1
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Sun BB, Suhre K, Gibson BW. Promises and Challenges of populational Proteomics in Health and Disease. Mol Cell Proteomics 2024; 23:100786. [PMID: 38761890 PMCID: PMC11193116 DOI: 10.1016/j.mcpro.2024.100786] [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: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Advances in proteomic assay technologies have significantly increased coverage and throughput, enabling recent increases in the number of large-scale population-based proteomic studies of human plasma and serum. Improvements in multiplexed protein assays have facilitated the quantification of thousands of proteins over a large dynamic range, a key requirement for detecting the lowest-ranging, and potentially the most disease-relevant, blood-circulating proteins. In this perspective, we examine how populational proteomic datasets in conjunction with other concurrent omic measures can be leveraged to better understand the genomic and non-genomic correlates of the soluble proteome, constructing biomarker panels for disease prediction, among others. Mass spectrometry workflows are discussed as they are becoming increasingly competitive with affinity-based array platforms in terms of speed, cost, and proteome coverage due to advances in both instrumentation and workflows. Despite much success, there remain considerable challenges such as orthogonal validation and absolute quantification. We also highlight emergent challenges associated with study design, analytical considerations, and data integration as population-scale studies are run in batches and may involve longitudinal samples collated over many years. Lastly, we take a look at the future of what the nascent next-generation proteomic technologies might provide to the analysis of large sets of blood samples, as well as the difficulties in designing large-scale studies that will likely require participation from multiple and complex funding sources and where data sharing, study designs, and financing must be solved.
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Affiliation(s)
- Benjamin B Sun
- Human Genetics, Informatics and Predictive Sciences, Bristol-Myers Squibb, Cambridge, Massachusetts, USA.
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Bradford W Gibson
- Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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2
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Guo W, Liu Y, Han Y, Tang H, Fan X, Wang C, Chen PR. Amplifiable protein identification via residue-resolved barcoding and composition code counting. Natl Sci Rev 2024; 11:nwae183. [PMID: 39055168 PMCID: PMC11272068 DOI: 10.1093/nsr/nwae183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 07/27/2024] Open
Abstract
Ultrasensitive protein identification is of paramount importance in basic research and clinical diagnostics but remains extremely challenging. A key bottleneck in preventing single-molecule protein sequencing is that, unlike the revolutionary nucleic acid sequencing methods that rely on the polymerase chain reaction (PCR) to amplify DNA and RNA molecules, protein molecules cannot be directly amplified. Decoding the proteins via amplification of certain fingerprints rather than the intact protein sequence thus represents an appealing alternative choice to address this formidable challenge. Herein, we report a proof-of-concept method that relies on residue-resolved DNA barcoding and composition code counting for amplifiable protein fingerprinting (AmproCode). In AmproCode, selective types of residues on peptides or proteins are chemically labeled with a DNA barcode, which can be amplified and quantified via quantitative PCR. The operation generates a relative ratio as the residue-resolved 'composition code' for each target protein that can be utilized as the fingerprint to determine its identity from the proteome database. We developed a database searching algorithm and applied it to assess the coverage of the whole proteome and secretome via computational simulations, proving the theoretical feasibility of AmproCode. We then designed the residue-specific DNA barcoding and amplification workflow, and identified different synthetic model peptides found in the secretome at as low as the fmol/L level for demonstration. These results build the foundation for an unprecedented amplifiable protein fingerprinting method. We believe that, in the future, AmproCode could ultimately realize single-molecule amplifiable identification of trace complex samples without further purification, and it may open a new avenue in the development of next-generation protein sequencing techniques.
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Affiliation(s)
- Weiming Guo
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yuan Liu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Han
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Huan Tang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chu Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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3
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Ohayon S, Taib L, Verma NC, Iarossi M, Bhattacharya I, Marom B, Huttner D, Meller A. Full-Length Single Protein Molecules Tracking and Counting in Thin Silicon Channels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2314319. [PMID: 38461367 DOI: 10.1002/adma.202314319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/25/2024] [Indexed: 03/11/2024]
Abstract
Emerging single-molecule protein sensing techniques are ushering in a transformative era in biomedical research. Nevertheless, challenges persist in realizing ultra-fast full-length protein sensing, including loss of molecular integrity due to protein fragmentation, biases introduced by antibodies affinity, identification of proteoforms, and low throughputs. Here, a single-molecule method for parallel protein separation and tracking is introduced, yielding multi-dimensional molecular properties used for their identification. Proteins are tagged by chemo-selective dual amino-acid specific labels and are electrophoretically separated by their mass/charge in custom-designed thin silicon channel with subwavelength height. This approach allows analysis of thousands of individual proteins within a few minutes by tracking their motion during the migration. The power of the method is demonstrated by quantifying a cytokine panel for host-response discrimination between viral and bacterial infections. Moreover, it is shown that two clinically-relevant splice isoforms of Vascular endothelial growth factor (VEGF) can be accurately quantified from human serum samples. Being non-destructive and compatible with full-length intact proteins, this method opens up ways for antibody-free single-protein molecule quantification.
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Affiliation(s)
- Shilo Ohayon
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Liran Taib
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | | | - Marzia Iarossi
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Ivy Bhattacharya
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Barak Marom
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Diana Huttner
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
| | - Amit Meller
- Department of Biomedical Engineering, Technion-IIT, Haifa, 3200003, Israel
- Russell Berrie Nanotechnology Institute, Technion-IIT, Haifa, 3200003, Israel
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4
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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5
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Nova IC, Ritmejeris J, Brinkerhoff H, Koenig TJR, Gundlach JH, Dekker C. Detection of phosphorylation post-translational modifications along single peptides with nanopores. Nat Biotechnol 2024; 42:710-714. [PMID: 37386295 PMCID: PMC11189593 DOI: 10.1038/s41587-023-01839-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/23/2023] [Indexed: 07/01/2023]
Abstract
Current methods to detect post-translational modifications of proteins, such as phosphate groups, cannot measure single molecules or differentiate between closely spaced phosphorylation sites. We detect post-translational modifications at the single-molecule level on immunopeptide sequences with cancer-associated phosphate variants by controllably drawing the peptide through the sensing region of a nanopore. We discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy for individual reads of single molecules.
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Affiliation(s)
- Ian C Nova
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Justas Ritmejeris
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Henry Brinkerhoff
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Theo J R Koenig
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA, USA
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands.
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6
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Filius M, van Wee R, de Lannoy C, Westerlaken I, Li Z, Kim SH, de Agrela Pinto C, Wu Y, Boons GJ, Pabst M, de Ridder D, Joo C. Full-length single-molecule protein fingerprinting. NATURE NANOTECHNOLOGY 2024; 19:652-659. [PMID: 38351230 DOI: 10.1038/s41565-023-01598-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/22/2023] [Indexed: 03/21/2024]
Abstract
Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoforms. Mass spectrometric methods, in particular, often provide only ambiguous information on post-translational modification sites, and sequences of co-existing modifications may not be resolved. Here we demonstrate fluorescence resonance energy transfer (FRET)-based single-molecule protein fingerprinting to map the location of individual amino acids and post-translational modifications within single full-length protein molecules. Our data show that both intrinsically disordered proteins and folded globular proteins can be fingerprinted with a subnanometer resolution, achieved by probing the amino acids one by one using single-molecule FRET via DNA exchange. This capability was demonstrated through the analysis of alpha-synuclein, an intrinsically disordered protein, by accurately quantifying isoforms in mixtures using a machine learning classifier, and by determining the locations of two O-GlcNAc moieties. Furthermore, we demonstrate fingerprinting of the globular proteins Bcl-2-like protein 1, procalcitonin and S100A9. We anticipate that our ability to perform proteoform identification with the ultimate sensitivity may unlock exciting new venues in proteomics research and biomarker-based diagnosis.
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Affiliation(s)
- Mike Filius
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Raman van Wee
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Carlos de Lannoy
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Ilja Westerlaken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Zeshi Li
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Sung Hyun Kim
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Department of Physics, Ewha Womans University, Seoul, Republic of Korea
| | - Cecilia de Agrela Pinto
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Yunfei Wu
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Geert-Jan Boons
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
- Department of Physics, Ewha Womans University, Seoul, Republic of Korea.
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7
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Emenike B, Czabala P, Farhi J, Swaminathan J, Anslyn EV, Spangle J, Raj M. Tertiary Amine Coupling by Oxidation for Selective Labeling of Dimethyl Lysine Post-Translational Modifications. J Am Chem Soc 2024; 146:10621-10631. [PMID: 38584362 PMCID: PMC11027136 DOI: 10.1021/jacs.4c00253] [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: 01/07/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Lysine dimethylation (Kme2) is a crucial post-translational modification (PTM) that regulates biological processes and is implicated in diseases. There is significant interest in globally identifying these methylation marks. Unfortunately, this remains challenging due to the lack of robust technologies for selectively labeling Kme2. To address this, we present a chemical method named tertiary amine coupling by oxidation (TACO). This method selectively modifies Kme2 to aldehydes using Selectfluor and a base. The resulting aldehydes from Kme2 were then functionalized using reductive amination, thiolamine, and oxime chemistry. We successfully demonstrated the versatility of TACO in selectively labeling Kme2 peptides and proteins in complex cell lysate mixtures with varying payloads, including affinity tags and fluorophores. We further showed the application of TACO chemistry for the identification of Kme2 sites at a single-molecule level by fluorosequencing. We discovered novel 30 Kme2 sites, in addition to previously known 5 Kme2 sites, by proteomics analysis of TACO-modified nuclear extracts. Our work establishes a unique strategy for covalently modifying Kme2, facilitating the global identification of low-abundance Kme2-PTMs and their sites within complex cell lysate mixtures.
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Affiliation(s)
- Benjamin Emenike
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Patrick Czabala
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jonathan Farhi
- Department
of Radiation Oncology, Emory University
School of Medicine, Atlanta, Georgia 30322, United States
| | - Jagannath Swaminathan
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer Spangle
- Department
of Radiation Oncology, Emory University
School of Medicine, Atlanta, Georgia 30322, United States
| | - Monika Raj
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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8
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Zhang M, Tang C, Wang Z, Chen S, Zhang D, Li K, Sun K, Zhao C, Wang Y, Xu M, Dai L, Lu G, Shi H, Ren H, Chen L, Geng J. Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore. Nat Methods 2024; 21:609-618. [PMID: 38443507 PMCID: PMC11009107 DOI: 10.1038/s41592-024-02208-7] [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: 10/19/2022] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
Precise identification and quantification of amino acids is crucial for many biological applications. Here we report a copper(II)-functionalized Mycobacterium smegmatis porin A (MspA) nanopore with the N91H substitution, which enables direct identification of all 20 proteinogenic amino acids when combined with a machine-learning algorithm. The validation accuracy reaches 99.1%, with 30.9% signal recovery. The feasibility of ultrasensitive quantification of amino acids was also demonstrated at the nanomolar range. Furthermore, the capability of this system for real-time analyses of two representative post-translational modifications (PTMs), one unnatural amino acid and ten synthetic peptides using exopeptidases, including clinically relevant peptides associated with Alzheimer's disease and cancer neoantigens, was demonstrated. Notably, our strategy successfully distinguishes peptides with only one amino acid difference from the hydrolysate and provides the possibility to infer the peptide sequence.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chao Tang
- Biosafety Laboratory of West China Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Zichun Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shanchuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mengying Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Haiyan Ren
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China.
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu, China.
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9
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Dorey A, Howorka S. Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics. Nat Chem 2024; 16:314-334. [PMID: 38448507 DOI: 10.1038/s41557-023-01322-x] [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: 08/30/2022] [Accepted: 07/14/2023] [Indexed: 03/08/2024]
Abstract
Sequencing of nucleic acids with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost and portability. This label-free method for sequencing at the single-molecule level is an achievement on its own. However, nanopores also show promise for the technologically even more challenging sequencing of polypeptides, something that could considerably benefit biological discovery, clinical diagnostics and homeland security, as current techniques lack portability and speed. Here we survey the biochemical innovations underpinning commercial and academic nanopore DNA/RNA sequencing techniques, and explore how these advances can fuel developments in future protein sequencing with nanopores.
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Affiliation(s)
- Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
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10
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Schlotter T, Kloter T, Hengsteler J, Yang K, Zhan L, Ragavan S, Hu H, Zhang X, Duru J, Vörös J, Zambelli T, Nakatsuka N. Aptamer-Functionalized Interface Nanopores Enable Amino Acid-Specific Peptide Detection. ACS NANO 2024; 18:6286-6297. [PMID: 38355286 PMCID: PMC10906075 DOI: 10.1021/acsnano.3c10679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/16/2024]
Abstract
Single-molecule proteomics based on nanopore technology has made significant advances in recent years. However, to achieve nanopore sensing with single amino acid resolution, several bottlenecks must be tackled: controlling nanopore sizes with nanoscale precision and slowing molecular translocation events. Herein, we address these challenges by integrating amino acid-specific DNA aptamers into interface nanopores with dynamically tunable pore sizes. A phenylalanine aptamer was used as a proof-of-concept: aptamer recognition of phenylalanine moieties led to the retention of specific peptides, slowing translocation speeds. Importantly, while phenylalanine aptamers were isolated against the free amino acid, the aptamers were determined to recognize the combination of the benzyl or phenyl and the carbonyl group in the peptide backbone, enabling binding to specific phenylalanine-containing peptides. We decoupled specific binding between aptamers and phenylalanine-containing peptides from nonspecific interactions (e.g., electrostatics and hydrophobic interactions) using optical waveguide lightmode spectroscopy. Aptamer-modified interface nanopores differentiated peptides containing phenylalanine vs. control peptides with structurally similar amino acids (i.e., tyrosine and tryptophan). When the duration of aptamer-target interactions inside the nanopore were prolonged by lowering the applied voltage, discrete ionic current levels with repetitive motifs were observed. Such reoccurring signatures in the measured signal suggest that the proposed method has the possibility to resolve amino acid-specific aptamer recognition, a step toward single-molecule proteomics.
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Affiliation(s)
- Tilman Schlotter
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Tom Kloter
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Julian Hengsteler
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Kyungae Yang
- Department
of Medicine, Columbia University Irving
Medical Center, New York, New York 10032, United States
| | - Lijian Zhan
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Sujeni Ragavan
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Haiying Hu
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Xinyu Zhang
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Jens Duru
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - János Vörös
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Tomaso Zambelli
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, 8092 Zürich, Switzerland
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11
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Lee S, Nouraein S, Kwon JJ, Huang Z, Wojick JA, Xia B, Corder G, Szablowski JO. Engineered serum markers for non-invasive monitoring of gene expression in the brain. Nat Biotechnol 2024:10.1038/s41587-023-02087-x. [PMID: 38200117 PMCID: PMC11233427 DOI: 10.1038/s41587-023-02087-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/04/2023] [Indexed: 01/12/2024]
Abstract
Measurement of gene expression in the brain requires invasive analysis of brain tissue or non-invasive methods that are limited by low sensitivity. Here we introduce a method for non-invasive, multiplexed, site-specific monitoring of endogenous gene or transgene expression in the brain through engineered reporters called released markers of activity (RMAs). RMAs consist of an easily detectable reporter and a receptor-binding domain that enables transcytosis across the brain endothelium. RMAs are expressed in the brain but exit into the blood, where they can be easily measured. We show that expressing RMAs at a single mouse brain site representing approximately 1% of the brain volume provides up to a 100,000-fold signal increase over the baseline. Expression of RMAs in tens to hundreds of neurons is sufficient for their reliable detection. We demonstrate that chemogenetic activation of cells expressing Fos-responsive RMA increases serum RMA levels >6-fold compared to non-activated controls. RMAs provide a non-invasive method for repeatable, multiplexed monitoring of gene expression in the intact animal brain.
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Affiliation(s)
- Sangsin Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
- Rice Neuroengineering Initiative, Rice University, Houston, TX, USA
| | - Shirin Nouraein
- Department of Bioengineering, Rice University, Houston, TX, USA
- Rice Neuroengineering Initiative, Rice University, Houston, TX, USA
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA
| | - James J Kwon
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Zhimin Huang
- Department of Bioengineering, Rice University, Houston, TX, USA
- Rice Neuroengineering Initiative, Rice University, Houston, TX, USA
| | - Jessica A Wojick
- Department of Psychiatry and Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Boao Xia
- Department of Bioengineering, Rice University, Houston, TX, USA
- Rice Neuroengineering Initiative, Rice University, Houston, TX, USA
| | - Gregory Corder
- Department of Psychiatry and Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jerzy O Szablowski
- Department of Bioengineering, Rice University, Houston, TX, USA.
- Rice Neuroengineering Initiative, Rice University, Houston, TX, USA.
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, USA.
- Applied Physics Program, Rice University, Houston, TX, USA.
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12
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Zhang Y, Yi Y, Li Z, Zhou K, Liu L, Wu HC. Peptide sequencing based on host-guest interaction-assisted nanopore sensing. Nat Methods 2024; 21:102-109. [PMID: 37957431 DOI: 10.1038/s41592-023-02095-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023]
Abstract
Direct protein sequencing technologies with improved sensitivity and throughput are still needed. Here, we propose an alternative method for peptide sequencing based on enzymatic cleavage and host-guest interaction-assisted nanopore sensing. We serendipitously discovered that the identity of any proteinogenic amino acid in a particular position of a phenylalanine-containing peptide could be determined via current blockage during translocation of the peptide through α-hemolysin nanopores in the presence of cucurbit[7]uril. Building upon this, we further present a proof-of-concept demonstration of peptide sequencing by sequentially cleaving off amino acids from C terminus of a peptide with carboxypeptidases, and then determining their identities and sequence with a peptide probe in nanopore. With future optimization, our results point to a different way of nanopore-based protein sequencing.
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Affiliation(s)
- Yun Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yakun Yi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyi Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Lei Liu
- Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
| | - Hai-Chen Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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13
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Wu X, Borca B, Sen S, Koslowski S, Abb S, Rosenblatt DP, Gallardo A, Mendieta-Moreno JI, Nachtigall M, Jelinek P, Rauschenbach S, Kern K, Schlickum U. Molecular sensitised probe for amino acid recognition within peptide sequences. Nat Commun 2023; 14:8335. [PMID: 38097575 PMCID: PMC10721870 DOI: 10.1038/s41467-023-43844-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformational freedom, however, the chemical identification of building blocks of these biopolymers often relies on the presence of markers, extensive simulations, or is not possible at all. Here, we present a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. A selective intermolecular interaction between the sensitiser attached at the tip-apex and the target amino acid on the surface induces an enhanced tunnelling conductance of one specific spectral feature, which can be mapped in spectroscopic imaging. Density functional theory calculations suggest a mechanism that relies on conformational changes of the sensitiser that are accompanied by local charge redistributions in the tunnelling junction, which, in turn, lower the tunnelling barrier at that specific part of the peptide.
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Affiliation(s)
- Xu Wu
- Max Planck Institute for Solid State Research, Stuttgart, Germany
- School of Integrated Circuits and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Bogdana Borca
- Institute of Applied Physics and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, 38104, Braunschweig, Germany
- National Institute of Materials Physics, 077125, Magurele, Romania
| | - Suman Sen
- Max Planck Institute for Solid State Research, Stuttgart, Germany
| | | | - Sabine Abb
- Max Planck Institute for Solid State Research, Stuttgart, Germany
| | | | - Aurelio Gallardo
- Institute of Physics of the Czech Academy of Science, Prague, Czech Republic
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | | | - Matyas Nachtigall
- Institute of Physics of the Czech Academy of Science, Prague, Czech Republic
| | - Pavel Jelinek
- Institute of Physics of the Czech Academy of Science, Prague, Czech Republic.
| | - Stephan Rauschenbach
- Max Planck Institute for Solid State Research, Stuttgart, Germany.
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Klaus Kern
- Max Planck Institute for Solid State Research, Stuttgart, Germany
- Institut de Physique, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Uta Schlickum
- Max Planck Institute for Solid State Research, Stuttgart, Germany.
- Institute of Applied Physics and Laboratory for Emerging Nanometrology, Technische Universität Braunschweig, 38104, Braunschweig, Germany.
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14
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Cobley JN. 50 shades of oxidative stress: A state-specific cysteine redox pattern hypothesis. Redox Biol 2023; 67:102936. [PMID: 37875063 PMCID: PMC10618833 DOI: 10.1016/j.redox.2023.102936] [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: 09/25/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
Oxidative stress is biochemically complex. Like primary colours, specific reactive oxygen species (ROS) and antioxidant inputs can be mixed to create unique "shades" of oxidative stress. Even a minimal redox module comprised of just 12 (ROS & antioxidant) inputs and 3 outputs (oxidative damage, cysteine-dependent redox-regulation, or both) yields over half a million "shades" of oxidative stress. The present paper proposes the novel hypothesis that: state-specific shades of oxidative stress, such as a discrete disease, are associated with distinct tell-tale cysteine oxidation patterns. The patterns are encoded by many parameters, from the identity of the oxidised proteins, the cysteine oxidation type, and magnitude. The hypothesis is conceptually grounded in distinct ROS and antioxidant inputs coalescing to produce unique cysteine oxidation outputs. And considers the potential biological significance of the holistic cysteine oxidation outputs. The literature supports the existence of state-specific cysteine oxidation patterns. Measuring and manipulating these patterns offer promising avenues for advancing oxidative stress research. The pattern inspired hypothesis provides a framework for understanding the complex biochemical nature of state-specific oxidative stress.
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Affiliation(s)
- James N Cobley
- Cysteine redox technology Group, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK.
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15
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Kipen J, Jaldén J. Beam search decoder for enhancing sequence decoding speed in single-molecule peptide sequencing data. PLoS Comput Biol 2023; 19:e1011345. [PMID: 37934778 PMCID: PMC10656014 DOI: 10.1371/journal.pcbi.1011345] [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: 07/12/2023] [Revised: 11/17/2023] [Accepted: 10/15/2023] [Indexed: 11/09/2023] Open
Abstract
Next-generation single-molecule protein sequencing technologies have the potential to significantly accelerate biomedical research. These technologies offer sensitivity and scalability for proteomic analysis. One auspicious method is fluorosequencing, which involves: cutting naturalized proteins into peptides, attaching fluorophores to specific amino acids, and observing variations in light intensity as one amino acid is removed at a time. The original peptide is classified from the sequence of light-intensity reads, and proteins can subsequently be recognized with this information. The amino acid step removal is achieved by attaching the peptides to a wall on the C-terminal and using a process called Edman Degradation to remove an amino acid from the N-Terminal. Even though a framework (Whatprot) has been proposed for the peptide classification task, processing times remain restrictive due to the massively parallel data acquisicion system. In this paper, we propose a new beam search decoder with a novel state formulation that obtains considerably lower processing times at the expense of only a slight accuracy drop compared to Whatprot. Furthermore, we explore how our novel state formulation may lead to even faster decoders in the future.
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Affiliation(s)
- Javier Kipen
- Division of Information Science and Engineering, Kungsliga Tekniska Högskolan, Stockholm, Stockholm, Sweden
| | - Joakim Jaldén
- Division of Information Science and Engineering, Kungsliga Tekniska Högskolan, Stockholm, Stockholm, Sweden
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16
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Motone K, Kontogiorgos-Heintz D, Wee J, Kurihara K, Yang S, Roote G, Fang Y, Cardozo N, Nivala J. Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563182. [PMID: 37905023 PMCID: PMC10614977 DOI: 10.1101/2023.10.19.563182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited in achieving this goal. Here, we establish a method for long-range, single-molecule reading of intact protein strands on a commercial nanopore sensor array. By using the ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieve single-amino acid level sensitivity, enabling sequencing of combinations of amino acid substitutions across long protein strands. For greater sequencing accuracy, we demonstrate the ability to reread individual protein molecules, spanning hundreds of amino acids in length, multiple times, and explore the potential for high accuracy protein barcode sequencing. Further, we develop a biophysical model that can simulate raw nanopore signals a priori, based on amino acid volume and charge, enhancing the interpretation of raw signal data. Finally, we apply these methods to examine intact, folded protein domains for complete end-to-end analysis. These results provide proof-of-concept for a platform that has the potential to identify and characterize full-length proteoforms at single-molecule resolution.
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Affiliation(s)
- Keisuke Motone
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- These authors contributed equally: Keisuke Motone, Daphne Kontogiorgos-Heintz
| | - Daphne Kontogiorgos-Heintz
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- These authors contributed equally: Keisuke Motone, Daphne Kontogiorgos-Heintz
| | - Jasmine Wee
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Kyoko Kurihara
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Sangbeom Yang
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Gwendolin Roote
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Yishu Fang
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Nicolas Cardozo
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- Paul. G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Science Institute, University of Washington, Seattle, WA, USA
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17
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Chen C, Song M, Li K, Yan S, Chen M, Geng J. E. coli outer membrane protein T (OmpT) nanopore for peptide sensing. Biochem Biophys Res Commun 2023; 677:132-140. [PMID: 37586211 DOI: 10.1016/j.bbrc.2023.05.125] [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: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 08/18/2023]
Abstract
Peptide detection methods with facility and high sensitivity are essential for diagnosing disease associated with peptide biomarkers. Nanopore sensing technology had emerged as a low cost, high-throughput, and scalable tool for peptide detection. The omptins family proteins which can form β-barrel pores have great potentials to be developed as nanopore biosensor. However, there are no study about the channel properties of E. coli OmpT and the development of OmpT as a nanopore biosensor. In this study, the OmpT biological nanopore channel was constructed with a conductance of 1.49 nS in 500 mM NaCl buffer and a three-step gating phenomenon under negative voltage higher than 100 mV and then was developed as a peptide biosensor which can detect peptide without the interfere of ssDNA and dNTPs. The OmpT constructed in this study has potential application in peptide detection, and also provides a new idea for the detection of peptides using the specific binding ability of protease.
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Affiliation(s)
- Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; School of Pharmacy, North Sichuan Medical College, Nanchong, 637000, China
| | - Mengxiao Song
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Shixin Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China; Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu 641400, China.
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18
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KIM S, KAMARULZAMAN L, TANIGUCHI Y. Recent methodological advances towards single-cell proteomics. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:306-327. [PMID: 37673661 PMCID: PMC10749393 DOI: 10.2183/pjab.99.021] [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: 02/14/2023] [Accepted: 07/20/2023] [Indexed: 09/08/2023]
Abstract
Studying the central dogma at the single-cell level has gained increasing attention to reveal hidden cell lineages and functions that cannot be studied using traditional bulk analyses. Nonetheless, most single-cell studies exploiting genomic and transcriptomic levels fail to address information on proteins that are central to many important biological processes. Single-cell proteomics enables understanding of the functional status of individual cells and is particularly crucial when the specimen is composed of heterogeneous entities of cells. With the growing importance of this field, significant methodological advancements have emerged recently. These include miniaturized and automated sample preparation, multi-omics analyses, and combined analyses of multiple techniques such as mass spectrometry and microscopy. Moreover, artificial intelligence and single-molecule detection technologies have advanced throughput and improved sensitivity limitations, respectively, over conventional methods. In this review, we summarize cutting-edge methodologies for single-cell proteomics and relevant emerging technologies that have been reported in the last 5 years, and provide an outlook on this research field.
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Affiliation(s)
- Sooyeon KIM
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Latiefa KAMARULZAMAN
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yuichi TANIGUCHI
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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19
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Vasunilashorn SM, Dillon ST, Marcantonio ER, Libermann TA. Application of Multiple Omics to Understand Postoperative Delirium Pathophysiology in Humans. Gerontology 2023; 69:1369-1384. [PMID: 37722373 PMCID: PMC10711777 DOI: 10.1159/000533789] [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: 01/24/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
Delirium, an acute change in cognition, is common, morbid, and costly, particularly among hospitalized older adults. Despite growing knowledge of its epidemiology, far less is known about delirium pathophysiology. Initial work understanding delirium pathogenesis has focused on assaying single or a limited subset of molecules or genetic loci. Recent technological advances at the forefront of biomarker and drug target discovery have facilitated application of multiple "omics" approaches aimed to provide a more complete understanding of complex disease processes such as delirium. At its basic level, "omics" involves comparison of genes (genomics, epigenomics), transcripts (transcriptomics), proteins (proteomics), metabolites (metabolomics), or lipids (lipidomics) in biological fluids or tissues obtained from patients who have a certain condition (i.e., delirium) and those who do not. Multi-omics analyses of these various types of molecules combined with machine learning and systems biology enable the discovery of biomarkers, biological pathways, and predictors of delirium, thus elucidating its pathophysiology. This review provides an overview of the most recent omics techniques, their current impact on identifying delirium biomarkers, and future potential in enhancing our understanding of delirium pathogenesis. We summarize challenges in identification of specific biomarkers of delirium and, more importantly, in discovering the mechanisms underlying delirium pathophysiology. Based on mounting evidence, we highlight a heightened inflammatory response as one common pathway in delirium risk and progression, and we suggest other promising biological mechanisms that have recently emerged. Advanced multiple omics approaches coupled with bioinformatics methodologies have great promise to yield important discoveries that will advance delirium research.
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Affiliation(s)
- Sarinnapha M. Vasunilashorn
- Division of General Medicine, Department of Medicine, Beth Israel Deaconess Medical Center (BIDMC), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Simon T. Dillon
- Harvard Medical School, Boston, MA, USA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, BIDMC, Boston, MA, USA
- Genomics, Proteomics, Bioinformatics and Systems Biology Center, BIDMC, Boston, MA, USA
| | - Edward R. Marcantonio
- Division of General Medicine, Department of Medicine, Beth Israel Deaconess Medical Center (BIDMC), Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gerontology, Department of Medicine, BIDMC, Boston, MA, USA
| | - Towia A. Libermann
- Harvard Medical School, Boston, MA, USA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, BIDMC, Boston, MA, USA
- Genomics, Proteomics, Bioinformatics and Systems Biology Center, BIDMC, Boston, MA, USA
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20
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Mapes JH, Stover J, Stout HD, Folsom TM, Babcock E, Loudwig S, Martin C, Austin MJ, Tu F, Howdieshell CJ, Simpson ZB, Blom T, Weaver D, Winkler D, Vander Velden K, Ossareh PM, Beierle JM, Somekh T, Bardo AM, Anslyn EV, Marcotte EM, Swaminathan J. Robust and scalable single-molecule protein sequencing with fluorosequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.558007. [PMID: 37745461 PMCID: PMC10516020 DOI: 10.1101/2023.09.15.558007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The need to accurately survey proteins and their modifications with ever higher sensitivities, particularly in clinical settings with limited samples, is spurring development of new single molecule proteomics technologies. Fluorosequencing is one such highly parallelized single molecule peptide sequencing platform, based on determining the sequence positions of select amino acid types within peptides to enable their identification and quantification from a reference database. Here, we describe substantial improvements to fluorosequencing, including identifying fluorophores compatible with the sequencing chemistry, mitigating dye-dye interactions through the use of extended polyproline linkers, and developing an end-to-end workflow for sample preparation and sequencing. We demonstrate by fluorosequencing peptides in mixtures and identifying a target neoantigen from a database of decoy MHC peptides, highlighting the potential of the technology for high sensitivity clinical applications.
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Affiliation(s)
| | | | - Heather D Stout
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | | | | | | | - Christopher Martin
- Erisyon, Inc. Austin, TX, 78752
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | | | - Fan Tu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | | | | | | | | | | | | | | | | | | | - Angela M Bardo
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jagannath Swaminathan
- Erisyon, Inc. Austin, TX, 78752
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
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21
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Wei X, Penkauskas T, Reiner JE, Kennard C, Uline MJ, Wang Q, Li S, Aksimentiev A, Robertson JW, Liu C. Engineering Biological Nanopore Approaches toward Protein Sequencing. ACS NANO 2023; 17:16369-16395. [PMID: 37490313 PMCID: PMC10676712 DOI: 10.1021/acsnano.3c05628] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Tadas Penkauskas
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
- School of Engineering, Brown University, Providence, RI 02912, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Celeste Kennard
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
| | - Mark J. Uline
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Sheng Li
- School of Data Science, University of Virginia, Charlottesville, VA 22903, United States
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joseph W.F. Robertson
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
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22
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Yu L, Kang X, Li F, Mehrafrooz B, Makhamreh A, Fallahi A, Foster JC, Aksimentiev A, Chen M, Wanunu M. Unidirectional single-file transport of full-length proteins through a nanopore. Nat Biotechnol 2023; 41:1130-1139. [PMID: 36624148 PMCID: PMC10329728 DOI: 10.1038/s41587-022-01598-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/02/2022] [Indexed: 01/10/2023]
Abstract
The electrical current blockade of a peptide or protein threading through a nanopore can be used as a fingerprint of the molecule in biosensor applications. However, threading of full-length proteins has only been achieved using enzymatic unfolding and translocation. Here we describe an enzyme-free approach for unidirectional, slow transport of full-length proteins through nanopores. We show that the combination of a chemically resistant biological nanopore, α-hemolysin (narrowest part is ~1.4 nm in diameter), and a high concentration guanidinium chloride buffer enables unidirectional, single-file protein transport propelled by an electroosmotic effect. We show that the mean protein translocation velocity depends linearly on the applied voltage and translocation times depend linearly on length, resembling the translocation dynamics of ssDNA. Using a supervised machine-learning classifier, we demonstrate that single-translocation events contain sufficient information to distinguish their threading orientation and identity with accuracies larger than 90%. Capture rates of protein are increased substantially when either a genetically encoded charged peptide tail or a DNA tag is added to a protein.
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Affiliation(s)
- Luning Yu
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Xinqi Kang
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Fanjun Li
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Behzad Mehrafrooz
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Ali Fallahi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Joshua C Foster
- Molecular and Cellular Biology Program, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Aleksei Aksimentiev
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Min Chen
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Program, University of Massachusetts at Amherst, Amherst, MA, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA.
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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23
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Smith MB, VanderVelden K, Blom T, Stout HD, Mapes JH, Folsom TM, Martin C, Bardo AM, Marcotte EM. Estimating error rates for single molecule protein sequencing experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549591. [PMID: 37502879 PMCID: PMC10370102 DOI: 10.1101/2023.07.18.549591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The practical application of new single molecule protein sequencing (SMPS) technologies requires accurate estimates of their associated sequencing error rates. Here, we describe the development and application of two distinct parameter estimation methods for analyzing SMPS reads produced by fluorosequencing. A Hidden Markov Model (HMM) based approach, extends whatprot, where we previously used HMMs for SMPS peptide-read matching. This extension offers a principled approach for estimating key parameters for fluorosequencing experiments, including missed amino acid cleavages, dye loss, and peptide detachment. Specifically, we adapted the Baum-Welch algorithm, a standard technique to estimate transition probabilities for an HMM using expectation maximization, but modified here to estimate a small number of parameter values directly rather than estimating every transition probability independently, which should help prevent overfitting. We demonstrate a high degree of accuracy on simulated data, but on experimental datasets, we observed that the model needed to be augmented with an additional error type, N-terminal blocking. This, in combination with data pre-processing, results in reasonable parameterizations of experimental datasets that agree with controlled experimental perturbations. A second independent implementation using a hybrid of DIRECT and Powell's method to reduce the root mean squared error (RMSE) between simulations and the real dataset was also developed. We compare these methods on both simulated and real data, finding that our Baum-Welch based approach outperforms DIRECT and Powell's method by most, but not all, criteria. Although some discrepancies between the results exist, we also find that both approaches provide similar error rate estimates from experimental single molecule fluorosequencing datasets.
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Affiliation(s)
- Matthew Beauregard Smith
- Oden Institute, The University of Texas at Austin, Austin, TX 78712
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | | | | | - Heather D Stout
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- Erisyon Inc., Austin TX 78752
| | | | | | | | - Angela M Bardo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
- Erisyon Inc., Austin TX 78752
| | - Edward M Marcotte
- Oden Institute, The University of Texas at Austin, Austin, TX 78712
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
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24
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Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins. Mol Cell 2023; 83:1936-1952.e7. [PMID: 37267908 PMCID: PMC10281453 DOI: 10.1016/j.molcel.2023.05.006] [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: 04/12/2022] [Revised: 01/29/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
Non-native conformations drive protein-misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well suited for elucidating them and their phenotypic effects. Especially intractable are the transient conformations populated by intrinsically disordered proteins. We describe an approach to systematically discover, stabilize, and purify native and non-native conformations, generated in vitro or in vivo, and directly link conformations to molecular, organismal, or evolutionary phenotypes. This approach involves high-throughput disulfide scanning (HTDS) of the entire protein. To reveal which disulfides trap which chromatographically resolvable conformers, we devised a deep-sequencing method for double-Cys variant libraries of proteins that precisely and simultaneously locates both Cys residues within each polypeptide. HTDS of the abundant E. coli periplasmic chaperone HdeA revealed distinct classes of disordered hydrophobic conformers with variable cytotoxicity depending on where the backbone was cross-linked. HTDS can bridge conformational and phenotypic landscapes for many proteins that function in disulfide-permissive environments.
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Affiliation(s)
- Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Victor Y Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kibum Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amir Bitran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sunia A Trauger
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Bogdan Budnik
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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25
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Seo JP, Trippett JS, Huang Z, Wang RZ, Lee S, Szablowski JO. Acoustically-Targeted Measurement of Transgene Expression in the Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541868. [PMID: 37292585 PMCID: PMC10245922 DOI: 10.1101/2023.05.23.541868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Gene expression is a critical component of brain physiology and activity, but monitoring this expression in the living brain represents a significant challenge. Here, we introduce a new paradigm called Recovery of Markers through InSonation (REMIS) for noninvasive measurement of gene expression in the brain with cell-type, spatial, and temporal specificity. Our approach relies on engineered protein markers that are designed to be expressed in neurons and exit into the interstitium. By applying ultrasound to targeted brain regions, these markers are released into the bloodstream, where they can be readily detected using biochemical techniques. REMIS can noninvasively confirm gene delivery and measure endogenous signaling in specific brain sites through a simple insonation and a subsequent blood test. Using REMIS, we successfully measured chemogenetic induction of neuronal activity in ultrasound-tar-geted brain regions. REMIS recovery of markers is reliable and demonstrated improved recovery of markers from the brain into the blood in every tested animal. Overall, our work establishes a noninvasive, spatially-specific means of monitoring gene delivery outcomes and endogenous signaling in mammalian brains, opening up possibilities for brain research and noninvasive monitoring of gene therapies in the brain.
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26
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Wang F, Zhao C, Zhao P, Chen F, Qiao D, Feng J. MoS 2 nanopore identifies single amino acids with sub-1 Dalton resolution. Nat Commun 2023; 14:2895. [PMID: 37210427 DOI: 10.1038/s41467-023-38627-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 05/22/2023] Open
Abstract
The sequencing of single protein molecules using nanopores is faced with a huge challenge due to the lack of resolution needed to resolve single amino acids. Here we report the direct experimental identification of single amino acids in nanopores. With atomically engineered regions of sensitivity comparable to the size of single amino acids, MoS2 nanopores provide a sub-1 Dalton resolution for discriminating the chemical group difference of single amino acids, including recognizing the amino acid isomers. This ultra-confined nanopore system is further used to detect the phosphorylation of individual amino acids, demonstrating its capability for reading post-translational modifications. Our study suggests that a sub-nanometer engineered pore has the potential to be applied in future chemical recognition and de novo protein sequencing at the single-molecule level.
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Affiliation(s)
- Fushi Wang
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Chunxiao Zhao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Pinlong Zhao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Fanfan Chen
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Dan Qiao
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China
| | - Jiandong Feng
- Laboratory of Experimental Physical Biology, Department of Chemistry, Zhejiang University, 310027, Hangzhou, China.
- Research Center for Quantum Sensing, Research Institute of Intelligent Sensing, Zhejiang Lab, 311121, Hangzhou, China.
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27
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Smith MB, Simpson ZB, Marcotte EM. Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier. PLoS Comput Biol 2023; 19:e1011157. [PMID: 37253025 PMCID: PMC10256185 DOI: 10.1371/journal.pcbi.1011157] [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: 01/19/2023] [Revised: 06/09/2023] [Accepted: 05/04/2023] [Indexed: 06/01/2023] Open
Abstract
We present a machine learning-based interpretive framework (whatprot) for analyzing single molecule protein sequencing data produced by fluorosequencing, a recently developed proteomics technology that determines sparse amino acid sequences for many individual peptide molecules in a highly parallelized fashion. Whatprot uses Hidden Markov Models (HMMs) to represent the states of each peptide undergoing the various chemical processes during fluorosequencing, and applies these in a Bayesian classifier, in combination with pre-filtering by a k-Nearest Neighbors (kNN) classifier trained on large volumes of simulated fluorosequencing data. We have found that by combining the HMM based Bayesian classifier with the kNN pre-filter, we are able to retain the benefits of both, achieving both tractable runtimes and acceptable precision and recall for identifying peptides and their parent proteins from complex mixtures, outperforming the capabilities of either classifier on its own. Whatprot's hybrid kNN-HMM approach enables the efficient interpretation of fluorosequencing data using a full proteome reference database and should now also enable improved sequencing error rate estimates.
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Affiliation(s)
| | | | - Edward M. Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
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28
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Mansuri MS, Williams K, Nairn AC. Uncovering biology by single-cell proteomics. Commun Biol 2023; 6:381. [PMID: 37031277 PMCID: PMC10082756 DOI: 10.1038/s42003-023-04635-2] [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: 08/01/2022] [Accepted: 02/25/2023] [Indexed: 04/10/2023] Open
Abstract
Recent technological advances have opened the door to single-cell proteomics that can answer key biological questions regarding how protein expression, post-translational modifications, and protein interactions dictate cell state in health and disease.
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Affiliation(s)
- M Shahid Mansuri
- Yale/NIDA Neuroproteomics Center and Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut, USA
| | - Kenneth Williams
- Yale/NIDA Neuroproteomics Center and Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center and Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, USA.
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29
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Marcassa G, Dascenco D, de Wit J. Proteomics-based synapse characterization: From proteins to circuits. Curr Opin Neurobiol 2023; 79:102690. [PMID: 36805717 DOI: 10.1016/j.conb.2023.102690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 01/10/2023] [Indexed: 02/19/2023]
Abstract
The highly heterogeneous nature of neuronal cell types and their connections presents a major challenge to the characterization of neural circuits at the protein level. New approaches now enable an increasingly sophisticated dissection of cell type- and cellular compartment-specific proteomes, as well as the profiling of the protein composition of specific synaptic connections. Here, we provide an overview of these approaches and discuss how they hold considerable promise toward unravelling the molecular mechanisms of neural circuit formation and function. Finally, we provide an outlook of technological developments that may bring the characterization of synaptic proteomes at the single-synapse level within reach.
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Affiliation(s)
- Gabriele Marcassa
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Dan Dascenco
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium. https://twitter.com/ddascenco
| | - Joris de Wit
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium.
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30
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31
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MacCoss MJ, Alfaro JA, Faivre DA, Wu CC, Wanunu M, Slavov N. Sampling the proteome by emerging single-molecule and mass spectrometry methods. Nat Methods 2023; 20:339-346. [PMID: 36899164 PMCID: PMC10044470 DOI: 10.1038/s41592-023-01802-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules, which has major implications in the development of proteomics technologies. We review strategies that have been helpful for counting billions of protein molecules by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and suggest that these strategies can benefit single-molecule methods, especially in mitigating the challenges of the wide dynamic range of the proteome.
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Affiliation(s)
- Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Javier Antonio Alfaro
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland.
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
- School of Informatics, University of Edinburgh, Edinburgh, UK.
| | - Danielle A Faivre
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christine C Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center and Barnett Institute, Northeastern University, Boston, MA, USA.
- Parallel Squared Technology Institute, Watertown, MA, USA.
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32
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Chen J, Gu Z, Xu Y, Deng M, Lai L, Pei J. QuoteTarget: A sequence-based transformer protein language model to identify potentially druggable protein targets. Protein Sci 2023; 32:e4555. [PMID: 36564866 PMCID: PMC9878469 DOI: 10.1002/pro.4555] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
The development of efficient computational methods for drug target protein identification can compensate for the high cost of experiments and is therefore of great significance for drug development. However, existing structure-based drug target protein-identification algorithms are limited by the insufficient number of proteins with experimentally resolved structures. Moreover, sequence-based algorithms cannot effectively extract information from protein sequences and thus display insufficient accuracy. Here, we combined the sequence-based self-supervised pretraining protein language model ESM1b with a graph convolutional neural network classifier to develop an improved, sequence-based drug target protein identification method. This complete model, named QuoteTarget, efficiently encodes proteins based on sequence information alone and achieves an accuracy of 95% with the nonredundant drug target and nondrug target datasets constructed for this study. When applied to all proteins from Homo sapiens, QuoteTarget identified 1213 potential undeveloped drug target proteins. We further inferred residue-binding weights from the well-trained network using the gradient-weighted class activation mapping (Grad-Cam) algorithm. Notably, we found that without any binding site information input, significant residues inferred by the model closely match the experimentally confirmed drug molecule-binding sites. Thus, our work provides a highly effective sequence-based identifier for drug target proteins, as well to yield new insights into recognizing drug molecule-binding sites. The entire model is available at https://github.com/Chenjxjx/drug-target-prediction.
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Affiliation(s)
- Jiaxiao Chen
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Zhonghui Gu
- Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Youjun Xu
- Infinite Intelligence PharmaBeijingChina
| | - Minghua Deng
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- School of Mathematical SciencesPeking UniversityBeijingChina
- Center for Statistical SciencePeking UniversityBeijingChina
| | - Luhua Lai
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- BNLMS, College of Chemistry and Molecular EngineeringPeking UniversityBeijingChina
- Research Unit of Drug Design MethodChinese Academy of Medical SciencesBeijingChina
| | - Jianfeng Pei
- Center for Quantitative BiologyAcademy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- Research Unit of Drug Design MethodChinese Academy of Medical SciencesBeijingChina
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33
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Callahan N, Siegall WB, Bergonzo C, Marino JP, Kelman Z. Contributions from ClpS surface residues in modulating N-terminal peptide binding and their implications for NAAB development. Protein Eng Des Sel 2023; 36:gzad007. [PMID: 37498171 DOI: 10.1093/protein/gzad007] [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: 03/14/2023] [Revised: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023] Open
Abstract
Numerous technologies are currently in development for use in next-generation protein sequencing platforms. A notable published approach employs fluorescently-tagged binding proteins to identity the N-terminus of immobilized peptides, in-between rounds of digestion. This approach makes use of N-terminal amino acid binder (NAAB) proteins, which would identify amino acids by chemical and shape complementarity. One source of NAABs is the ClpS protein family, which serve to recruit proteins to bacterial proteosomes based on the identity of the N-terminal amino acid. In this study, a Thermosynechococcus vestitus (also known as Thermosynechococcus elongatus) ClpS2 protein was used as the starting point for direct evolution of an NAAB with affinity and specificity for N-terminal leucine. Enriched variants were analyzed and shown to improve the interaction between the ClpS surface and the peptide chain, without increasing promiscuity. Interestingly, interactions were found that were unanticipated which favor different charged residues located at position 5 from the N-terminus of a target peptide.
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Affiliation(s)
- Nicholas Callahan
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - William B Siegall
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Christina Bergonzo
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards & Technology (NIST), 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards & Technology (NIST), 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research (IBBR), National Institute of Standards & Technology (NIST) and the University of Maryland (UMD), 9600 Gudelsky Drive, Rockville, MD 20850, USA
- National Institute of Standards & Technology (NIST), 100 Bureau Drive, Gaithersburg, MD 20899, USA
- Biomolecular Labeling Laboratory, IBBR, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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34
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He H, Wu C, Saqib M, Hao R. Single-molecule fluorescence methods for protein biomarker analysis. Anal Bioanal Chem 2023:10.1007/s00216-022-04502-9. [PMID: 36609860 DOI: 10.1007/s00216-022-04502-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
Proteins have been considered key building blocks of life. In particular, the protein content of an organism and a cell offers significant information for the in-depth understanding of the disease and biological processes. Single-molecule protein detection/sequencing tools will revolutionize clinical (proteomics) research, offering ultrasensitivity for low-abundance biomarker (protein) detection, which is important for the realization of early-stage disease diagnosis and single-cell proteomics. This improved detection/measurement capability delivers new sets of techniques to explore new frontiers and address important challenges in various interdisciplinary areas including nanostructured materials, molecular medicine, molecular biology, and chemistry. Importantly, fluorescence-based methods have emerged as indispensable tools for single protein detection/sequencing studies, providing a higher signal-to-noise ratio (SNR). Improvements in fluorescent dyes/probes and detector capabilities coupled with advanced (image) analysis strategies have fueled current developments for single protein biomarker detections. For example, in comparison to conventional ELISA (i.e., based on ensembled measurements), single-molecule fluorescence detection is more sensitive, faster, and more accurate with reduced background, high-throughput, and so on. In comparison to MS sequencing, fluorescence-based single-molecule protein sequencing can achieve the sequencing of peptides themselves with higher sensitivity. This review summarizes various typical single-molecule detection technologies including their methodology (modes of operation), detection limits, advantages and drawbacks, and current challenges with recent examples. We describe the fluorescence-based single-molecule protein sequencing/detection based on five kinds of technologies such as fluorosequencing, N-terminal amino acid binder, nanopore light sensing, and DNA nanotechnology. Finally, we present our perspective for developing high-performance fluorescence-based sequencing/detection techniques.
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Affiliation(s)
- Haihan He
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chuhong Wu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Muhammad Saqib
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.,Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China. .,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
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35
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Püntener S, Rivera-Fuentes P. Single-Molecule Peptide Identification Using Fluorescence Blinking Fingerprints. J Am Chem Soc 2023; 145:1441-1447. [PMID: 36603184 PMCID: PMC9853850 DOI: 10.1021/jacs.2c12561] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The ability to identify peptides with single-molecule sensitivity would lead to next-generation proteomics methods for basic research and clinical applications. Existing single-molecule peptide sequencing methods can read some amino acid sequences, but they are limited in their ability to distinguish between similar amino acids or post-translational modifications. Here, we demonstrate that the fluorescence intermittency of a peptide labeled with a spontaneously blinking fluorophore contains information about the structure of the peptide. Using a deep learning algorithm, this single-molecule blinking pattern can be used to identify the peptide. This method can distinguish between peptides with different sequences, peptides with the same sequence but different phosphorylation patterns, and even peptides that differ only by the presence of epimerized residues. This study builds the foundation for a targeted proteomics method with single-molecule sensitivity.
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Affiliation(s)
- Salome Püntener
- Institute
of Chemical Sciences and Engineering, Ecole
Polytechnique Fédéral de Lausanne, CH-1015 Lausanne, Switzerland,Department
of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Pablo Rivera-Fuentes
- Institute
of Chemical Sciences and Engineering, Ecole
Polytechnique Fédéral de Lausanne, CH-1015 Lausanne, Switzerland,Department
of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland,
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36
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He X, Liu X, Zuo F, Shi H, Jing J. Artificial intelligence-based multi-omics analysis fuels cancer precision medicine. Semin Cancer Biol 2023; 88:187-200. [PMID: 36596352 DOI: 10.1016/j.semcancer.2022.12.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 01/02/2023]
Abstract
With biotechnological advancements, innovative omics technologies are constantly emerging that have enabled researchers to access multi-layer information from the genome, epigenome, transcriptome, proteome, metabolome, and more. A wealth of omics technologies, including bulk and single-cell omics approaches, have empowered to characterize different molecular layers at unprecedented scale and resolution, providing a holistic view of tumor behavior. Multi-omics analysis allows systematic interrogation of various molecular information at each biological layer while posing tricky challenges regarding how to extract valuable insights from the exponentially increasing amount of multi-omics data. Therefore, efficient algorithms are needed to reduce the dimensionality of the data while simultaneously dissecting the mysteries behind the complex biological processes of cancer. Artificial intelligence has demonstrated the ability to analyze complementary multi-modal data streams within the oncology realm. The coincident development of multi-omics technologies and artificial intelligence algorithms has fuelled the development of cancer precision medicine. Here, we present state-of-the-art omics technologies and outline a roadmap of multi-omics integration analysis using an artificial intelligence strategy. The advances made using artificial intelligence-based multi-omics approaches are described, especially concerning early cancer screening, diagnosis, response assessment, and prognosis prediction. Finally, we discuss the challenges faced in multi-omics analysis, along with tentative future trends in this field. With the increasing application of artificial intelligence in multi-omics analysis, we anticipate a shifting paradigm in precision medicine becoming driven by artificial intelligence-based multi-omics technologies.
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Affiliation(s)
- Xiujing He
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Xiaowei Liu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Fengli Zuo
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Hubing Shi
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Jing Jing
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China.
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37
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38
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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39
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Sampath G. A binary/digital approach to amino acid identification and its application to peptide sequencing and protein identification. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2022; 45:94. [PMID: 36445647 DOI: 10.1140/epje/s10189-022-00246-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
A binary/digital method is proposed in theory for the identification of single amino acids (AAs) in the bulk or with a few molecules from a single binary measurement. Combined with Edman degradation (or other cleaving method), it can be used to sequence a peptide or identify the parent protein from a partial sequence. The approach is centered on the superspecificity property of transfer RNAs (tRNAs). Markedly different from conventional and recent single molecule (SM) sequencing methods based on analog measurements, it changes the analytical question 'Which AA is it?' to the much simpler one 'Is there an AA in the detection space?'. Each of 20 terminal residues cleaved from 20 copies of a peptide enters a different cavity with a unique tRNA; tRNA charging (or binding with AA) occurs only in the cavity with the cognate AA. The bound AA or the AA separated from the tRNA is detected with a single binary measurement; its identity is known from the position of the single high bit in the resulting 20-bit output. Alternatively, a 20-stage pipeline can be used with sparse samples. Detection of the bound AA can be done optically by tagging the AAs with a fluorescent dye, or of the freed AA electrically with a nanopore. Necessary conditions for accurate AA identification are satisfied in principle; related computations and simulation results are presented. A modified version that can be used for de novo sequencing in parallel of large numbers of peptides immobilized on a glass slide with the tRNAs carrying a fluorescent tag is also proposed. Both methods can be used for protein identification from partial sequences containing 2 or 3 AA types by using only the corresponding tRNAs. Experiments may be performed to validate them, followed by translation into practice with existing technology; potential implementation issues are discussed. Binary/digital amino acid identification for peptide sequencing.
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40
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Reed BD, Meyer MJ, Abramzon V, Ad O, Ad O, Adcock P, Ahmad FR, Alppay G, Ball JA, Beach J, Belhachemi D, Bellofiore A, Bellos M, Beltrán JF, Betts A, Bhuiya MW, Blacklock K, Boer R, Boisvert D, Brault ND, Buxbaum A, Caprio S, Choi C, Christian TD, Clancy R, Clark J, Connolly T, Croce KF, Cullen R, Davey M, Davidson J, Elshenawy MM, Ferrigno M, Frier D, Gudipati S, Hamill S, He Z, Hosali S, Huang H, Huang L, Kabiri A, Kriger G, Lathrop B, Li A, Lim P, Liu S, Luo F, Lv C, Ma X, McCormack E, Millham M, Nani R, Pandey M, Parillo J, Patel G, Pike DH, Preston K, Pichard-Kostuch A, Rearick K, Rearick T, Ribezzi-Crivellari M, Schmid G, Schultz J, Shi X, Singh B, Srivastava N, Stewman SF, Thurston TR, Thurston TR, Trioli P, Tullman J, Wang X, Wang YC, Webster EAG, Zhang Z, Zuniga J, Patel SS, Griffiths AD, van Oijen AM, McKenna M, Dyer MD, Rothberg JM. Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device. Science 2022; 378:186-192. [PMID: 36227977 DOI: 10.1126/science.abo7651] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Studies of the proteome would benefit greatly from methods to directly sequence and digitally quantify proteins and detect posttranslational modifications with single-molecule sensitivity. Here, we demonstrate single-molecule protein sequencing using a dynamic approach in which single peptides are probed in real time by a mixture of dye-labeled N-terminal amino acid recognizers and simultaneously cleaved by aminopeptidases. We annotate amino acids and identify the peptide sequence by measuring fluorescence intensity, lifetime, and binding kinetics on an integrated semiconductor chip. Our results demonstrate the kinetic principles that allow recognizers to identify multiple amino acids in an information-rich manner that enables discrimination of single amino acid substitutions and posttranslational modifications. With further development, we anticipate that this approach will offer a sensitive, scalable, and accessible platform for single-molecule proteomic studies and applications.
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Affiliation(s)
| | | | | | - Omer Ad
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | - Omer Ad
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | - Pat Adcock
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | - Gün Alppay
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mel Davey
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | | | | | | | | | | | - Zhaoyu He
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | | | - Le Huang
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | - Ali Kabiri
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | | | - An Li
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | - Peter Lim
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | | | - Caixia Lv
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | | | | | - Roger Nani
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xin Wang
- Quantum-Si, Inc., Guilford, CT 06437, USA
| | | | | | | | | | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Andrew D Griffiths
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, Paris, France
| | - Antoine M van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
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41
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Romero Romero ML, Landerer C, Poehls J, Toth‐Petroczy A. Phenotypic mutations contribute to protein diversity and shape protein evolution. Protein Sci 2022; 31:e4397. [PMID: 36040266 PMCID: PMC9375231 DOI: 10.1002/pro.4397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022]
Abstract
Errors in DNA replication generate genetic mutations, while errors in transcription and translation lead to phenotypic mutations. Phenotypic mutations are orders of magnitude more frequent than genetic ones, yet they are less understood. Here, we review the types of phenotypic mutations, their quantifications, and their role in protein evolution and disease. The diversity generated by phenotypic mutation can facilitate adaptive evolution. Indeed, phenotypic mutations, such as ribosomal frameshift and stop codon readthrough, sometimes serve to regulate protein expression and function. Phenotypic mutations have often been linked to fitness decrease and diseases. Thus, understanding the protein heterogeneity and phenotypic diversity caused by phenotypic mutations will advance our understanding of protein evolution and have implications on human health and diseases.
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Affiliation(s)
- Maria Luisa Romero Romero
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Jonas Poehls
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
| | - Agnes Toth‐Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany
- Center for Systems Biology Dresden Dresden Germany
- Cluster of Excellence Physics of Life TU Dresden Dresden Germany
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42
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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43
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Xie T, Brady A, Velarde C, Vaccarello DN, Callahan NW, Marino JP, Orski SV. Selective C-Terminal Conjugation of Protease-Derived Native Peptides for Proteomic Measurements. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9119-9128. [PMID: 35856835 DOI: 10.1021/acs.langmuir.2c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bottom-up proteomic experiments often require selective conjugation or labeling of the N- and/or C-termini of peptides resulting from proteolytic digestion. For example, techniques based on surface fluorescence imaging are emerging as a promising route to high-throughput protein sequencing but require the generation of peptide surface arrays immobilized through single C-terminal point attachment while leaving the N-terminus free. While several robust approaches are available for selective N-terminal conjugation, it has proven to be much more challenging to implement methods for selective labeling or conjugation of the C-termini that can discriminate between the C-terminal carboxyl group and other carboxyl groups on aspartate and glutamate residues. Further, many approaches based on conjugation through amide bond formation require protection of the N-terminus to avoid unwanted cross-linking reactions. To overcome these challenges, herein, we describe a new strategy for single-point selective immobilization of peptides generated by protease digestion via the C-terminus. The method involves immobilization of peptides via lysine amino acids which are found naturally at the C-terminal end of cleaved peptides from digestions of certain serine endoproteinases, like LysC. This lysine and the N-terminus, the sole two primary amines in the peptide fragments, are chemically reacted with a custom phenyl isothiocyanate (EPITC) that contains an alkyne handle. Subsequent exposure of the double-modified peptides to acid selectively cleaves the N-terminal amino acid, while the modified C-terminus lysine remains unchanged. The alkyne-modified peptides with free N-termini can then be immobilized on an azide surface through standard click chemistry. Using this general approach, surface functionalization is demonstrated using a combination of X-ray photoelectron spectroscopy (XPS), ellipsometry, and atomic force microscopy (AFM).
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Affiliation(s)
- Tian Xie
- National Institute of Standards & Technology, Gaithersburg, Maryland 20899, United States
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
- Georgetown University, Washington, District of Columbia, 20057, United States
| | - Alexandria Brady
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - Cecilia Velarde
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - David N Vaccarello
- National Institute of Standards & Technology, Gaithersburg, Maryland 20899, United States
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - Nicholas W Callahan
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - John P Marino
- National Institute of Standards & Technology, Gaithersburg, Maryland 20899, United States
- University of Maryland - Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, United States
| | - Sara V Orski
- National Institute of Standards & Technology, Gaithersburg, Maryland 20899, United States
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44
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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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45
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Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics 2022; 21:100254. [PMID: 35654359 PMCID: PMC9256833 DOI: 10.1016/j.mcpro.2022.100254] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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Affiliation(s)
- Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
| | - Thomas P Conrads
- Inova Women's Service Line, Inova Health System, Falls Church, Virginia, USA
| | - Richard R Drake
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Ravi Iyengar
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Emma Lundberg
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Salvatore Sechi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Institute in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marc Vidal
- Department of Genetics, Harvard University, Cambridge, Massachusetts, USA
| | - Christine Vogel
- New York University Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - David R Walt
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Wyss Institute at Harvard University, Boston, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
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46
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Brewer KD, Shi SM, Wyss-Coray T. Unraveling protein dynamics to understand the brain - the next molecular frontier. Mol Neurodegener 2022; 17:45. [PMID: 35717317 PMCID: PMC9206758 DOI: 10.1186/s13024-022-00546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
The technological revolution to measure global gene expression at the single-cell level is currently transforming our knowledge of the brain and neurological diseases, leading from a basic understanding of genetic regulators and risk factors to one of more complex gene interactions and biological pathways. Looking ahead, our next challenge will be the reliable measurement and understanding of proteins. We describe in this review how to apply new, powerful methods of protein labeling, tracking, and detection. Recent developments of these methods now enable researchers to uncover protein mechanisms in vivo that may previously have only been hypothesized. These methods are also useful for discovering new biology because how proteins regulate systemic interactions is not well understood in most cases, such as how they travel through the bloodstream to distal targets or cross the blood–brain barrier. Genetic sequencing of DNA and RNA have enabled many great discoveries in the past 20 years, and now, the protein methods described here are creating a more complete picture of how cells to whole organisms function. It is likely that these developments will generate another transformation in biomedical research and our understanding of the brain and will ultimately allow for patient-specific medicine on a protein level.
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Affiliation(s)
- Kyle D Brewer
- ChEM-H, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Sophia M Shi
- ChEM-H, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- ChEM-H, Stanford University, Stanford, CA, USA. .,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA. .,Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
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47
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Bachman JL, Wight CD, Bardo AM, Johnson AM, Pavlich CI, Boley AJ, Wagner HR, Swaminathan J, Iverson BL, Marcotte EM, Anslyn EV. Evaluating the Effect of Dye-Dye Interactions of Xanthene-Based Fluorophores in the Fluorosequencing of Peptides. Bioconjug Chem 2022; 33:1156-1165. [PMID: 35622964 DOI: 10.1021/acs.bioconjchem.2c00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A peptide sequencing scheme utilizing fluorescence microscopy and Edman degradation to determine the amino acid position in fluorophore-labeled peptides was recently reported, referred to as fluorosequencing. It was observed that multiple fluorophores covalently linked to a peptide scaffold resulted in a decrease in the anticipated fluorescence output and worsened the single-molecule fluorescence analysis. In this study, we report an improvement in the photophysical properties of fluorophore-labeled peptides by incorporating long and flexible (PEG)10 linkers at the peptide attachment points. Long linkers to the fluorophores were installed using copper-catalyzed azide-alkyne cycloaddition conditions. The photophysical properties of these peptides were analyzed in solution and immobilized on a microscope slide at the single-molecule level under peptide fluorosequencing conditions. Solution-phase fluorescence analysis showed improvements in both quantum yield and fluorescence lifetime with the long linkers. While on the solid support, photometry measurements showed significant increases in fluorescence brightness and 20 to 60% improvements in the ability to determine the amino acid position with fluorosequencing. This spatial distancing strategy demonstrates improvements in the peptide sequencing platform and provides a general approach for improving the photophysical properties in fluorophore-labeled macromolecules.
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Affiliation(s)
- James L Bachman
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Christopher D Wight
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Angela M Bardo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Amber M Johnson
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Cyprian I Pavlich
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Alexander J Boley
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Holden R Wagner
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jagannath Swaminathan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Brent L Iverson
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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48
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Abstract
Despite tremendous gains over the past decade, methods for characterizing proteins have generally lagged behind those for nucleic acids, which are characterized by extremely high sensitivity, dynamic range, and throughput. However, the ability to directly characterize proteins at nucleic acid levels would address critical biological challenges such as more sensitive medical diagnostics, deeper protein quantification, large-scale measurement, and discovery of alternate protein isoforms and modifications and would open new paths to single-cell proteomics. In response to this need, there has been a push to radically improve protein sequencing technologies by taking inspiration from high-throughput nucleic acid sequencing, with a particular focus on developing practical methods for single-molecule protein sequencing (SMPS). SMPS technologies fall generally into three categories: sequencing by degradation (e.g., mass spectrometry or fluorosequencing), sequencing by transit (e.g., nanopores or quantum tunneling), and sequencing by affinity (as in DNA hybridization-based approaches). We describe these diverse approaches, which range from those that are already experimentally well-supported to the merely speculative, in this nascent field striving to reformulate proteomics.
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Affiliation(s)
- Brendan M Floyd
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, USA; ,
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, Texas, USA; ,
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49
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Gomes AV. How a 300-word publication changed protein biochemistry –the power of Edman degradation. Arch Biochem Biophys 2022; 726:109304. [DOI: 10.1016/j.abb.2022.109304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
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50
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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