | - Jin Zi
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Liang Lin
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Quanhui Wang
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , BeiChen West Road, Beijing 100101, China
| | - Xin Liu
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Bo Wen
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Siqi Liu
- BGI-Shenzhen , 11 Build, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , BeiChen West Road, Beijing 100101, China
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86
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Shukla HD, Mahmood J, Vujaskovic Z. Integrated proteo-genomic approach for early diagnosis and prognosis of cancer. Cancer Lett 2015; 369:28-36. [DOI: 10.1016/j.canlet.2015.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/05/2015] [Accepted: 08/05/2015] [Indexed: 12/28/2022]
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87
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Kim YI, Lee J, Choi YJ, Seo J, Park J, Lee SY, Cho JY. Proteogenomic Study beyond Chromosome 9: New Insight into Expressed Variant Proteome and Transcriptome in Human Lung Adenocarcinoma Tissues. J Proteome Res 2015; 14:5007-16. [PMID: 26584007 DOI: 10.1021/acs.jproteome.5b00544] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This is a report of a human proteome project (HPP) related to chromosome 9 (Chr 9). To reveal missing proteins and undiscovered features in proteogenomes, both LC-MS/MS analysis and next-generation RNA sequencing (RNA-seq)-based identification and characterization were conducted on five pairs of lung adenocarcinoma tumors and adjacent nontumor tissues. Before our previous Chromosome-Centric Human Proteome Project (C-HPP) special issue, there were 170 remaining missing proteins on Chr 9 (neXtProt 2013.09.26 rel.); 133 remain at present (neXtProt 2015.04.28 rel.). In the proteomics study, we found two missing protein candidates that require follow-up work and one unrevealed protein across all chromosomes. RNA-seq analysis detected RNA expression for four nonsynonymous (NS) single nucleotide polymorphisms (SNPs) (in CDH17, HIST1H1T, SAPCD2, and ZNF695) and three synonymous SNPs (in CDH17, CST1, and HNF1A) in all five tumor tissues but not in any of the adjacent normal tissues. By constructing a cancer patient sample-specific protein database based on individual RNA-seq data and by searching the proteomics data from the same sample, we identified four missense mutations in four genes (LTF, HDLBP, TF, and HBD). Two of these mutations were found in tumor samples but not in paired normal tissues. In summary, our proteogenomic study of human primary lung tumor tissues detected additional and revealed novel missense mutations and synonymous SNP signatures, some of which are specific to lung cancers. Data from mass spectrometry have been deposited in the ProteomeXchange with the identifier PXD002523.
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Affiliation(s)
- Yong-In Kim
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, South Korea
| | - Jongan Lee
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, South Korea
| | - Young-Jin Choi
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, South Korea.,ProtAnBio , Seoul 08826, South Korea
| | - Jawon Seo
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, South Korea
| | - Jisook Park
- Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, South Korea
| | - Soo-Youn Lee
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, South Korea.,Department of Clinical Pharmacology & Therapeutics, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul 06351, South Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 PLUS Program for Creative Veterinary Science Research and Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University , Seoul 08826, South Korea
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88
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Low TY, Heck AJ. Reconciling proteomics with next generation sequencing. Curr Opin Chem Biol 2015; 30:14-20. [PMID: 26590485 DOI: 10.1016/j.cbpa.2015.10.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
Both genomics and proteomics technologies have matured in the last decade to a level where they are able to deliver system-wide data on the qualitative and quantitative abundance of their respective molecular entities, that is DNA/RNA and proteins. A next logical step is the collective use of these technologies, ideally gathering data on matching samples. The first large scale so-called proteogenomics studies are emerging, and display the benefits each of these layers of analysis has on the other layers to together generate more meaningful insight into the connection between the phenotype/physiology and genotype of the system under study. Here we review a selected number of these studies, highlighting what they can uniquely deliver. We also discuss the future potential and remaining challenges, from a somewhat proteome biased perspective.
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Affiliation(s)
- Teck Yew Low
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert Jr Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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89
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Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB. A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma. PLoS One 2015; 10:e0142162. [PMID: 26539827 PMCID: PMC4634858 DOI: 10.1371/journal.pone.0142162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/19/2015] [Indexed: 11/19/2022] Open
Abstract
We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma. Data are available via ProteomeXchange with identifier PXD002622.
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Affiliation(s)
- Paul A. Stewart
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Katja Parapatics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Eric A. Welsh
- Cancer Informatics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - André C. Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Haoyun Cao
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - John M. Koomen
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Steven A. Eschrich
- Cancer Informatics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
| | - Keiryn L. Bennett
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090 Vienna, Austria
| | - Eric B. Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America 33612
- * E-mail:
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90
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Reich HN, Sabelnykova VY, Boutros PC. Matching Kidneys and Urines: Establishing Noninvasive Surrogates of Intrarenal Events in Primary Glomerulonephritis. Semin Nephrol 2015. [PMID: 26215863 DOI: 10.1016/j.semnephrol.2015.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Kidney biopsy is the gold standard procedure for providing diagnostic and prognostic information for patients with glomerular-based diseases, however, the utility of this procedure for assessing longitudinal disease activity is limited. The intense search for noninvasive biomarkers of kidney disease activity and injury is driven in large part by the inherent risks of the kidney biopsy procedure and limited information derived from the morphologic description of biopsy findings. Furthermore, gaps in our understanding of the core intrarenal molecular processes underlying the development and progression of glomerular-based diseases has limited the development of effective targeted therapy. In this review, we discuss the potential utility of molecular analysis of the urine to provide a dynamic window into intrarenal molecular and morphologic responses. We focus on molecular analysis of the urine to identify noninvasive surrogate markers of kidney responses, with the goal of using these biomarkers as more sensitive indicators of progression and tissue-level responses to therapeutic interventions in patients with primary glomerulonephritis.
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Affiliation(s)
- Heather N Reich
- The Toronto Glomerulonephritis Registry, University Health Network, Gabor Zellerman Chair in Nephrology Research at the University of Toronto Department of Medicine, Toronto, Ontario, Canada.
| | - Veronica Y Sabelnykova
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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91
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Boellner S, Becker KF. Recent progress in protein profiling of clinical tissues for next-generation molecular diagnostics. Expert Rev Mol Diagn 2015. [DOI: 10.1586/14737159.2015.1070098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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92
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Nagy PL, Mansukhani M. The role of clinical genomic testing in diagnosis and discovery of pathogenic mutations. Expert Rev Mol Diagn 2015. [PMID: 26202666 DOI: 10.1586/14737159.2015.1071667] [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: 11/08/2022]
Abstract
Next-generation sequencing in clinical practice allows for a critical review of the literature to evaluate disease relatedness of specific genes and pathogenicity of individual mutations, while providing an important discovery tool for new disease genes and disease-causing mutations. Data obtained from large panels, whole exome or whole genome sequencing, performed for constitutional or cancer cases, need to be managed in a transparent, yet powerful analytical framework. Assessment of reported pathogenic potential of a variant or disease association of a gene requires careful consideration of population allele frequency, variant data from parents, and precise, yet concise phenotypic description of the entire family and other individuals or families that have the same variant. The full potential for discovery can only be realized if there is data sharing between clinicians performing the interpretation worldwide and structural biologists, analytical chemists and cell biologists interested and knowledgeable of the structure and function of the genes involved.
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Affiliation(s)
- Peter L Nagy
- a Department of Pathology and Cell Biology, Columbia University, Laboratory of Personalized Genomic Medicine, 630 West 168 Street, 10032, New York, NY, USA
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93
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Polyakova A, Kuznetsova K, Moshkovskii S. Proteogenomics meets cancer immunology: mass spectrometric discovery and analysis of neoantigens. Expert Rev Proteomics 2015; 12:533-41. [DOI: 10.1586/14789450.2015.1070100] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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94
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Methionine to isothreonine conversion as a source of false discovery identifications of genetically encoded variants in proteogenomics. J Proteomics 2015; 120:169-78. [DOI: 10.1016/j.jprot.2015.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 03/03/2015] [Accepted: 03/07/2015] [Indexed: 01/07/2023]
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95
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Onco-proteogenomics identifies urinary S100A9 and GRN as potential combinatorial biomarkers for early diagnosis of hepatocellular carcinoma. BBA CLINICAL 2015; 3:205-13. [PMID: 26675302 PMCID: PMC4669941 DOI: 10.1016/j.bbacli.2015.02.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC), the major type of liver cancer, is among the most lethal cancers owing to its aggressive nature and frequently late detection. Therefore, the possibility to identify early diagnostic markers could be of significant benefit. Urine has especially become one of the most attractive body fluids in biomarker discovery as it can be obtained non-invasively in large quantities and is stable as compared with other body fluids. To identify potential protein biomarker for early diagnosis of HCC, we explored protein expression profiles in urine from HCC patients and normal controls (n = 44) by shotgun proteomics using nano-liquid chromatography coupled tandem mass spectrometry (nanoLC–MS/MS) and stable isotope dimethyl labeling. We have systematically mapped 91 proteins with differential expressions (p < 0.05), which included 8 down-regulated microtubule proteins and 83 up-regulated proteins involved in signal and inflammation response. Further integrated proteogenomic approach composed of proteomic, genomic and transcriptomic analysis identified that S100A9 and GRN were co-amplified (p < 0.001) and co-expressed (p < 0.01) in HCC tumors and urine samples. In addition, the amplifications of S100A9 or GRN were found to be associated with poor survival in HCC patients, and their co-amplification was also prognosed worse overall survival than individual ones. Our results suggest that urinary S100A9 and GRN as potential combinatorial biomarkers can be applied to early diagnosis of hepatocellular carcinoma and highlight the utility of onco-proteogenomics for identifying protein markers that can be applied to disease-oriented translational medicine. An integrated proteogenomic analysis is applied to identify biomarkers for HCC. Genomic amplifications of S100A9 and GRN co-occur in tumors from HCC patients. S100A9 and GRN are co-expressed in tumor and urine samples from HCC patients. Amplifications of S100A9 and GRN are associated with poor survival of HCC patients.
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96
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Faulkner S, Dun MD, Hondermarck H. Proteogenomics: emergence and promise. Cell Mol Life Sci 2015; 72:953-7. [PMID: 25609363 PMCID: PMC11113406 DOI: 10.1007/s00018-015-1837-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/08/2015] [Accepted: 01/12/2015] [Indexed: 12/14/2022]
Abstract
Proteogenomics, or the integration of proteomics with genomics and transcriptomics, is emerging as the next step towards a unified understanding of cellular functions. Looking globally and simultaneously at gene structure, RNA expression, protein synthesis and post-translational modifications have become technically feasible and offer a new perspective to molecular processes. Recent publications have highlighted the value of proteogenomics in oncology for defining the molecular signature of human tumors, and translation to other areas of biomedicine and life sciences is anticipated. This mini-review will discuss recent developments, challenges and perspectives in proteogenomics.
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Affiliation(s)
- Sam Faulkner
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy and Hunter Medical Research Institute, Life Science Building, University of Newcastle, Callaghan, NSW 2308 Australia
| | - Matthew D. Dun
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy and Hunter Medical Research Institute, Life Science Building, University of Newcastle, Callaghan, NSW 2308 Australia
| | - Hubert Hondermarck
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy and Hunter Medical Research Institute, Life Science Building, University of Newcastle, Callaghan, NSW 2308 Australia
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97
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Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nat Methods 2015; 11:1114-25. [PMID: 25357241 DOI: 10.1038/nmeth.3144] [Citation(s) in RCA: 505] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/22/2014] [Indexed: 12/19/2022]
Abstract
Proteogenomics is an area of research at the interface of proteomics and genomics. In this approach, customized protein sequence databases generated using genomic and transcriptomic information are used to help identify novel peptides (not present in reference protein sequence databases) from mass spectrometry-based proteomic data; in turn, the proteomic data can be used to provide protein-level evidence of gene expression and to help refine gene models. In recent years, owing to the emergence of new sequencing technologies such as RNA-seq and dramatic improvements in the depth and throughput of mass spectrometry-based proteomics, the pace of proteogenomic research has greatly accelerated. Here I review the current state of proteogenomic methods and applications, including computational strategies for building and using customized protein sequence databases. I also draw attention to the challenge of false positive identifications in proteogenomics and provide guidelines for analyzing the data and reporting the results of proteogenomic studies.
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Affiliation(s)
- Alexey I Nesvizhskii
- 1] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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98
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Alfaro JA, Sinha A, Kislinger T, Boutros PC. Erratum: Onco-proteogenomics: cancer proteomics joins forces with genomics. Nat Methods 2015. [DOI: 10.1038/nmeth0215-160b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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99
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Sepiashvili L, Waggott D, Hui A, Shi W, Su S, Ignatchenko A, Ignatchenko V, Laureano M, Huang SH, Xu W, Weinreb I, Waldron J, O'Sullivan B, Irish JC, Boutros PC, Liu FF, Kislinger T. Integrated omic analysis of oropharyngeal carcinomas reveals human papillomavirus (HPV)-dependent regulation of the activator protein 1 (AP-1) pathway. Mol Cell Proteomics 2014; 13:3572-84. [PMID: 25271301 DOI: 10.1074/mcp.m114.041764] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
HPV-positive oropharyngeal carcinoma (OPC) patients have superior outcomes relative to HPV-negative patients, but the underlying mechanisms remain poorly understood. We conducted a proteomic investigation of HPV-positive (n = 27) and HPV-negative (n = 26) formalin-fixed paraffin-embedded OPC biopsies to acquire insights into the biological pathways that correlate with clinical behavior. Among the 2,633 proteins identified, 174 were differentially abundant. These were enriched for proteins related to cell cycle, DNA replication, apoptosis, and immune response. The differential abundances of cortactin and methylthioadenosine phosphorylase were validated by immunohistochemistry in an independent cohort of 29 OPC samples (p = 0.023 and p = 0.009, respectively). An additional 1,124 proteins were independently corroborated through comparison to a published proteomic dataset of OPC. Furthermore, utilizing the Cancer Genome Atlas, we conducted an integrated investigation of OPC, attributing mechanisms underlying differential protein abundances to alterations in mutation, copy number, methylation, and mRNA profiles. A key finding of this integration was the identification of elevated cortactin oncoprotein levels in HPV-negative OPCs. These proteins might contribute to reduced survival in these patients via their established role in radiation resistance. Through interrogation of Cancer Genome Atlas data, we demonstrated that activation of the β1-integrin/FAK/cortactin/JNK1 signaling axis and associated differential regulation of activator protein 1 transcription factor target genes are plausible consequences of elevated cortactin protein levels.
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Affiliation(s)
- Lusia Sepiashvili
- From the ‡Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7; §Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5T 2M9
| | - Daryl Waggott
- ¶Informatics & Biocomputing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 0A3
| | - Angela Hui
- §Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5T 2M9
| | - Wei Shi
- §Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5T 2M9
| | - Susie Su
- ‖Division of Biostatistics, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Alex Ignatchenko
- §Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5T 2M9
| | - Vladimir Ignatchenko
- §Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5T 2M9
| | - Marissa Laureano
- §Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5T 2M9
| | - Shao Hui Huang
- **Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Wei Xu
- ‖Division of Biostatistics, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Ilan Weinreb
- ‡‡Department of Pathology, University of Toronto, Toronto, Ontario, Canada M5G 2C4
| | - John Waldron
- **Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Brian O'Sullivan
- **Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Jonathan C Irish
- §§Department of Surgery, University of Toronto, Toronto, Ontario, Canada M5G 2M9
| | - Paul C Boutros
- From the ‡Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7; ¶Informatics & Biocomputing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada M5G 0A3; ¶¶Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada M5G 0A3
| | - Fei-Fei Liu
- From the ‡Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7; §Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5T 2M9; **Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada M5G 2M9;
| | - Thomas Kislinger
- From the ‡Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada M5G 1L7; §Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada M5T 2M9;
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