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Xu T, Wang Q, Wang Q, Sun L. Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4664-4682. [PMID: 38973469 PMCID: PMC11257149 DOI: 10.1039/d4ay00651h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
Proteoforms are all forms of protein molecules from the same gene because of variations at the DNA, RNA, and protein levels, e.g., alternative splicing and post-translational modifications (PTMs). Delineation of proteins in a proteoform-specific manner is crucial for understanding their biological functions. Mass spectrometry (MS)-intensive top-down proteomics (TDP) is promising for comprehensively characterizing intact proteoforms in complex biological systems. It has achieved substantial progress in technological development, including sample preparation, proteoform separations, MS instrumentation, and bioinformatics tools. In a single TDP study, thousands of proteoforms can be identified and quantified from a cell lysate. It has also been applied to various biomedical research to better our understanding of protein function in regulating cellular processes and to discover novel proteoform biomarkers of diseases for early diagnosis and therapeutic development. This review covers the most recent technological development and biomedical applications of MS-intensive TDP.
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Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
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2
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Roberts DS, Loo JA, Tsybin YO, Liu X, Wu S, Chamot-Rooke J, Agar JN, Paša-Tolić L, Smith LM, Ge Y. Top-down proteomics. NATURE REVIEWS. METHODS PRIMERS 2024; 4:38. [PMID: 39006170 PMCID: PMC11242913 DOI: 10.1038/s43586-024-00318-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 07/16/2024]
Abstract
Proteoforms, which arise from post-translational modifications, genetic polymorphisms and RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is essential to unravel the intricacies of biological systems and bridge the gap between genotypes and phenotypes. By analysing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and can decipher protein function, uncover disease mechanisms and advance precision medicine. This Primer explores TDP, including the underlying principles, recent advances and an outlook on the future. The experimental section discusses instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques and data collection. The results section looks at how to decipher raw data, visualize intact protein spectra and unravel data analysis. Additionally, proteoform identification, characterization and quantification are summarized, alongside approaches for statistical analysis. Various applications are described, including the human proteoform project and biomedical, biopharmaceutical and clinical sciences. These are complemented by discussions on measurement reproducibility, limitations and a forward-looking perspective that outlines areas where the field can advance, including potential future applications.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California - Los Angeles, Los Angeles, CA, USA
| | | | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
| | | | - Jeffrey N Agar
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
- Department of Cell and Regenerative Biology, Human Proteomics Program, University of Wisconsin - Madison, Madison, WI, USA
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3
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Sadeghi S, Chen W, Wang Q, Wang Q, Fang F, Liu X, Sun L. Pilot Evaluation of the Long-Term Reproducibility of Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Top-Down Proteomics of a Complex Proteome Sample. J Proteome Res 2024; 23:1399-1407. [PMID: 38417052 PMCID: PMC11002928 DOI: 10.1021/acs.jproteome.3c00872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/01/2024]
Abstract
Mass spectrometry (MS)-based top-down proteomics (TDP) has revolutionized biological research by measuring intact proteoforms in cells, tissues, and biofluids. Capillary zone electrophoresis-tandem MS (CZE-MS/MS) is a valuable technique for TDP, offering a high peak capacity and sensitivity for proteoform separation and detection. However, the long-term reproducibility of CZE-MS/MS in TDP remains unstudied, which is a crucial aspect for large-scale studies. This work investigated the long-term qualitative and quantitative reproducibility of CZE-MS/MS for TDP for the first time, focusing on a yeast cell lysate. Over 1000 proteoforms were identified per run across 62 runs using one linear polyacrylamide (LPA)-coated separation capillary, highlighting the robustness of the CZE-MS/MS technique. However, substantial decreases in proteoform intensity and identification were observed after some initial runs due to proteoform adsorption onto the capillary inner wall. To address this issue, we developed an efficient capillary cleanup procedure using diluted ammonium hydroxide, achieving high qualitative and quantitative reproducibility for the yeast sample across at least 23 runs. The data underscore the capability of CZE-MS/MS for large-scale quantitative TDP of complex samples, signaling its readiness for deployment in broad biological applications. The MS RAW files were deposited in ProteomeXchange Consortium with the data set identifier of PXD046651.
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Affiliation(s)
- Seyed
Amirhossein Sadeghi
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Wenrong Chen
- Department
of BioHealth Informatics, Indiana University-Purdue
University Indianapolis, 535 W Michigan Street, Indianapolis, Indiana 46202, United States
| | - Qianyi Wang
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianjie Wang
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Fei Fang
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Xiaowen Liu
- Deming
Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, Louisiana 70112, United States
| | - Liangliang Sun
- Department
of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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4
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Huang CF, Kline JT, Negrão F, Robey MT, Toby TK, Durbin KR, Fellers RT, Friedewald JJ, Levitsky J, Abecassis MMI, Melani RD, Kelleher NL, Fornelli L. Targeted Quantification of Proteoforms in Complex Samples by Proteoform Reaction Monitoring. Anal Chem 2024; 96:3578-3586. [PMID: 38354049 PMCID: PMC11008684 DOI: 10.1021/acs.analchem.3c05578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Existing mass spectrometric assays used for sensitive and specific measurements of target proteins across multiple samples, such as selected/multiple reaction monitoring (SRM/MRM) or parallel reaction monitoring (PRM), are peptide-based methods for bottom-up proteomics. Here, we describe an approach based on the principle of PRM for the measurement of intact proteoforms by targeted top-down proteomics, termed proteoform reaction monitoring (PfRM). We explore the ability of our method to circumvent traditional limitations of top-down proteomics, such as sensitivity and reproducibility. We also introduce a new software program, Proteoform Finder (part of ProSight Native), specifically designed for the easy analysis of PfRM data. PfRM was initially benchmarked by quantifying three standard proteins. The linearity of the assay was shown over almost 3 orders of magnitude in the femtomole range, with limits of detection and quantification in the low femtomolar range. We later applied our multiplexed PfRM assay to complex samples to quantify biomarker candidates in peripheral blood mononuclear cells (PBMCs) from liver-transplanted patients, suggesting their possible translational applications. These results demonstrate that PfRM has the potential to contribute to the accurate quantification of protein biomarkers for diagnostic purposes and to improve our understanding of disease etiology at the proteoform level.
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Affiliation(s)
- Che-Fan Huang
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Jake T Kline
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Fernanda Negrão
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew T Robey
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - Timothy K Toby
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Kenneth R Durbin
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - Ryan T Fellers
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteinaceous, Inc., Evanston, Illinois 60201, United States
| | - John J Friedewald
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Josh Levitsky
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Michael M I Abecassis
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Luca Fornelli
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma 73019, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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5
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Kaczmarczyk JA, Whiteley GR, Blonder J. Detection and Quantitation of Endogenous Membrane-Bound RAS Proteins and KRAS Mutants in Cancer Cell Lines Using 1D-SDS-PAGE LC-MS 2. Methods Mol Biol 2024; 2823:269-289. [PMID: 39052226 DOI: 10.1007/978-1-0716-3922-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
In healthy cells, membrane-anchored wild-type RAS proteins (i.e., HRAS, KRAS4A, KRAS4B, and NRAS) regulate critical cellular processes (e.g., proliferation, differentiation, survival). When mutated, RAS proteins are principal oncogenic drivers in approximately 30% of all human cancers. Among them, KRAS mutants are found in nearly 80% of all patients diagnosed with RAS-driven malignancies and are regarded as high-priority anti-cancer drug targets. Due to the lack of highly qualified/specific RAS isoform and mutant RAS monoclonal antibodies, there is a vital need for an effective antibody-free approach capable of identifying and quantifying membrane-bound RAS proteins in isoform- and mutation-specific manner. Here, we describe the development of a simple antibody-free protocol that relies on ultracentrifugation to isolate the membrane fraction coupled with single-dimensional (1D) sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to fractionate and enrich membrane-bound endogenous RAS isoforms. Next, bottom-up proteomics that utilizes in-gel digestion followed by reversed-phase high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS2) is used for detection and relative quantitation of all wild-type RAS proteins (i.e., HRAS, KRAS4A, KRAS4B, and NRAS) and corresponding RAS mutants (e.g., G12D, G13D, G12S, G12V). Notably, this simple 1D-SDS-PAGE-HPLC-MS2-based protocol can be automated and widely applied to multiple cancer cell lines to investigate concentration changes in membrane-bound endogenous RAS proteins and corresponding mutants in the context of drug discovery.
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Affiliation(s)
- Jan A Kaczmarczyk
- Meso Scale Diagnostics, Rockville, MD, USA.
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Gordon R Whiteley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Josip Blonder
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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6
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D'Ippolito RA, Scheidemantle GM, Smith BP, Powell K, Eury S, Neish A, Mehalko J, Beaumont L, Fer N, Wall V, Burgan W, Maciag AE, Esposito D, DeHart CJ. FLAG-KRAS4B as a Model System for KRAS4B Proteoform and PTM Evaluation by Mass Spectrometry. Methods Mol Biol 2024; 2797:299-322. [PMID: 38570469 DOI: 10.1007/978-1-0716-3822-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Prior analysis of intact and modified protein forms (proteoforms) of KRAS4B isolated from cell lines and tumor samples by top-down mass spectrometry revealed the presence of novel posttranslational modifications (PTMs) and potential evidence of context-specific KRAS4B modifications. However, low endogenous proteoform signal resulted in ineffective characterization, making it difficult to visualize less abundant PTMs or perform follow-up PTM validation using standard proteomic workflows. The NCI RAS Initiative has developed a model system, whereby KRAS4B bearing an N-terminal FLAG tag can be stably expressed within a panel of cancer cell lines. Herein, we present a method for combining immunoprecipitation with complementary proteomic methods to directly analyze N-terminally FLAG-tagged KRAS4B proteoforms and PTMs. We provide detailed protocols for FLAG-KRAS4B purification, proteoform analysis by targeted top-down LC-MS/MS, and validation of abundant PTMs by bottom-up LC-MS/MS with example results.
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Affiliation(s)
- Robert A D'Ippolito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Grace M Scheidemantle
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brian P Smith
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Katie Powell
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott Eury
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Abigail Neish
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jennifer Mehalko
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lauren Beaumont
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nicole Fer
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vanessa Wall
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William Burgan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anna E Maciag
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Caroline J DeHart
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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7
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D'Ippolito RA, Scheidemantle GM, Rabara D, Abreu Blanco M, Ramakrishnan N, Widmeyer SRT, Messing S, Turner D, Maciag AE, Stephen AG, Esposito D, McCormick F, Nissley DV, DeHart CJ. Determining KRAS4B-Targeting Compound Specificity by Top-Down Mass Spectrometry. Methods Mol Biol 2024; 2823:291-310. [PMID: 39052227 DOI: 10.1007/978-1-0716-3922-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
We present a novel method to determine engagement and specificity of KRAS4B-targeting compounds in vitro. By employing top-down mass spectrometry (MS), which analyzes intact and modified protein molecules (proteoforms), we can directly visualize and confidently characterize each KRAS4B species within compound-treated samples. Moreover, by employing targeted MS2 fragmentation, we can precisely localize each compound molecule to a specific residue on a given KRAS4B proteoform. This method allows us to comprehensively evaluate compound specificity, clearly detect nonspecific binding events, and determine the order and frequency with which they occur. We provide two proof-of-concept examples of our method employing publicly available compounds, along with detailed protocols for sample preparation, top-down MS data acquisition, targeted proteoform MS2 fragmentation, and analysis of the resulting data. Our results demonstrate the concentration dependence of KRAS4B-compound engagement and highlight the ability of top-down MS to directly map compound binding location(s) without disrupting the KRAS4B primary structure. Our hope is that this novel method may help accelerate the identification of new successful targeted inhibitors for KRAS4B and other RAS isoforms.
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Affiliation(s)
- Robert A D'Ippolito
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Grace M Scheidemantle
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dana Rabara
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maria Abreu Blanco
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nitya Ramakrishnan
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephanie R T Widmeyer
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simon Messing
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - David Turner
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anna E Maciag
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dominic Esposito
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Frank McCormick
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Caroline J DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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8
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Guil-Luna S, Sanchez-Montero MT, Rodríguez-Ariza A. S-Nitrosylation at the intersection of metabolism and autophagy: Implications for cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:189012. [PMID: 37918453 DOI: 10.1016/j.bbcan.2023.189012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Metabolic plasticity, which determines tumour growth and metastasis, is now understood to be a flexible and context-specific process in cancer metabolism. One of the major pathways contributing to metabolic adaptations in eucaryotic cells is autophagy, a cellular degradation and recycling process that is activated during periods of starvation or stress to maintain metabolite and biosynthetic intermediate levels. Consequently, there is a close association between the metabolic adaptive capacity of tumour cells and autophagy-related pathways in cancer. Additionally, nitric oxide regulates protein function and signalling through S-nitrosylation, a post-translational modification that can also impact metabolism and autophagy. The primary objective of this review is to provide an up-to-date overview of the role of S-nitrosylation at the intersection of metabolism and autophagy in cancer. First, we will outline the involvement of S-nitrosylation in the metabolic adaptations that occur in tumours. Then, we will discuss the multifaceted role of autophagy in cancer, the interplay between metabolism and autophagy during tumour progression, and the contribution of S-nitrosylation to autophagic dysregulation in cancer. Finally, we will present insights into relevant therapeutic aspects and discuss prospects for the future.
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Affiliation(s)
- Silvia Guil-Luna
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain; Department of Comparative Anatomy and Pathology, Faculty of Veterinary Medicine of Córdoba, University of Córdoba, Córdoba, Spain
| | | | - Antonio Rodríguez-Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain; Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain.
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9
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Chambers AG, Chain DC, Sweet SM, Song Z, Martin PL, Ellis MJ, Rooney C, Kim YJ. Mass spectrometry quantifies target engagement for a KRASG12C inhibitor in FFPE tumor tissue. Clin Proteomics 2023; 20:47. [PMID: 37880622 PMCID: PMC10599008 DOI: 10.1186/s12014-023-09435-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Quantification of drug-target binding is critical for confirming that drugs reach their intended protein targets, understanding the mechanism of action, and interpreting dose-response relationships. For covalent inhibitors, target engagement can be inferred by free target levels before and after treatment. Targeted mass spectrometry assays offer precise protein quantification in complex biological samples and have been routinely applied in pre-clinical studies to quantify target engagement in frozen tumor tissues for oncology drug development. However, frozen tissues are often not available from clinical trials so it is critical that assays are applicable to formalin-fixed, paraffin-embedded (FFPE) tissues in order to extend mass spectrometry-based target engagement studies into clinical settings. METHODS Wild-type RAS and RASG12C was quantified in FFPE tissues by a highly optimized targeted mass spectrometry assay that couples high-field asymmetric waveform ion mobility spectrometry (FAIMS) and parallel reaction monitoring (PRM) with internal standards. In a subset of samples, technical reproducibility was evaluated by analyzing consecutive tissue sections from the same tumor block and biological variation was accessed among adjacent tumor regions in the same tissue section. RESULTS Wild-type RAS protein was measured in 32 clinical non-small cell lung cancer tumors (622-2525 amol/µg) as measured by FAIMS-PRM mass spectrometry. Tumors with a known KRASG12C mutation (n = 17) expressed a wide range of RASG12C mutant protein (127-2012 amol/µg). The variation in wild-type RAS and RASG12C measurements ranged 0-18% CV across consecutive tissue sections and 5-20% CV among adjacent tissue regions. Quantitative target engagement was then demonstrated in FFPE tissues from 2 xenograft models (MIA PaCa-2 and NCI-H2122) treated with a RASG12C inhibitor (AZD4625). CONCLUSIONS This work illustrates the potential to expand mass spectrometry-based proteomics in preclinical and clinical oncology drug development through analysis of FFPE tumor biopsies.
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Affiliation(s)
- Andrew G Chambers
- Early Oncology, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - David C Chain
- Early Oncology, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Steve M Sweet
- Early Oncology, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Zifeng Song
- Early Oncology, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Philip L Martin
- Early Oncology, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | - Matthew J Ellis
- Early Oncology, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA
| | | | - Yeoun Jin Kim
- Early Oncology, AstraZeneca, One MedImmune Way, Gaithersburg, MD, 20878, USA.
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10
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Jin L, Wang F, Wang X, Harvey BP, Bi Y, Hu C, Cui B, Darcy AT, Maull JW, Phillips BR, Kim Y, Jenkins GJ, Sornasse TR, Tian Y. Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All THeoretical Mass Spectra (SWATH) Proteomics Workflow. Proteomes 2023; 11:32. [PMID: 37873874 PMCID: PMC10594463 DOI: 10.3390/proteomes11040032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune and inflammatory disease. Plasma biomarkers are critical for understanding disease mechanisms, treatment effects, and diagnosis. Mass spectrometry-based proteomics is a powerful tool for unbiased biomarker discovery. However, plasma proteomics is significantly hampered by signal interference from high-abundance proteins, low overall protein coverage, and high levels of missing data from data-dependent acquisition (DDA). To achieve quantitative proteomics analysis for plasma samples with a balance of throughput, performance, and cost, we developed a workflow incorporating plate-based high abundance protein depletion and sample preparation, comprehensive peptide spectral library building, and data-independent acquisition (DIA) SWATH mass spectrometry-based methodology. In this study, we analyzed plasma samples from both RA patients and healthy donors. The results showed that the new workflow performance exceeded that of the current state-of-the-art depletion-based plasma proteomic platforms in terms of both data quality and proteome coverage. Proteins from biological processes related to the activation of systemic inflammation, suppression of platelet function, and loss of muscle mass were enriched and differentially expressed in RA. Some plasma proteins, particularly acute-phase reactant proteins, showed great power to distinguish between RA patients and healthy donors. Moreover, protein isoforms in the plasma were also analyzed, providing even deeper proteome coverage. This workflow can serve as a basis for further application in discovering plasma biomarkers of other diseases.
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Affiliation(s)
- Liang Jin
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Fei Wang
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Xue Wang
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Bohdan P. Harvey
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Yingtao Bi
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Chenqi Hu
- DMPK, Takeda Development Center Americas Inc., Cambridge, MA 02142, USA; (C.H.)
| | - Baoliang Cui
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Anhdao T. Darcy
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - John W. Maull
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Ben R. Phillips
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Youngjae Kim
- DMPK, Takeda Development Center Americas Inc., Cambridge, MA 02142, USA; (C.H.)
| | - Gary J. Jenkins
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Thierry R. Sornasse
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
| | - Yu Tian
- Research & Development, AbbVie, North Chicago, IL 60064, USA; (L.J.); (B.P.H.); (B.C.); (A.T.D.); (J.W.M.); (T.R.S.)
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11
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Kitamura N, Galligan JJ. A global view of the human post-translational modification landscape. Biochem J 2023; 480:1241-1265. [PMID: 37610048 PMCID: PMC10586784 DOI: 10.1042/bcj20220251] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Post-translational modifications (PTMs) provide a rapid response to stimuli, finely tuning metabolism and gene expression and maintain homeostasis. Advances in mass spectrometry over the past two decades have significantly expanded the list of known PTMs in biology and as instrumentation continues to improve, this list will surely grow. While many PTMs have been studied in detail (e.g. phosphorylation, acetylation), the vast majority lack defined mechanisms for their regulation and impact on cell fate. In this review, we will highlight the field of PTM research as it currently stands, discussing the mechanisms that dictate site specificity, analytical methods for their detection and study, and the chemical tools that can be leveraged to define PTM regulation. In addition, we will highlight the approaches needed to discover and validate novel PTMs. Lastly, this review will provide a starting point for those interested in PTM biology, providing a comprehensive list of PTMs and what is known regarding their regulation and metabolic origins.
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Affiliation(s)
- Naoya Kitamura
- Department of Pharmacology and College of Pharmacy, University of Arizona, Tucson, Arizona 85721, U.S.A
| | - James J. Galligan
- Department of Pharmacology and College of Pharmacy, University of Arizona, Tucson, Arizona 85721, U.S.A
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12
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Wang Q, Fang F, Sun L. Pilot investigation of magnetic nanoparticle-based immobilized metal affinity chromatography for efficient enrichment of phosphoproteoforms for mass spectrometry-based top-down proteomics. Anal Bioanal Chem 2023; 415:4521-4531. [PMID: 37017721 PMCID: PMC10540245 DOI: 10.1007/s00216-023-04677-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/06/2023]
Abstract
Protein phosphorylation is a vital and common post-translational modification (PTM) in cells, modulating various biological processes and diseases. Comprehensive top-down proteomics of phosphorylated proteoforms (phosphoproteoforms) in cells and tissues is essential for a better understanding of the roles of protein phosphorylation in fundamental biological processes and diseases. Mass spectrometry (MS)-based top-down proteomics of phosphoproteoforms remains challenging due to their relatively low abundance. Herein, we investigated magnetic nanoparticle-based immobilized metal affinity chromatography (IMAC, Ti4+, and Fe3+) for selective enrichment of phosphoproteoforms for MS-based top-down proteomics. The IMAC method achieved reproducible and highly efficient enrichment of phosphoproteoforms from simple and complex protein mixtures. It outperformed one commercial phosphoprotein enrichment kit regarding the capture efficiency and recovery of phosphoproteins. Reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) analyses of yeast cell lysates after IMAC (Ti4+ or Fe3+) enrichment produced roughly 100% more phosphoproteoform identifications compared to without IMAC enrichment. Importantly, the phosphoproteoforms identified after Ti4+-IMAC or Fe3+-IMAC enrichment correspond to proteins with much lower overall abundance compared to that identified without the IMAC treatment. We also revealed that Ti4+-IMAC and Fe3+-IMAC could enrich different pools of phosphoproteoforms from complex proteomes and the combination of those two methods will be useful for further improving the phosphoproteoform coverage from complex samples. The results clearly demonstrate the value of our magnetic nanoparticle-based Ti4+-IMAC and Fe3+-IMAC for advancing top-down MS characterization of phosphoproteoforms in complex biological systems.
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Affiliation(s)
- Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI, 48824, USA.
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13
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Leonard B, Danna V, Gorham L, Davison M, Chrisler W, Kim DN, Gerbasi VR. Shaping Nanobodies and Intrabodies against Proteoforms. Anal Chem 2023; 95:8747-8751. [PMID: 37235478 PMCID: PMC10269583 DOI: 10.1021/acs.analchem.3c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023]
Abstract
Proteoforms expand genomic diversity and direct developmental processes. While high-resolution mass spectrometry has accelerated characterization of proteoforms, molecular techniques working to bind and disrupt the function of specific proteoforms have lagged behind. In this study, we worked to develop intrabodies capable of binding specific proteoforms. We employed a synthetic camelid nanobody library expressed in yeast to identify nanobody binders of different SARS-CoV-2 receptor binding domain (RBD) proteoforms. Importantly, employment of the positive and negative selection mechanisms inherent to the synthetic system allowed for amplification of nanobody-expressing yeast that bind to the original (Wuhan strain RBD) but not the E484 K (Beta variant) mutation. Nanobodies raised against specific RBD proteoforms were validated by yeast-2-hybrid analysis and sequence comparisons. These results provide a framework for development of nanobodies and intrabodies that target proteoforms.
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Affiliation(s)
- Bojana Leonard
- Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vincent Danna
- Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - Leo Gorham
- Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - Michelle Davison
- Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - William Chrisler
- Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - Doo Nam Kim
- Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vincent R. Gerbasi
- Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
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14
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Basharat AR, Zang Y, Sun L, Liu X. TopFD: A Proteoform Feature Detection Tool for Top-Down Proteomics. Anal Chem 2023; 95:8189-8196. [PMID: 37196155 DOI: 10.1021/acs.analchem.2c05244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Top-down liquid chromatography-mass spectrometry (LC-MS) analyzes intact proteoforms and generates mass spectra containing peaks of proteoforms with various isotopic compositions, charge states, and retention times. An essential step in top-down MS data analysis is proteoform feature detection, which aims to group these peaks into peak sets (features), each containing all peaks of a proteoform. Accurate protein feature detection enhances the accuracy in MS-based proteoform identification and quantification. Here, we present TopFD, a software tool for top-down MS feature detection that integrates algorithms for proteoform feature detection, feature boundary refinement, and machine learning models for proteoform feature evaluation. We performed extensive benchmarking of TopFD, ProMex, FlashDeconv, and Xtract using seven top-down MS data sets and demonstrated that TopFD outperforms other tools in feature accuracy, reproducibility, and feature abundance reproducibility.
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Affiliation(s)
- Abdul Rehman Basharat
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Yong Zang
- Department of Biostatistics and Health Data Sciences, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaowen Liu
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
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15
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Ras protein abundance correlates with Ras isoform mutation patterns in cancer. Oncogene 2023; 42:1224-1232. [PMID: 36864243 PMCID: PMC10079525 DOI: 10.1038/s41388-023-02638-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/04/2023]
Abstract
Activating mutations of Ras genes are often observed in cancer. The protein products of the three Ras genes are almost identical. However, for reasons that remain unclear, KRAS is far more frequently mutated than the other Ras isoforms in cancer and RASopathies. We have quantified HRAS, NRAS, KRAS4A and KRAS4B protein abundance across a large panel of cell lines and healthy tissues. We observe consistent patterns of KRAS > NRAS»HRAS protein expression in cells that correlate with the rank order of Ras mutation frequencies in cancer. Our data provide support for the model of a sweet-spot of Ras dosage mediating isoform-specific contributions to cancer and development. We suggest that in most cases, being the most abundant Ras isoform correlates with occupying the sweet-spot and that HRAS and NRAS expression is usually insufficient to promote oncogenesis when mutated. However, our results challenge the notion that rare codons mechanistically underpin the predominance of KRAS mutant cancers. Finally, direct measurement of mutant versus wildtype KRAS protein abundance revealed a frequent imbalance that may suggest additional non-gene duplication mechanisms for optimizing oncogenic Ras dosage.
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16
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Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. MASS SPECTROMETRY REVIEWS 2023; 42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.
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Affiliation(s)
| | - Venus Baghalabadi
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Subin R C K Rajendran
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, Nova Scotia, Canada
| | - Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hammam Said
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ziheng Dang
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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17
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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18
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Turan HT, Meuwly M. Local Hydration Control and Functional Implications Through S-Nitrosylation of Proteins: Kirsten Rat Sarcoma Virus (K-RAS) and Hemoglobin (Hb). J Phys Chem B 2023; 127:1526-1539. [PMID: 36757772 DOI: 10.1021/acs.jpcb.2c07371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
S-nitrosylation, the covalent addition of NO to the thiol side chain of cysteine, is an important post-transitional modification (PTM) that can affect the function of proteins. As such, PTMs extend and diversify protein function and thus characterizing consequences of PTM at a molecular level is of great interest. Although PTMs can be detected through various direct/indirect methods, they lack the capability to investigate the modifications with molecular detail. In the present work local and global structural dynamics, their correlation, the hydration structure, and the infrared spectroscopy for WT and S-nitrosylated Kirsten rat sarcoma virus (K-RAS) and hemoglobin (Hb) are characterized from molecular dynamics simulations. It is found that attaching NO to Cys118 in K-RAS rigidifies the protein in the Switch-I region which has functional implications, whereas for Hb, nitrosylation at Cys93 at the β1 chain increases the flexibility of secondary structural motives for Hb in its T0 and R4 conformational substates. Solvent water access decreased by 40% after nitrosylation in K-RAS, similar to Hb for which, however, local hydration of the R4SNO state is yet lower than for T0SNO. Finally, S-nitrosylation leads to detectable peaks for the NO stretch frequency, but the congested IR spectral region will make experimental detection of these bands difficult. Overall, S-nitrosylation in these two proteins is found to influence hydration, protein flexibility, and conformational dynamics which are all eventually involved in protein regulation and function at a molecular level.
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Affiliation(s)
- Haydar Taylan Turan
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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19
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Carrillo-Rodriguez P, Selheim F, Hernandez-Valladares M. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps. Cancers (Basel) 2023; 15:cancers15020555. [PMID: 36672506 PMCID: PMC9856946 DOI: 10.3390/cancers15020555] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The qualitative and quantitative evaluation of proteome changes that condition cancer development can be achieved with liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise several steps such as sample selection, sample processing including labeling, MS acquisition methods, statistical treatment, and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. Moreover, we review major bioinformatics tools for interpreting and visualizing proteomics results and suggest the most popular machine learning techniques for the selection of predictive biomarkers. Finally, we consider the approximation of proteomics strategies for clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them.
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Affiliation(s)
- Paula Carrillo-Rodriguez
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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20
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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21
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McCool EN, Xu T, Chen W, Beller NC, Nolan SM, Hummon AB, Liu X, Sun L. Deep top-down proteomics revealed significant proteoform-level differences between metastatic and nonmetastatic colorectal cancer cells. SCIENCE ADVANCES 2022; 8:eabq6348. [PMID: 36542699 PMCID: PMC9770947 DOI: 10.1126/sciadv.abq6348] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 11/18/2022] [Indexed: 05/23/2023]
Abstract
Understanding cancer metastasis at the proteoform level is crucial for discovering previously unknown protein biomarkers for cancer diagnosis and drug development. We present the first top-down proteomics (TDP) study of a pair of isogenic human nonmetastatic and metastatic colorectal cancer (CRC) cell lines (SW480 and SW620). We identified 23,622 proteoforms of 2332 proteins from the two cell lines, representing nearly fivefold improvement in the number of proteoform identifications (IDs) compared to previous TDP datasets of human cancer cells. We revealed substantial differences between the SW480 and SW620 cell lines regarding proteoform and single amino acid variant (SAAV) profiles. Quantitative TDP unveiled differentially expressed proteoforms between the two cell lines, and the corresponding genes had diversified functions and were closely related to cancer. Our study represents a pivotal advance in TDP toward the characterization of human proteome in a proteoform-specific manner, which will transform basic and translational biomedical research.
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Affiliation(s)
- Elijah N. McCool
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Wenrong Chen
- Department of BioHealth Informatics, Indiana University–Purdue University Indianapolis, 719 Indiana Avenue, Indianapolis, IN 46202, USA
| | - Nicole C. Beller
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Scott M. Nolan
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
- The Comprehensive Cancer Center, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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22
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Adams LM, DeHart CJ, Drown BS, Anderson LC, Bocik W, Boja ES, Hiltke TM, Hendrickson CL, Rodriguez H, Caldwell M, Vafabakhsh R, Kelleher NL. Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling. J Biol Chem 2022; 299:102768. [PMID: 36470426 PMCID: PMC9808003 DOI: 10.1016/j.jbc.2022.102768] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
The KRAS gene is one of the most frequently mutated oncogenes in human cancer and gives rise to two isoforms, KRAS4A and KRAS4B. KRAS post-translational modifications (PTMs) have the potential to influence downstream signaling. However, the relationship between KRAS PTMs and oncogenic mutations remains unclear, and the extent of isoform-specific modification is unknown. Here, we present the first top-down proteomics study evaluating both KRAS4A and KRAS4B, resulting in 39 completely characterized proteoforms across colorectal cancer cell lines and primary tumor samples. We determined which KRAS PTMs are present, along with their relative abundance, and that proteoforms of KRAS4A versus KRAS4B are differentially modified. Moreover, we identified a subset of KRAS4B proteoforms lacking the C185 residue and associated C-terminal PTMs. By confocal microscopy, we confirmed that this truncated GFP-KRAS4BC185∗ proteoform is unable to associate with the plasma membrane, resulting in a decrease in mitogen-activated protein kinase signaling pathway activation. Collectively, our study provides a reference set of functionally distinct KRAS proteoforms and the colorectal cancer contexts in which they are present.
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Affiliation(s)
- Lauren M. Adams
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Caroline J. DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Bryon S. Drown
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Lissa C. Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, Florida, USA
| | - William Bocik
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Emily S. Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | - Tara M. Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | | | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda Maryland, USA
| | - Michael Caldwell
- Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
| | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA,Department of Chemistry, Northwestern University, Evanston, Illinois, USA,Division of Hematology and Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA,For correspondence: Neil L. Kelleher
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23
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Urbiola-Salvador V, Miroszewska D, Jabłońska A, Qureshi T, Chen Z. Proteomics approaches to characterize the immune responses in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119266. [PMID: 35390423 DOI: 10.1016/j.bbamcr.2022.119266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/01/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Despite the dynamic development of cancer research, annually millions of people die of cancer. The human immune system is the major 'guard' against tumor development. Unfortunately, cancer cells have the ability to evade the immune system and continue to grow. The proper understanding of the intricate immune response in tumorigenesis remains the holy grail of cancer immunology and designing effective immunotherapy. To decode the immune responses in cancer, in recent years, proteomics studies have received considerable attention. Proteomics studies focus on the detection and quantification of proteins, which are the effectors of biological functions, and as such, are proven to reflect the cell state more accurately, in comparison to genomic or transcriptomic studies. In this review, we discuss the proteomics studies applied to characterize the immune responses in cancer and tumor immune microenvironment heterogeneity. Further, we describe emerging single-cell proteomics approaches that have the potential to be applied in cancer immunity studies.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Agnieszka Jabłońska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Talha Qureshi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
| | - Zhi Chen
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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24
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Yang M, Hu H, Su P, Thomas PM, Camarillo JM, Greer JB, Early BP, Fellers RT, Kelleher NL, Laskin J. Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. Angew Chem Int Ed Engl 2022; 61:e202200721. [PMID: 35446460 PMCID: PMC9276647 DOI: 10.1002/anie.202200721] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Indexed: 01/28/2023]
Abstract
Unraveling the complexity of biological systems relies on the development of new approaches for spatially resolved proteoform‐specific analysis of the proteome. Herein, we employ nanospray desorption electrospray ionization mass spectrometry imaging (nano‐DESI MSI) for the proteoform‐selective imaging of biological tissues. Nano‐DESI generates multiply charged protein ions, which is advantageous for their structural characterization using tandem mass spectrometry (MS/MS) directly on the tissue. Proof‐of‐concept experiments demonstrate that nano‐DESI MSI combined with on‐tissue top‐down proteomics is ideally suited for the proteoform‐selective imaging of tissue sections. Using rat brain tissue as a model system, we provide the first evidence of differential proteoform expression in different regions of the brain.
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Affiliation(s)
- Manxi Yang
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
| | - Hang Hu
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
| | - Pei Su
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Paul M. Thomas
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Jeannie M. Camarillo
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Joseph B. Greer
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Bryan P. Early
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Ryan T. Fellers
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular BiosciencesNorthwestern University2145 Sheridan RoadEvanstonIL 60208USA
| | - Julia Laskin
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN 47907USA
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25
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Jooß K, McGee JP, Kelleher NL. Native Mass Spectrometry at the Convergence of Structural Biology and Compositional Proteomics. Acc Chem Res 2022; 55:1928-1937. [PMID: 35749283 DOI: 10.1021/acs.accounts.2c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ConspectusBiology is driven by a vast set of molecular interactions that evolved over billions of years. Just as covalent modifications like acetylations and phosphorylations can change a protein's function, so too can noncovalent interactions with metals, small molecules, and other proteins. However, much of the language of protein-level biology is left either undiscovered or inferred, as traditional methods used in the field of proteomics use conditions that dissociate noncovalent interactions and denature proteins.Just in the past few years, mass spectrometry (MS) has evolved the capacity to preserve and subsequently characterize the complete composition of endogenous protein complexes. Using this "native" type of mass spectrometry, a complex can be activated to liberate some or all of its subunits, typically via collisions with neutral gas or solid surfaces and isolated before further characterization ("Native Top-Down MS," or nTDMS). The subunit mass, the parent ion mass, and the fragment ions of the activated subunits can be used to piece together the precise molecular composition of the parent complex. When performed en masse in discovery mode (i.e., "native proteomics"), the interactions of life─including protein modifications─will eventually be clarified and linked to dysfunction in human disease states.In this Account, we describe the current and future components of the native MS toolkit, covering the challenges the field faces to characterize ever larger bioassemblies. Each of the three pillars of native proteomics are addressed: (i) separations, (ii) top-down mass spectrometry, and (iii) integration with structural biology. Complexes such as endogenous nucleosomes can be targeted now using nTDMS, whereas virus particles, exosomes, and high-density lipoprotein particles will be tackled in the coming few years. The future work to adequately address the size and complexity of mega- to gigadalton complexes will include native separations, single ion mass spectrometry, and new data types. The use of nTDMS in discovery mode will incorporate native-compatible separation techniques to maximize the number of proteoforms in complexes identified. With a new wave of innovations, both targeted and discovery mode nTDMS will expand to include extremely scarce and exceedingly heterogeneous bioassemblies. Understanding the proteinaceous interactions of life and how they go wrong (e.g., misfolding, forming complexes in dysfunctional stoichiometries and configurations) will not only inform the development of life-restoring therapeutics but also deepen our understanding of life at the molecular level.
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Affiliation(s)
- Kevin Jooß
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - John P McGee
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States.,Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
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26
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Yang M, Hu H, Su P, Thomas PM, Camarillo JM, Greer JB, Early BP, Fellers RT, Kelleher NL, Laskin J. Proteoform‐Selective Imaging of Tissues Using Mass Spectrometry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Manxi Yang
- Purdue University Department of Chemistry chemistry 560 Oval Dr. 47906 West Lafayette UNITED STATES
| | - Hang Hu
- Purdue University Chemistry UNITED STATES
| | - Pei Su
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Paul M. Thomas
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | | | - Joseph B. Greer
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Bryan P. Early
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Ryan T. Fellers
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Neil L. Kelleher
- Northwestern University Chemistry and Molecular Biosciences UNITED STATES
| | - Julia Laskin
- Purdue University Department of Chemistry 560 Oval Dr. 47907 West Lafayette UNITED STATES
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27
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Wang C, Liang Y, Zhao B, Liang Z, Zhang L, Zhang Y. Ethane-Bridged Hybrid Monolithic Column with Large Mesopores for Boosting Top-Down Proteomic Analysis. Anal Chem 2022; 94:6172-6179. [PMID: 35412811 DOI: 10.1021/acs.analchem.1c05234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Top-down proteomics is challenged by the high complexity of biological samples. The coelution of intact proteins results in overlapped mass spectra, and hence, an increased peak capacity for protein separation is needed. Herein, ethane-bridged hybrid monoliths with well-defined large mesopores were successfully prepared based on the sol-gel condensation of 1,2-bis(trimethoxysilyl)ethane and tetramethoxysilane, followed by two-step base etching of the Si-O-Si domain while maintaining the Si-C-C-Si domain in the structure. Relatively homogeneous macropores of 1.1 μm and large mesopores of 24 nm were obtained, permitting fast mass transfer of large molecules and efficient diffusion without obstruction. The use of less hydrophobic C1 ligand further sharpened the peak shape and improved peak capacity. A 120 cm-long capillary column was used for top-down proteomic analysis of E. coli lysates under low backpressure with 16 MPa. High peak capacity of 646 was achieved within 240 min gradient. With MS/MS analysis, 959 proteoforms corresponding to 263 proteins could be unambiguously identified from E. coli lysates in a single run. Furthermore, to illustrate the separation performance for large proteoforms, such monoliths were applied to top-down analysis of the SEC fraction of E. coli lysates with Mw ranging from 30 to 70 kDa. With highly effective separation, 347 large proteoforms with Mw higher than 30 kDa were detected in the single 75 min run. These results showed great potential for top-down proteomic analysis in complex samples.
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Affiliation(s)
- Chao Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Baofeng Zhao
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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28
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Drown BS, Jooß K, Melani RD, Lloyd-Jones C, Camarillo JM, Kelleher NL. Mapping the Proteoform Landscape of Five Human Tissues. J Proteome Res 2022; 21:1299-1310. [PMID: 35413190 PMCID: PMC9087339 DOI: 10.1021/acs.jproteome.2c00034] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A functional understanding of the human body requires structure-function studies of proteins at scale. The chemical structure of proteins is controlled at the transcriptional, translational, and post-translational levels, creating a variety of products with modulated functions within the cell. The term "proteoform" encapsulates this complexity at the level of chemical composition. Comprehensive mapping of the proteoform landscape in human tissues necessitates analytical techniques with increased sensitivity and depth of coverage. Here, we took a top-down proteomics approach, combining data generated using capillary zone electrophoresis (CZE) and nanoflow reversed-phase liquid chromatography (RPLC) hyphenated to mass spectrometry to identify and characterize proteoforms from the human lungs, heart, spleen, small intestine, and kidneys. CZE and RPLC provided complementary post-translational modification and proteoform selectivity, thereby enhancing the overall proteome coverage when used in combination. Of the 11,466 proteoforms identified in this study, 7373 (64%) were not reported previously. Large differences in the protein and proteoform level were readily quantified, with initial inferences about proteoform biology operative in the analyzed organs. Differential proteoform regulation of defensins, glutathione transferases, and sarcomeric proteins across tissues generate hypotheses about how they function and are regulated in human health and disease.
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Affiliation(s)
- Bryon S Drown
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Kevin Jooß
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Cameron Lloyd-Jones
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Jeannie M Camarillo
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
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29
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Simanshu DK, Morrison DK. A Structure is Worth a Thousand Words: New Insights for RAS and RAF Regulation. Cancer Discov 2022; 12:899-912. [PMID: 35046094 PMCID: PMC8983508 DOI: 10.1158/2159-8290.cd-21-1494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
Abstract
The RAS GTPases are frequently mutated in human cancer, with KRAS being the predominant tumor driver. For many years, it has been known that the structure and function of RAS are integrally linked, as structural changes induced by GTP binding or mutational events determine the ability of RAS to interact with regulators and effectors. Recently, a wealth of information has emerged from structures of specific KRAS mutants and from structures of multiprotein complexes containing RAS and/or RAF, an essential effector of RAS. These structures provide key insights regarding RAS and RAF regulation as well as promising new strategies for therapeutic intervention. SIGNIFICANCE The RAS GTPases are major drivers of tumorigenesis, and for RAS proteins to exert their full oncogenic potential, they must interact with the RAF kinases to initiate ERK cascade signaling. Although binding to RAS is typically a prerequisite for RAF to become an activated kinase, determining the molecular mechanisms by which this interaction results in RAF activation has been a challenging task. A major advance in understanding this process and RAF regulation has come from recent structural studies of various RAS and RAF multiprotein signaling complexes, revealing new avenues for drug discovery.
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Affiliation(s)
- Dhirendra K. Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Deborah K. Morrison
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
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30
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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31
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Kemper EK, Zhang Y, Dix MM, Cravatt BF. Global profiling of phosphorylation-dependent changes in cysteine reactivity. Nat Methods 2022; 19:341-352. [PMID: 35228727 PMCID: PMC8920781 DOI: 10.1038/s41592-022-01398-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023]
Abstract
Proteomics has revealed that the ~20,000 human genes engender a far greater number of proteins, or proteoforms, that are diversified in large part by post-translational modifications (PTMs). How such PTMs affect protein structure and function is an active area of research but remains technically challenging to assess on a proteome-wide scale. Here, we describe a chemical proteomic method to quantitatively relate serine/threonine phosphorylation to changes in the reactivity of cysteine residues, a parameter that can affect the potential for cysteines to be post-translationally modified or engaged by covalent drugs. Leveraging the extensive high-stoichiometry phosphorylation occurring in mitotic cells, we discover numerous cysteines that exhibit phosphorylation-dependent changes in reactivity on diverse proteins enriched in cell cycle regulatory pathways. The discovery of bidirectional changes in cysteine reactivity often occurring in proximity to serine/threonine phosphorylation events points to the broad impact of phosphorylation on the chemical reactivity of proteins and the future potential to create small-molecule probes that differentially target proteoforms with PTMs.
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Affiliation(s)
- Esther K Kemper
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Yuanjin Zhang
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Melissa M Dix
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin F Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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32
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Hollas MAR, Robey M, Fellers R, LeDuc R, Thomas P, Kelleher N. The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms. Nucleic Acids Res 2022; 50:D526-D533. [PMID: 34986596 PMCID: PMC8728143 DOI: 10.1093/nar/gkab1086] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/06/2021] [Accepted: 11/14/2021] [Indexed: 01/01/2023] Open
Abstract
The Human Proteoform Atlas (HPfA) is a web-based repository of experimentally verified human proteoforms on-line at http://human-proteoform-atlas.org and is a direct descendant of the Consortium of Top-Down Proteomics' (CTDP) Proteoform Atlas. Proteoforms are the specific forms of protein molecules expressed by our cells and include the unique combination of post-translational modifications (PTMs), alternative splicing and other sources of variation deriving from a specific gene. The HPfA uses a FAIR system to assign persistent identifiers to proteoforms which allows for redundancy calling and tracking from prior and future studies in the growing community of proteoform biology and measurement. The HPfA is organized around open ontologies and enables flexible classification of proteoforms. To achieve this, a public registry of experimentally verified proteoforms was also created. Submission of new proteoforms can be processed through email vianrtdphelp@northwestern.edu, and future iterations of these proteoform atlases will help to organize and assign function to proteoforms, their PTMs and their complexes in the years ahead.
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Affiliation(s)
- Michael A R Hollas
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Matthew T Robey
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Ryan T Fellers
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Richard D LeDuc
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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33
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Luu GT, Sanchez LM. Toward improvement of screening through mass spectrometry-based proteomics: ovarian cancer as a case study. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116679. [PMID: 34744497 PMCID: PMC8570641 DOI: 10.1016/j.ijms.2021.116679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Ovarian cancer is one of the leading causes of cancer related deaths affecting United States women. Early-stage detection of ovarian cancer has been linked to increased survival, however, current screening methods, such as biomarker testing, have proven to be ineffective in doing so. Therefore, further developments are necessary to be able to achieve positive patient prognosis. Ongoing efforts are being made in biomarker discovery towards clinical applications in screening for early-stage ovarian cancer. In this perspective, we discuss and provide examples for several workflows employing mass spectrometry-based proteomics towards protein biomarker discovery and characterization in the context of ovarian cancer; workflows include protein identification and characterization as well as intact protein profiling. We also discuss the opportunities to merge these workflows for a multiplexed approach for biomarkers. Lastly, we provide our insight as to future developments that may serve to enhance biomarker discovery workflows while also considering translational potential.
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Affiliation(s)
- Gordon T Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St. Santa Cruz, CA, 95064
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High St. Santa Cruz, CA, 95064
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34
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Guzman NA, Guzman DE. Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression. Biomolecules 2021; 11:1443. [PMID: 34680076 PMCID: PMC8533156 DOI: 10.3390/biom11101443] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 09/29/2021] [Indexed: 01/08/2023] Open
Abstract
Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structural changes of each proteoform of a particular protein is essential to elucidate the complex molecular mechanisms that guide the course of disease. Clinical proteomics therefore holds the potential to offer further insight into disease pathology, progression, and prevention. Nevertheless, more technologically advanced diagnostic methods are needed to improve the reliability and clinical applicability of proteomics in preventive medicine. In this manuscript, we review the use of immunoaffinity capillary electrophoresis (IACE) as an emerging powerful diagnostic tool to isolate, separate, detect and characterize proteoform biomarkers obtained from liquid biopsy. IACE is an affinity capture-separation technology capable of isolating, concentrating and analyzing a wide range of biomarkers present in biological fluids. Isolation and concentration of target analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. IACE has the potential to generate rapid results with significant accuracy, leading to reliability and reproducibility in diagnosing and monitoring disease. Additionally, IACE has the capability of monitoring the efficacy of therapeutic agents by quantifying companion and complementary protein biomarkers. With advancements in telemedicine and artificial intelligence, the implementation of proteoform biomarker detection and analysis may significantly improve our capacity to identify medical conditions early and intervene in ways that improve health outcomes for individuals and populations.
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Affiliation(s)
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08543, USA;
- Division of Hospital Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
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35
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The evolution of evolutionary processes in organismal and cancer evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:43-48. [PMID: 34509467 DOI: 10.1016/j.pbiomolbio.2021.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/22/2022]
Abstract
The evolution of early life and of contemporary viruses has been driven in significant part by random genetic mutations, while modern unicellular and organismal evolution primarily leverages evolved, efficient and active cell biology processes for adaptive changes prior to selection. Random mutations are often buffered by cell homeostasis, or they have a negative role, e.g., by causing death or monogenic diseases, or by triggering real-time cancer evolution. Accordingly, the Modern Synthesis theory no longer adequately describes the efficient, often punctuated and at times directionally adaptive natural genetic engineering (NGE) processes deduced from the DNA record of evolution. Similarly, the somatic mutation theory (SMT) of cancer describes driver mutations that can trigger oncogenesis, and passenger mutations characteristic of periods of genetic microevolution in cancer. At the precancerous stage, most somatic mutations are repaired or buffered in the cell, aberrant cells are removed, or organismal bioelectric tissue signals or other physiological functional networks maintain control of rogue, mutated cells. However, the SMT is not sufficient to describe the observed punctuated macroevolution of cancer-cell genes, chromosomes, karyotypes and epigenomes, nor of expressed cancer-cell transcriptomes, proteomes and epiproteomes, which include non-DNA-templated post-translational modifications, protein-protein interactions and metabolites. Moreover, punctuated cancer cell macroevolution often culminates in macro-effects, which include epithelial-mesenchymal transitions (EMT), cancer cell polyploidies and even giant multinucleated cancer cells that drive cancer progression, therapy resistance and metastasis. All of this cancer-cell evolution competes in a molecular and cellular arms race with host immune cells and antibodies, as well as with the host tumor microenvironment. Empirically observed punctuated, multilevel and multiclonal cancer macroevolution, and the concomitant, rapid co-development of the host immune system and tumor microenvironment, can occur with the efficiency, speed and lethality of cancer that is enabled by evolved, active natural genetic engineering (NGE) mechanisms. NGE affects both vertical cancer-cell genomic inheritance and evolution towards therapy resistance and metastasis, as well as viral or cancer-cell exosome vector-driven horizontal gene transfers that contributes to cancer cell cooperation, or to transforming previously non-cancerous somatic cells into destabilized cancer cells during metastasis. In addition, externally driven, irreversible and transferable (EDIT) adaptations are exemplified by mitotically heritable, non-templated cancer cell epigenetics, and by mitotically heritable cancer-cell surface protein and lipid glycosylation, as important examples of fast time-scale molecular evolution mechanisms in which genes are followers, similar to evo-devo processes in organismal evolution.
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Abstract
Biological mass spectrometry (MS) encompasses a range of methods for characterizing proteins and other biomolecules. MS is uniquely powerful for the structural analysis of endogenous protein complexes, which are often heterogeneous, poorly abundant, and refractive to characterization by other methods. Here, we focus on how biological MS can contribute to the study of endogenous protein complexes, which we define as complexes expressed in the physiological host and purified intact, as opposed to reconstituted complexes assembled from heterologously expressed components. Biological MS can yield information on complex stoichiometry, heterogeneity, topology, stability, activity, modes of regulation, and even structural dynamics. We begin with a review of methods for isolating endogenous complexes. We then describe the various biological MS approaches, focusing on the type of information that each method yields. We end with future directions and challenges for these MS-based methods.
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Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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37
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Campbell SL, Philips MR. Post-translational modification of RAS proteins. Curr Opin Struct Biol 2021; 71:180-192. [PMID: 34365229 DOI: 10.1016/j.sbi.2021.06.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 06/25/2021] [Indexed: 11/26/2022]
Abstract
Mutations of RAS genes drive cancer more frequently than any other oncogene. RAS proteins integrate signals from a wide array of receptors and initiate downstream signaling through pathways that control cellular growth. RAS proteins are fundamentally binary molecular switches in which the off/on state is determined by the binding of GDP or GTP, respectively. As such, the intrinsic and regulated nucleotide-binding and hydrolytic properties of the RAS GTPase were historically believed to account for the entirety of the regulation of RAS signaling. However, it is increasingly clear that RAS proteins are also regulated by a vast array of post-translational modifications (PTMs). The current challenge is to understand what are the functional consequences of these modifications and which are physiologically relevant. Because PTMs are catalyzed by enzymes that may offer targets for drug discovery, the study of RAS PTMs has been a high priority for RAS biologists.
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Affiliation(s)
| | - Mark R Philips
- Perlmutter Cancer Center, NYU Grossman School of Medicine, USA
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38
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Production and Membrane Binding of N-Terminally Acetylated, C-Terminally Farnesylated and Carboxymethylated KRAS4b. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:105-116. [PMID: 33977473 DOI: 10.1007/978-1-0716-1190-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recombinant mammalian proteins are routinely produced in E. coli and thus lack post-translational modifications. KRAS4b is processed at both the N- and C-terminus, resulting in an acetylation of the N-terminus (at Thr, after aminopeptidase removal of the original N-term Met) and farnesylation/carboxymethylation of the C-terminal Cys (after proteolytic cleavage of the original C-terminal three amino acids, Val-Iso-Met). Processing of KRAS enables it to associate with the plasma membrane and fulfill its function in cell signaling. We describe here the production of recombinant KRAS4b from our modified baculovirus/insect cell expression system that accurately incorporates these in vivo modifications to allow experiments that anchor KRAS4b to membrane mimetics (e.g., nanodiscs and liposomes).
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Choi IK, Jiang T, Kankara SR, Wu S, Liu X. TopMSV: A Web-Based Tool for Top-Down Mass Spectrometry Data Visualization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1312-1318. [PMID: 33780241 PMCID: PMC8172439 DOI: 10.1021/jasms.0c00460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Top-down mass spectrometry (MS) investigates intact proteoforms for proteoform identification, characterization, and quantification. Data visualization plays an essential role in top-down MS data analysis because proteoform identification and characterization often involve manual data inspection to determine the molecular masses of highly charged ions and validate unexpected alterations in identified proteoforms. While many software tools have been developed for MS data visualization, there is still a lack of web-based visualization software designed for top-down MS. Here, we present TopMSV, a web-based tool for top-down MS data processing and visualization. TopMSV provides interactive views of top-down MS data using a web browser. It integrates software tools for spectral deconvolution and proteoform identification and uses analysis results of the tools to annotate top-down MS data.
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Affiliation(s)
- In Kwon Choi
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Tianze Jiang
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Sreekanth Reddy Kankara
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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40
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Shen X, Xu T, Hakkila B, Hare M, Wang Q, Wang Q, Beckman JS, Sun L. Capillary Zone Electrophoresis-Electron-Capture Collision-Induced Dissociation on a Quadrupole Time-of-Flight Mass Spectrometer for Top-Down Characterization of Intact Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1361-1369. [PMID: 33749270 PMCID: PMC8576897 DOI: 10.1021/jasms.0c00484] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Mass spectrometry (MS)-based denaturing top-down proteomics (dTDP) requires high-capacity separation and extensive gas-phase fragmentation of proteoforms. Herein, we coupled capillary zone electrophoresis (CZE) to electron-capture collision-induced dissociation (ECciD) on an Agilent 6545 XT quadrupole time-of-flight (Q-TOF) mass spectrometer for dTDP for the first time. During ECciD, the protein ions were first fragmented using ECD, followed by further activation and fragmentation by applying a CID potential. In this pilot study, we optimized the CZE-ECciD method for small proteins (lower than 20 kDa) regarding the charge state of protein parent ions for fragmentation and the CID potential applied to maximize the protein backbone cleavage coverage and the number of sequence-informative fragment ions. The CZE-ECciD Q-TOF platform provided extensive backbone cleavage coverage for three standard proteins lower than 20 kDa from only single charge states in a single CZE-MS/MS run in the targeted MS/MS mode, including ubiquitin (97%, +7, 8.6 kDa), superoxide dismutase (SOD, 87%, +17, 16 kDa), and myoglobin (90%, +16, 17 kDa). The CZE-ECciD method produced comparable cleavage coverage of small proteins (i.e., myoglobin) with direct-infusion MS studies using electron transfer dissociation (ETD), activated ion-ETD, and combinations of ETD and collision-based fragmentation on high-end orbitrap mass spectrometers. The results render CZE-ECciD a new tool for dTDP to enhance both separation and gas-phase fragmentation of proteoforms.
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Affiliation(s)
- Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Blake Hakkila
- e-MSion, Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
| | - Mike Hare
- e-MSion, Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
| | - Qianjie Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Joseph S Beckman
- e-MSion, Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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41
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Melby JA, Roberts DS, Larson EJ, Brown KA, Bayne EF, Jin S, Ge Y. Novel Strategies to Address the Challenges in Top-Down Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1278-1294. [PMID: 33983025 PMCID: PMC8310706 DOI: 10.1021/jasms.1c00099] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Top-down mass spectrometry (MS)-based proteomics is a powerful technology for comprehensively characterizing proteoforms to decipher post-translational modifications (PTMs) together with genetic variations and alternative splicing isoforms toward a proteome-wide understanding of protein functions. In the past decade, top-down proteomics has experienced rapid growth benefiting from groundbreaking technological advances, which have begun to reveal the potential of top-down proteomics for understanding basic biological functions, unraveling disease mechanisms, and discovering new biomarkers. However, many challenges remain to be comprehensively addressed. In this Account & Perspective, we discuss the major challenges currently facing the top-down proteomics field, particularly in protein solubility, proteome dynamic range, proteome complexity, data analysis, proteoform-function relationship, and analytical throughput for precision medicine. We specifically review the major technology developments addressing these challenges with an emphasis on our research group's efforts, including the development of top-down MS-compatible surfactants for protein solubilization, functionalized nanoparticles for the enrichment of low-abundance proteoforms, strategies for multidimensional chromatography separation of proteins, and a new comprehensive user-friendly software package for top-down proteomics. We have also made efforts to connect proteoforms with biological functions and provide our visions on what the future holds for top-down proteomics.
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Affiliation(s)
- Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Eli J Larson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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42
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Ahsan N, Rao RSP, Wilson RS, Punyamurtula U, Salvato F, Petersen M, Ahmed MK, Abid MR, Verburgt JC, Kihara D, Yang Z, Fornelli L, Foster SB, Ramratnam B. Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches. Proteomics 2021; 21:e2000279. [PMID: 33860983 PMCID: PMC8250252 DOI: 10.1002/pmic.202000279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022]
Abstract
While protein–protein interaction is the first step of the SARS‐CoV‐2 infection, recent comparative proteomic profiling enabled the identification of over 11,000 protein dynamics, thus providing a comprehensive reflection of the molecular mechanisms underlying the cellular system in response to viral infection. Here we summarize and rationalize the results obtained by various mass spectrometry (MS)‐based proteomic approaches applied to the functional characterization of proteins and pathways associated with SARS‐CoV‐2‐mediated infections in humans. Comparative analysis of cell‐lines versus tissue samples indicates that our knowledge in proteome profile alternation in response to SARS‐CoV‐2 infection is still incomplete and the tissue‐specific response to SARS‐CoV‐2 infection can probably not be recapitulated efficiently by in vitro experiments. However, regardless of the viral infection period, sample types, and experimental strategies, a thorough cross‐comparison of the recently published proteome, phosphoproteome, and interactome datasets led to the identification of a common set of proteins and kinases associated with PI3K‐Akt, EGFR, MAPK, Rap1, and AMPK signaling pathways. Ephrin receptor A2 (EPHA2) was identified by 11 studies including all proteomic platforms, suggesting it as a potential future target for SARS‐CoV‐2 infection mechanisms and the development of new therapeutic strategies. We further discuss the potentials of future proteomics strategies for identifying prognostic SARS‐CoV‐2 responsive age‐, gender‐dependent, tissue‐specific protein targets.
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Affiliation(s)
- Nagib Ahsan
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - R. Shyama Prasad Rao
- Biostatistics and Bioinformatics DivisionYenepoya Research CenterYenepoya UniversityMangaluruIndia
| | - Rashaun S. Wilson
- Keck Mass Spectrometry and Proteomics ResourceYale UniversityNew HavenConnecticutUSA
| | - Ujwal Punyamurtula
- COBRE Center for Cancer Research DevelopmentProteomics Core FacilityRhode Island HospitalProvidenceRhode IslandUSA
| | - Fernanda Salvato
- Department of Plant and Microbial BiologyCollege of Agriculture and Life SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Max Petersen
- Signal Transduction Lab, Division of Hematology/OncologyRhode Island Hospital, Warren Alpert Medical School, Brown UniversityProvidenceRhode IslandUSA
| | - Mohammad Kabir Ahmed
- Department of BiochemistryFaculty of MedicineUniversiti Kuala Lumpur Royal College of Medicine PerakIpohPerakMalaysia
| | - M. Ruhul Abid
- Department of SurgeryCardiovascular Research CenterRhode Island HospitalWarren Alpert Medical SchoolBrown UniversityProvidenceRhode IslandUSA
| | - Jacob C. Verburgt
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Daisuke Kihara
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
- Department of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
| | - Zhibo Yang
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - Luca Fornelli
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
- Department of BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Steven B. Foster
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - Bharat Ramratnam
- COBRE Center for Cancer Research DevelopmentProteomics Core FacilityRhode Island HospitalProvidenceRhode IslandUSA
- Division of Infectious DiseasesDepartment of MedicineWarren Alpert Medical SchoolBrown UniversityProvidenceRhode IslandUSA
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43
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Huang M, Wang Y. GLOBAL AND TARGETED PROFILING OF GTP-BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2021; 40:215-235. [PMID: 32519381 PMCID: PMC7725852 DOI: 10.1002/mas.21637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/15/2020] [Indexed: 05/05/2023]
Abstract
GTP-binding proteins are among the most important enzyme families that are involved in a plethora of biological processes. However, owing to the enormous diversity of the nucleotide-binding protein family, comprehensive analyses of the expression level, structure, activity, and regulatory mechanisms of GTP-binding proteins remain challenging with the use of conventional approaches. The many advances in mass spectrometry (MS) instrumentation and data acquisition methods, together with a variety of enrichment approaches in sample preparation, render MS a powerful tool for the comprehensive characterizations of the activities and expression levels of various GTP-binding proteins. We review herein the recent developments in the application of MS-based techniques, together with general and widely used affinity enrichment approaches, for the proteome-wide and targeted capture, identification, and quantification of GTP-binding proteins. The working principles, advantages, and limitations of various strategies for profiling the expression level, activity, posttranslational modifications, and interactome of GTP-binding proteins are discussed. It can be envisaged that future applications of MS-based proteomics will lead to a better understanding about the roles of GTP-binding proteins in different biological processes and human diseases. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Ming Huang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA 92521, USA
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
- Correspondence author: Yinsheng Wang. Telephone: (951)827-2700;
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44
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Tsang O, Wong JWH. Proteogenomic interrogation of cancer cell lines: an overview of the field. Expert Rev Proteomics 2021; 18:221-232. [PMID: 33877947 DOI: 10.1080/14789450.2021.1914594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: Cancer cell lines (CCLs) have been a major resource for cancer research. Over the past couple of decades, they have been instrumental in omic profiling method development and as model systems to generate new knowledge in cell and cancer biology. More recently, with the increasing amount of genomic, transcriptomic and proteomic data being generated in hundreds of CCLs, there is growing potential for integrative proteogenomic data analyses to be performed.Areas covered: In this review, we first describe the most commonly used proteome profiling methods in CCLs. We then discuss how these proteomics data can be integrated with genomics data for proteogenomics analyses. Finally, we highlight some of the recent biological discoveries that have arisen from proteogenomics analyses of CCLs.Expert opinion: Protegeonomics analyses of CCLs have so far enabled the discovery of novel proteins and proteoforms. It has also improved our understanding of biological processes including post-transcriptional regulation of protein abundance and the presentation of antigens by major histocompatibility complex alleles. With proteomics data to be generated in hundreds to thousands of CCLs in coming years, there will be further potential for large-scale proteogenomics analyses and data integration with the phenotypically well-characterized CCLs.
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Affiliation(s)
- Olson Tsang
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Jason W H Wong
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR.,School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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45
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Xu T, Sun L. A Mini Review on Capillary Isoelectric Focusing-Mass Spectrometry for Top-Down Proteomics. Front Chem 2021; 9:651757. [PMID: 33898392 PMCID: PMC8063032 DOI: 10.3389/fchem.2021.651757] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/16/2021] [Indexed: 01/24/2023] Open
Abstract
Mass spectrometry (MS)-based top-down proteomics (TDP) requires high-resolution separation of proteoforms before electrospray ionization (ESI)-MS and tandem mass spectrometry (MS/MS). Capillary isoelectric focusing (cIEF)-ESI-MS and MS/MS could be an ideal method for TDP because cIEF can enable separation of proteoforms based on their isoelectric points (pIs) with ultra-high resolution. cIEF-ESI-MS has been well-recognized for protein characterization since 1990s. However, the widespread adoption of cIEF-MS for the characterization of proteoforms had been impeded by several technical challenges, including the lack of highly sensitive and robust ESI interface for coupling cIEF to MS, ESI suppression of analytes from ampholytes, and the requirement of manual operations. In this mini review, we summarize the technical improvements of cIEF-ESI-MS for characterizing proteoforms and highlight some recent applications to hydrophobic proteins, urinary albumin variants, charge variants of monoclonal antibodies, and large-scale TDP of complex proteomes.
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Affiliation(s)
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, United States
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46
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López CA, Agarwal A, Van QN, Stephen AG, Gnanakaran S. Unveiling the Dynamics of KRAS4b on Lipid Model Membranes. J Membr Biol 2021; 254:201-216. [PMID: 33825026 PMCID: PMC8052243 DOI: 10.1007/s00232-021-00176-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/16/2021] [Indexed: 12/23/2022]
Abstract
Small GTPase proteins are ubiquitous and responsible for regulating several processes related to cell growth and differentiation. Mutations that stabilize their active state can lead to uncontrolled cell proliferation and cancer. Although these proteins are well characterized at the cellular scale, the molecular mechanisms governing their functions are still poorly understood. In addition, there is limited information about the regulatory function of the cell membrane which supports their activity. Thus, we have studied the dynamics and conformations of the farnesylated KRAS4b in various membrane model systems, ranging from binary fluid mixtures to heterogeneous raft mimics. Our approach combines long time-scale coarse-grained (CG) simulations and Markov state models to dissect the membrane-supported dynamics of KRAS4b. Our simulations reveal that protein dynamics is mainly modulated by the presence of anionic lipids and to some extent by the nucleotide state (activation) of the protein. In addition, our results suggest that both the farnesyl and the polybasic hypervariable region (HVR) are responsible for its preferential partitioning within the liquid-disordered (Ld) domains in membranes, potentially enhancing the formation of membrane-driven signaling platforms.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | - Animesh Agarwal
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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47
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Melby JA, de Lange WJ, Zhang J, Roberts DS, Mitchell SD, Tucholski T, Kim G, Kyrvasilis A, McIlwain SJ, Kamp TJ, Ralphe JC, Ge Y. Functionally Integrated Top-Down Proteomics for Standardized Assessment of Human Induced Pluripotent Stem Cell-Derived Engineered Cardiac Tissues. J Proteome Res 2021; 20:1424-1433. [PMID: 33395532 DOI: 10.1021/acs.jproteome.0c00830] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three-dimensional (3D) human induced pluripotent stem cell-derived engineered cardiac tissues (hiPSC-ECTs) have emerged as a promising alternative to two-dimensional hiPSC-cardiomyocyte monolayer systems because hiPSC-ECTs are a closer representation of endogenous cardiac tissues and more faithfully reflect the relevant cardiac pathophysiology. The ability to perform functional and molecular assessments using the same hiPSC-ECT construct would allow for more reliable correlation between observed functional performance and underlying molecular events, and thus is critically needed. Herein, for the first time, we have established an integrated method that permits sequential assessment of functional properties and top-down proteomics from the same single hiPSC-ECT construct. We quantitatively determined the differences in isometric twitch force and the sarcomeric proteoforms between two groups of hiPSC-ECTs that differed in the duration of time of 3D-ECT culture. Importantly, by using this integrated method we discovered a new and strong correlation between the measured contractile parameters and the phosphorylation levels of alpha-tropomyosin between the two groups of hiPSC-ECTs. The integration of functional assessments together with molecular characterization by top-down proteomics in the same hiPSC-ECT construct enables a holistic analysis of hiPSC-ECTs to accelerate their applications in disease modeling, cardiotoxicity, and drug discovery. Data are available via ProteomeXchange with identifier PXD022814.
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Affiliation(s)
- Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Willem J de Lange
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jianhua Zhang
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Stanford D Mitchell
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gina Kim
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Andreas Kyrvasilis
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Sean J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - J Carter Ralphe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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48
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Adams LM, DeHart CJ, Kelleher NL. Precise Characterization of KRAS4B Proteoforms by Combining Immunoprecipitation with Top-Down Mass Spectrometry. Methods Mol Biol 2021; 2262:47-64. [PMID: 33977470 PMCID: PMC8543976 DOI: 10.1007/978-1-0716-1190-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The characterization of biologically relevant post-translational modifications (PTMs) on KRAS4B has historically been carried out through methodologies such as immunoblotting with PTM-specific antibodies or peptide-based proteomic methods. While these methods have the potential to identify a given PTM on KRAS4B, they are incapable of characterizing or distinguishing the different molecular forms or proteoforms of KRAS4B from those of related RAS isoforms. We present a method that combines immunoprecipitation of KRAS4B with top-down mass spectrometry (IP-TDMS), thus enabling the precise characterization of intact KRAS4B proteoforms. We provide detailed protocols for the IP, LC-MS/MS, and data analysis comprising a successful IP-TDMS assay in the contexts of cancer cell lines and tissue samples.
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Affiliation(s)
- Lauren M Adams
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Caroline J DeHart
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Neil L Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
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49
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Brown KA, Tucholski T, Alpert AJ, Eken C, Wesemann L, Kyrvasilis A, Jin S, Ge Y. Top-Down Proteomics of Endogenous Membrane Proteins Enabled by Cloud Point Enrichment and Multidimensional Liquid Chromatography-Mass Spectrometry. Anal Chem 2020; 92:15726-15735. [PMID: 33231430 PMCID: PMC7968110 DOI: 10.1021/acs.analchem.0c02533] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Although top-down proteomics has emerged as a powerful strategy to characterize proteins in biological systems, the analysis of endogenous membrane proteins remains challenging due to their low solubility, low abundance, and the complexity of the membrane subproteome. Here, we report a simple but effective enrichment and separation strategy for top-down proteomics of endogenous membrane proteins enabled by cloud point extraction and multidimensional liquid chromatography coupled to high-resolution mass spectrometry (MS). The cloud point extraction efficiently enriched membrane proteins using a single extraction, eliminating the need for time-consuming ultracentrifugation steps. Subsequently, size-exclusion chromatography (SEC) with an MS-compatible mobile phase (59% water, 40% isopropanol, 1% formic acid) was used to remove the residual surfactant and fractionate intact proteins (6-115 kDa). The fractions were separated further by reversed-phase liquid chromatography (RPLC) coupled with MS for protein characterization. This method was applied to human embryonic kidney cells and cardiac tissue lysates to enable the identification of 188 and 124 endogenous integral membrane proteins, respectively, some with as many as 19 transmembrane domains.
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Affiliation(s)
- Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Andrew J. Alpert
- PolyLC Inc., Columbia, Maryland 21045, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Christian Eken
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Lucas Wesemann
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Andreas Kyrvasilis
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
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50
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Lu H, Martí J. Influence of Cholesterol on the Orientation of the Farnesylated GTP-Bound KRas-4B Binding with Anionic Model Membranes. MEMBRANES 2020; 10:E364. [PMID: 33266473 PMCID: PMC7700388 DOI: 10.3390/membranes10110364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/02/2023]
Abstract
The Ras family of proteins is tethered to the inner leaflet of the cell membranes which plays an essential role in signal transduction pathways that promote cellular proliferation, survival, growth, and differentiation. KRas-4B, the most mutated Ras isoform in different cancers, has been under extensive study for more than two decades. Here we have focused our interest on the influence of cholesterol on the orientations that KRas-4B adopts with respect to the plane of the anionic model membranes. How cholesterol in the bilayer might modulate preferences for specific orientation states is far from clear. Herein, after analyzing data from in total 4000 ns-long molecular dynamics (MD) simulations for four KRas-4B systems, properties such as the area per lipid and thickness of the membrane as well as selected radial distribution functions, penetration of different moieties of KRas-4B, and internal conformational fluctuations of flexible moieties in KRas-4B have been calculated. It has been shown that high cholesterol content in the plasma membrane (PM) favors one orientation state (OS1), exposing the effector-binding loop for signal transduction in the cell from the atomic level. We confirm that high cholesterol in the PM helps KRas-4B mutant stay in its constitutively active state, which suggests that high cholesterol intake can increase mortality and may promote cancer progression for cancer patients. We propose that during the treatment of KRas-4B-related cancers, reducing the cholesterol level in the PM and sustaining cancer progression by controlling the plasma cholesterol intake might be taken into account in anti-cancer therapies.
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Affiliation(s)
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, 08034 Barcelona, Spain;
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