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Huang HT, Lumpkin RJ, Tsai RW, Su S, Zhao X, Xiong Y, Chen J, Mageed N, Donovan KA, Fischer ES, Sellers WR. Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates. Nat Chem Biol 2024; 20:1227-1236. [PMID: 38514884 DOI: 10.1038/s41589-024-01590-9] [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: 07/13/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Protein ubiquitylation controls diverse processes within eukaryotic cells, including protein degradation, and is often dysregulated in disease. Moreover, small-molecule degraders that redirect ubiquitylation activities toward disease targets are an emerging and promising therapeutic class. Over 600 E3 ubiquitin ligases are expressed in humans, but their substrates remain largely elusive, necessitating the development of new methods for their discovery. Here we report the development of E3-substrate tagging by ubiquitin biotinylation (E-STUB), a ubiquitin-specific proximity labeling method that biotinylates ubiquitylated substrates in proximity to an E3 ligase of interest. E-STUB accurately identifies the direct ubiquitylated targets of protein degraders, including collateral targets and ubiquitylation events that do not lead to substrate degradation. It also detects known substrates of E3 ligase CRBN and VHL with high specificity. With the ability to elucidate proximal ubiquitylation events, E-STUB may facilitate the development of proximity-inducing therapeutics and act as a generalizable method for E3-substrate mapping.
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Affiliation(s)
- Hai-Tsang Huang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan W Tsai
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Shuyao Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xu Zhao
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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2
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Zare A, Salehi S, Bader J, Schneider C, Fischer U, Veh A, Arampatzi P, Mann M, Briese M, Sendtner M. hnRNP R promotes O-GlcNAcylation of eIF4G and facilitates axonal protein synthesis. Nat Commun 2024; 15:7430. [PMID: 39198412 PMCID: PMC11358521 DOI: 10.1038/s41467-024-51678-y] [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: 10/16/2023] [Accepted: 08/12/2024] [Indexed: 09/01/2024] Open
Abstract
Motoneurons critically depend on precise spatial and temporal control of translation for axon growth and the establishment and maintenance of neuromuscular connections. While defects in local translation have been implicated in the pathogenesis of motoneuron disorders, little is known about the mechanisms regulating axonal protein synthesis. Here, we report that motoneurons derived from Hnrnpr knockout mice show reduced axon growth accompanied by lowered synthesis of cytoskeletal and synaptic components in axons. Mutant mice display denervated neuromuscular junctions and impaired motor behavior. In axons, hnRNP R is a component of translation initiation complexes and, through interaction with O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (Ogt), modulates O-GlcNAcylation of eIF4G. Restoring axonal O-GlcNAc levels rescued local protein synthesis and axon growth defects of hnRNP R knockout motoneurons. Together, these findings demonstrate a function of hnRNP R in controlling the local production of key factors required for axon growth and formation of neuromuscular innervations.
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Affiliation(s)
- Abdolhossein Zare
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Saeede Salehi
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Jakob Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Cornelius Schneider
- Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Wuerzburg, Wuerzburg, Germany
| | - Alexander Veh
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany
| | | | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Briese
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Wuerzburg, Wuerzburg, Germany.
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3
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Li Q, Wang S, Wang J, Chen L, Liu W, Li Z, Xu J, Deng Z, Zhou Y. Mechanism of Phloretin Accumulation in Malus hupehensis Grown at High Altitudes: Evidence from Quantitative 4D Proteomics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39166542 DOI: 10.1021/acs.jafc.4c04487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Phloretin is a natural dihydrochalcone (DHC) that exhibits various pharmacological and therapeutic activities. Malus hupehensis Rehd. (M. hupehensis) is widely planted in the middle of China and its leaves contain an extremely high content of phloridzin, a glycosylated derivative of phloretin. In the present study, we observed a significant increase in phloretin content in the leaves of M. hupehensis planted at high altitudes. To investigate the mechanisms of phloretin accumulation, we explored changes in the proteome profiles of M. hupehensis plants grown at various altitudes. The results showed that at high altitudes, photosynthesis- and DHC biosynthesis-related proteins were downregulated and upregulated, respectively, leading to reduced chlorophyll content and DHC accumulation in the leaves. Moreover, we identified a novel phloridzin-catalyzing glucosidase whose expression level was significantly increased in high-altitude-cultivated plants. This work provided a better understanding of the mechanism of phloretin accumulation and effective and economic strategies for phloretin production.
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Affiliation(s)
- Qing Li
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Suzhou 215500, China
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China
| | - Shanshan Wang
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junzhi Wang
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China
| | - Lijun Chen
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China
| | - Wenrui Liu
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ziyan Li
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Suzhou 215500, China
| | - Jingyuan Xu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Suzhou 215500, China
| | - Zhangshuang Deng
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China
| | - Yiqing Zhou
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Suzhou 215500, China
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang 443002, China
- Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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4
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Wu E, Xu G, Xie D, Qiao L. Data-independent acquisition in metaproteomics. Expert Rev Proteomics 2024:1-10. [PMID: 39152734 DOI: 10.1080/14789450.2024.2394190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
INTRODUCTION Metaproteomics offers insights into the function of complex microbial communities, while it is also capable of revealing microbe-microbe and host-microbe interactions. Data-independent acquisition (DIA) mass spectrometry is an emerging technology, which holds great potential to achieve deep and accurate metaproteomics with higher reproducibility yet still facing a series of challenges due to the inherent complexity of metaproteomics and DIA data. AREAS COVERED This review offers an overview of the DIA metaproteomics approaches, covering aspects such as database construction, search strategy, and data analysis tools. Several cases of current DIA metaproteomics studies are presented to illustrate the procedures. Important ongoing challenges are also highlighted. Future perspectives of DIA methods for metaproteomics analysis are further discussed. Cited references are searched through and collected from Google Scholar and PubMed. EXPERT OPINION Considering the inherent complexity of DIA metaproteomics data, data analysis strategies specifically designed for interpretation are imperative. From this point of view, we anticipate that deep learning methods and de novo sequencing methods will become more prevalent in the future, potentially improving protein coverage in metaproteomics. Moreover, the advancement of metaproteomics also depends on the development of sample preparation methods, data analysis strategies, etc. These factors are key to unlocking the full potential of metaproteomics.
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Affiliation(s)
- Enhui Wu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Chemistry, Fudan University, Shanghai, China
| | - Guanyang Xu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Dong Xie
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liang Qiao
- Department of Chemistry, Fudan University, Shanghai, China
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5
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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6
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Paulke NJ, Fleischhacker C, Wegener JB, Riedemann GC, Cretu C, Mushtaq M, Zaremba N, Möbius W, Zühlke Y, Wedemeyer J, Liebmann L, Gorshkova AA, Kownatzki-Danger D, Wagner E, Kohl T, Wichmann C, Jahn O, Urlaub H, Toischer K, Hasenfuß G, Moser T, Preobraschenski J, Lenz C, Rog-Zielinska EA, Lehnart SE, Brandenburg S. Dysferlin Enables Tubular Membrane Proliferation in Cardiac Hypertrophy. Circ Res 2024; 135:554-574. [PMID: 39011635 DOI: 10.1161/circresaha.124.324588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Cardiac hypertrophy compensates for increased biomechanical stress of the heart induced by prevalent cardiovascular pathologies but can result in heart failure if left untreated. Here, we hypothesized that the membrane fusion and repair protein dysferlin is critical for the integrity of the transverse-axial tubule (TAT) network inside cardiomyocytes and contributes to the proliferation of TAT endomembranes during pressure overload-induced cardiac hypertrophy. METHODS Stimulated emission depletion and electron microscopy were used to localize dysferlin in mouse and human cardiomyocytes. Data-independent acquisition mass spectrometry revealed the cardiac dysferlin interactome and proteomic changes of the heart in dysferlin-knockout mice. After transverse aortic constriction, we compared the hypertrophic response of wild-type versus dysferlin-knockout hearts and studied TAT network remodeling mechanisms inside cardiomyocytes by live-cell membrane imaging. RESULTS We localized dysferlin in a vesicular compartment in nanometric proximity to contact sites of the TAT network with the sarcoplasmic reticulum, a.k.a. junctional complexes for Ca2+-induced Ca2+ release. Interactome analyses demonstrated a novel protein interaction of dysferlin with the membrane-tethering sarcoplasmic reticulum protein juncophilin-2, a putative interactor of L-type Ca2+ channels and ryanodine receptor Ca2+ release channels in junctional complexes. Although the dysferlin-knockout caused a mild progressive phenotype of dilated cardiomyopathy, global proteome analysis revealed changes preceding systolic failure. Following transverse aortic constriction, dysferlin protein expression was significantly increased in hypertrophied wild-type myocardium, while dysferlin-knockout animals presented markedly reduced left-ventricular hypertrophy. Live-cell membrane imaging showed a profound reorganization of the TAT network in wild-type left-ventricular myocytes after transverse aortic constriction with robust proliferation of axial tubules, which critically depended on the increased expression of dysferlin within newly emerging tubule components. CONCLUSIONS Dysferlin represents a new molecular target in cardiac disease that protects the integrity of tubule-sarcoplasmic reticulum junctional complexes for regulated excitation-contraction coupling and controls TAT network reorganization and tubular membrane proliferation in cardiomyocyte hypertrophy induced by pressure overload.
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Affiliation(s)
- Nora Josefine Paulke
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Carolin Fleischhacker
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Justus B Wegener
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Gabriel C Riedemann
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Constantin Cretu
- Biochemistry of Membrane Dynamics Group, Institute for Auditory Neuroscience and InnerEarLab (C.C., J.P.), University Medical Center Göttingen, Germany
| | - Mufassra Mushtaq
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Nina Zaremba
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Wiebke Möbius
- Department of Neurogenetics, Electron Microscopy, City Campus (W.M.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Yannik Zühlke
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Jasper Wedemeyer
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Lorenz Liebmann
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Anastasiia A Gorshkova
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Daniel Kownatzki-Danger
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Now with Institute of Transfusion Medicine, University Hospital Schleswig-Holstein; Kiel, Germany (D.K.-D)
| | - Eva Wagner
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Tobias Kohl
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
| | - Carolin Wichmann
- Molecular Architecture of Synapses Group, Institute for Auditory Neuroscience and InnerEarLab and Center for Biostructural Imaging of Neurodegeneration (C.W.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Olaf Jahn
- Translational Neuroproteomics Group, Department of Psychiatry and Psychotherapy (O.J.), University Medical Center Göttingen, Germany
- Neuroproteomics Group, Department of Molecular Neurobiology (O.J.)
| | - Henning Urlaub
- Department of Clinical Chemistry (H.U., C.L.), University Medical Center Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany (H.U., C.L.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Karl Toischer
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Germany (K.T., G.H., S.E.L.)
| | - Gerd Hasenfuß
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Germany (K.T., G.H., S.E.L.)
| | - Tobias Moser
- Institute for Auditory Neuroscience and InnerEarLab (T.M.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Julia Preobraschenski
- Biochemistry of Membrane Dynamics Group, Institute for Auditory Neuroscience and InnerEarLab (C.C., J.P.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Christof Lenz
- Department of Clinical Chemistry (H.U., C.L.), University Medical Center Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany (H.U., C.L.)
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
| | - Eva A Rog-Zielinska
- Institute for Experimental Cardiovascular Medicine, University Heart Center and Faculty of Medicine, University of Freiburg, Germany (E.A.R.-Z.)
| | - Stephan E Lehnart
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Germany (K.T., G.H., S.E.L.)
| | - Sören Brandenburg
- Department of Cardiology and Pneumology (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., K.T., G.H., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center (N.J.P., C.F., J.B.W., G.C.R., M.M., N.Z., Y.Z., J.W., L.L., A.A.G., D.K.-D., E.W., T.K., S.E.L., S.B.), University Medical Center Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany (W.M., C.W., H.U., K.T., G.H., T.M., J.P., C.L., S.E.L., S.B.)
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7
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Ma Q, Sun J, Liu Q, Fu J, Wen Y, Zhang F, Wu Y, Zhang X, Gong L, Zhang W. Identification of a biomarker to predict doxorubicin/cisplatin chemotherapy efficacy in osteosarcoma patients using primary, recurrent and metastatic specimens. Transl Oncol 2024; 49:102098. [PMID: 39153366 DOI: 10.1016/j.tranon.2024.102098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/23/2024] [Accepted: 08/11/2024] [Indexed: 08/19/2024] Open
Abstract
BACKGROUND Doxorubicin and cisplatin are both first-line chemotherapeutics for osteosarcoma (OS) treatment. However, the efficacy of doxorubicin/cisplatin chemotherapy varies considerably. Thus, identifying an efficient diagnostic biomarker to distinguish patients with good and poor responses to doxorubicin/cisplatin chemotherapy is of paramount importance. METHODS To predict the efficacy of doxorubicin/cisplatin chemotherapy, we analyzed the differentially expressed proteins in 37 resected OS samples, which were categorized into the primary group (PG), the recurrent group (RG) and the metastatic group (MG). The characteristics of the enriched differentially expressed proteins were assessed via GO and KEGG analyses. Protein‒protein interactions were identified to determine the relationships among the differentially expressed proteins. Receiver operating characteristic (ROC) curve analyses were performed to explore the clinical significance of the differentially expressed proteins. Parallel reaction monitoring (PRM) was used to validate the candidate proteins. Immunohistochemical (IHC) staining was performed to confirm the expression of cathepsin (CTSG) in patients with good and poor response to doxorubicin/cisplatin. RESULTS A total of 9458 proteins were identified and quantified, among which 143 and 208 exhibited significant changes (|log2FC|>1, p < 0.05) in the RG and MG compared with the PG, respectively. GO and KEGG enrichment led to the identification of neutrophil extracellular traps (NETs). ROC curve analyses revealed 74 and 86 proteins with areas under the curve greater than 0.7 in the RG and MG, respectively. PRM validation revealed the statistical significance of CTSG, which is involved in NET formation, at the protein level in both the RG and MG. IHC staining of another cohort revealed that CTSG was prominently upregulated in the poor response group after treatment with doxorubicin/cisplatin. CONCLUSION CTSG and its associated NETs are potential biomarkers with which the efficacy of doxorubicin/cisplatin chemotherapy could be predicted in OS patients.
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Affiliation(s)
- Qiong Ma
- Department of Pathology, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China; Orthopedic Oncology Institute, Department of Orthopedic Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China
| | - Jin Sun
- Orthopedic Oncology Institute, Department of Orthopedic Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China
| | - Qiao Liu
- Department of Pathology, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China
| | - Jin Fu
- Department of Pathology, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China
| | - Yanhua Wen
- Orthopedic Oncology Institute, Department of Orthopedic Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China
| | - Fuqin Zhang
- Department of Pathology, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China
| | - Yonghong Wu
- Orthopedic Oncology Institute, Department of Orthopedic Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China
| | - Xiaoyu Zhang
- Orthopedic Oncology Institute, Department of Orthopedic Surgery, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China
| | - Li Gong
- Department of Pathology, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China.
| | - Wei Zhang
- Department of Pathology, Tangdu Hospital, Air Force Medical University, 569 Xinsi Road, Xi'an 710038, China.
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8
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Fleischer S, Nash TR, Tamargo MA, Lock RI, Venturini G, Morsink M, Graney PL, Li V, Lamberti MJ, Liberman M, Kim Y, Tavakol DN, Zhuang RZ, Whitehead J, Friedman RA, Soni RK, Seidman JG, Seidman CE, Geraldino-Pardilla L, Winchester R, Vunjak-Novakovic G. An engineered human cardiac tissue model reveals contributions of systemic lupus erythematosus autoantibodies to myocardial injury. NATURE CARDIOVASCULAR RESEARCH 2024:10.1038/s44161-024-00525-w. [PMID: 39195859 DOI: 10.1038/s44161-024-00525-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 07/18/2024] [Indexed: 08/29/2024]
Abstract
Systemic lupus erythematosus (SLE) is a heterogenous autoimmune disease that affects multiple organs, including the heart. The mechanisms of myocardial injury in SLE remain poorly understood. In this study, we engineered human cardiac tissues and cultured them with IgG from patients with SLE, with and without myocardial involvement. IgG from patients with elevated myocardial inflammation exhibited increased binding to apoptotic cells within cardiac tissues subjected to stress, whereas IgG from patients with systolic dysfunction exhibited enhanced binding to the surface of live cardiomyocytes. Functional assays and RNA sequencing revealed that, in the absence of immune cells, IgG from patients with systolic dysfunction altered cellular composition, respiration and calcium handling. Phage immunoprecipitation sequencing (PhIP-seq) confirmed distinctive IgG profiles between patient subgroups. Coupling IgG profiling with cell surfaceome analysis identified four potential pathogenic autoantibodies that may directly affect the myocardium. Overall, these insights may improve patient risk stratification and inform the development of new therapeutic strategies.
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Affiliation(s)
- Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Manuel A Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Roberta I Lock
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Margaretha Morsink
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Vanessa Li
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Morgan J Lamberti
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Daniel N Tavakol
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jaron Whitehead
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Robert Winchester
- Department of Medicine, Columbia University, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
- College of Dental Medicine, Columbia University, New York, NY, USA.
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9
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Ball B, Sukumaran A, Krieger JR, Geddes-McAlister J. Comparative Cross-Kingdom DDA- and DIA-PASEF Proteomic Profiling Reveals Novel Determinants of Fungal Virulence and a Putative Druggable Target. J Proteome Res 2024. [PMID: 39140824 DOI: 10.1021/acs.jproteome.4c00255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Accurate and reliable detection of fungal pathogens presents an important hurdle to manage infections, especially considering that fungal pathogens, including the globally important human pathogen, Cryptococcus neoformans, have adapted diverse mechanisms to survive the hostile host environment and moderate virulence determinant production during coinfections. These pathogen adaptations present an opportunity for improvements (e.g., technological and computational) to better understand the interplay between a host and a pathogen during disease to uncover new strategies to overcome infection. In this study, we performed comparative proteomic profiling of an in vitro coinfection model across a range of fungal and bacterial burden loads in macrophages. Comparing data-dependent acquisition and data-independent acquisition enabled with parallel accumulation serial fragmentation technology, we quantified changes in dual-perspective proteome remodeling. We report enhanced and novel detection of pathogen proteins with data-independent acquisition-parallel accumulation serial fragmentation (DIA-PASEF), especially for fungal proteins during single and dual infection of macrophages. Further characterization of a fungal protein detected only with DIA-PASEF uncovered a novel determinant of fungal virulence, including altered capsule and melanin production, thermotolerance, and macrophage infectivity, supporting proteomics advances for the discovery of a novel putative druggable target to suppress C. neoformans pathogenicity.
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Affiliation(s)
- Brianna Ball
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Arjun Sukumaran
- Department of Molecular and Cellular Biology, University of Guelph, Guelph N1G 2W1, Ontario, Canada
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10
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Lan L, He H, Zhang J. An integration of neuroimaging and serum proteomics analysis suggests immune and inflammation are associated with white matter microstructure changes in cerebral small vessel disease with depressive symptoms. J Stroke Cerebrovasc Dis 2024; 33:107921. [PMID: 39137823 DOI: 10.1016/j.jstrokecerebrovasdis.2024.107921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 08/04/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024] Open
Abstract
INTRODUCTION Depressive symptoms are a common concomitant of cerebral small vessel disease (CSVD), of which pathogenesis requires more study. White matter microstructural abnormalities and proteomic alternation have been widely reported regarding depression in the elderly with CSVD. Exploring the relationship between cerebral white matter microstructural alterations and serum proteins may complete the explanation of molecular mechanisms for the findings from neuroimaging research of CSVD combined with depressive symptoms. METHODS An untargeted proteomics approach based on mass spectrometry was used to obtain serum proteomic profiles, which were clustered into co-expression protein modules. White matter microstructural integrity was measured using the FMRIB Software Library (FSL) and MATLAB to analyze diffusion tensor imaging (DTI) data and calculate the differences in fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) for 50 regions of interest (ROI). Integrating the proteome with the DTI results, weighted gene co-expression analysis (WGCNA) was used to identify protein modules related to white matter microstructural alterations, and the proteins of the corresponding modules were analyzed for functional enrichment through bioinformatics techniques. RESULTS DTI measurements were analCerebral small vessel disease (CSVD); Depression; Diffusion tensor imaging (DTI); Proteomics; Inflammationyzed between individuals with CSVD and depressive symptoms (CSVD+D) (n = 24) and those without depressive symptoms (CSVD-D) (n = 35). Results showed an overall increase in MD, AD, and RD within the left hemisphere of the CSVD+D group, suggesting widespread loss of white matter integrity and axonal demyelination, including left superior longitudinal fasciculus (SLF), left posterior corona radiata (PCR) and right external capsule (EC). We identified two protein modules associated with DTI diffusivity, and functional enrichment analyses revealed that complement and coagulation cascades and immune responses participate in the alternation of white matter microstructure in the CSVD+D group. CONCLUSION The results suggested immune- and inflammation-related mechanism was associated with white matter microstructure changes in CSVD with depressive symptoms.
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Affiliation(s)
- Liuyi Lan
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan, Hubei 430071, China
| | - Haoying He
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan, Hubei 430071, China
| | - Junjian Zhang
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan, Hubei 430071, China.
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11
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Panigrahi A, Hunt AL, Assis D, Willetts M, Kallakury BV, Davidson B, Conrads TP, Goldman R. dia-PASEF Proteomics of Tumor and Stroma LMD Enriched from Archived HNSCC Samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607341. [PMID: 39149249 PMCID: PMC11326218 DOI: 10.1101/2024.08.09.607341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
We employed laser microdissection to selectively harvest tumor cells and stroma from the microenvironment of formalin-fixed, paraffin-embedded head and neck squamous cell carcinoma (HNSCC) tissues. The captured HNSCC tissue fractions were analyzed by quantitative mass spectrometry-based proteomics using a data independent analysis approach. In paired samples, we achieved excellent proteome coverage having quantified 6,668 proteins with a median quantitative coefficient of variation under 10%. We observed significant differences in relevant functional pathways between the spatially resolved tumor and stroma regions. Our results identified extracellular matrix (ECM) as a major component enriched in the stroma, including many cancer associated fibroblast signature proteins in this compartment. We demonstrate the potential for comparative deep proteome analysis from very low starting input in a scalable format that is useful to decipher the alterations in tumor and the stromal microenvironment. Correlating such results with clinical features or disease progression will likely enable identification of novel targets for disease classification and interventions.
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Affiliation(s)
- Aswini Panigrahi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
| | - Allison L Hunt
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Annandale, VA 22003, USA
| | | | | | - Bhaskar V Kallakury
- Department of Pathology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Bruce Davidson
- Department of Otolaryngology-Head and Neck Surgery, Medstar Georgetown University Hospital, Washington, DC, United States
| | - Thomas P Conrads
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Annandale, VA 22003, USA
| | - Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
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12
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Hofer SJ, Daskalaki I, Bergmann M, Friščić J, Zimmermann A, Mueller MI, Abdellatif M, Nicastro R, Masser S, Durand S, Nartey A, Waltenstorfer M, Enzenhofer S, Faimann I, Gschiel V, Bajaj T, Niemeyer C, Gkikas I, Pein L, Cerrato G, Pan H, Liang Y, Tadic J, Jerkovic A, Aprahamian F, Robbins CE, Nirmalathasan N, Habisch H, Annerer E, Dethloff F, Stumpe M, Grundler F, Wilhelmi de Toledo F, Heinz DE, Koppold DA, Rajput Khokhar A, Michalsen A, Tripolt NJ, Sourij H, Pieber TR, de Cabo R, McCormick MA, Magnes C, Kepp O, Dengjel J, Sigrist SJ, Gassen NC, Sedej S, Madl T, De Virgilio C, Stelzl U, Hoffmann MH, Eisenberg T, Tavernarakis N, Kroemer G, Madeo F. Spermidine is essential for fasting-mediated autophagy and longevity. Nat Cell Biol 2024:10.1038/s41556-024-01468-x. [PMID: 39117797 DOI: 10.1038/s41556-024-01468-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: 04/04/2024] [Accepted: 07/02/2024] [Indexed: 08/10/2024]
Abstract
Caloric restriction and intermittent fasting prolong the lifespan and healthspan of model organisms and improve human health. The natural polyamine spermidine has been similarly linked to autophagy enhancement, geroprotection and reduced incidence of cardiovascular and neurodegenerative diseases across species borders. Here, we asked whether the cellular and physiological consequences of caloric restriction and fasting depend on polyamine metabolism. We report that spermidine levels increased upon distinct regimens of fasting or caloric restriction in yeast, flies, mice and human volunteers. Genetic or pharmacological blockade of endogenous spermidine synthesis reduced fasting-induced autophagy in yeast, nematodes and human cells. Furthermore, perturbing the polyamine pathway in vivo abrogated the lifespan- and healthspan-extending effects, as well as the cardioprotective and anti-arthritic consequences of fasting. Mechanistically, spermidine mediated these effects via autophagy induction and hypusination of the translation regulator eIF5A. In summary, the polyamine-hypusination axis emerges as a phylogenetically conserved metabolic control hub for fasting-mediated autophagy enhancement and longevity.
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Affiliation(s)
- Sebastian J Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Ioanna Daskalaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Martina Bergmann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Jasna Friščić
- Department of Dermatology, Allergy and Venerology, University of Lübeck, Lübeck, Germany
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Melanie I Mueller
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Mahmoud Abdellatif
- BioTechMed Graz, Graz, Austria
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Division of Cardiology, Medical University of Graz, Graz, Austria
| | - Raffaele Nicastro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Sarah Masser
- BioTechMed Graz, Graz, Austria
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Sylvère Durand
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Alexander Nartey
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Mara Waltenstorfer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Sarah Enzenhofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Isabella Faimann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Verena Gschiel
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Thomas Bajaj
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Christine Niemeyer
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Ilias Gkikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
- Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece
| | - Lukas Pein
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Giulia Cerrato
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Hui Pan
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - YongTian Liang
- Institute for Biology and Genetics, Freie Universität Berlin, Berlin, Germany
- Cluster of Excellence, NeuroCure, Berlin, Germany
| | - Jelena Tadic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Andrea Jerkovic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Fanny Aprahamian
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Christine E Robbins
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Nitharsshini Nirmalathasan
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Hansjörg Habisch
- Research Unit Integrative Structural Biology, Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, Graz, Austria
| | - Elisabeth Annerer
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | | | - Michael Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | - Daniel E Heinz
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Daniela A Koppold
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Pediatrics, Division of Oncology and Hematology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Internal Medicine and Nature-based Therapies, Immanuel Hospital Berlin, Berlin, Germany
| | - Anika Rajput Khokhar
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Michalsen
- Institute of Social Medicine, Epidemiology and Health Economics, corporate member of Freie Universität Berlin and Humboldt-Universität, Charité-Universitätsmedizin, Berlin, Germany
- Department of Internal Medicine and Nature-based Therapies, Immanuel Hospital Berlin, Berlin, Germany
| | - Norbert J Tripolt
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Harald Sourij
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas R Pieber
- BioTechMed Graz, Graz, Austria
- Interdisciplinary Metabolic Medicine Trials Unit, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
- Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- HEALTH - Institute for Biomedical Research and Technologies, Joanneum Research Forschungsgesellschaft, Graz, Austria
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Mark A McCormick
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Christoph Magnes
- HEALTH - Institute for Biomedical Research and Technologies, Joanneum Research Forschungsgesellschaft, Graz, Austria
| | - Oliver Kepp
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Stephan J Sigrist
- Institute for Biology and Genetics, Freie Universität Berlin, Berlin, Germany
- Cluster of Excellence, NeuroCure, Berlin, Germany
| | - Nils C Gassen
- Neurohomeostasis Research Group, Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Simon Sedej
- BioTechMed Graz, Graz, Austria
- Division of Cardiology, Medical University of Graz, Graz, Austria
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Tobias Madl
- BioTechMed Graz, Graz, Austria
- Research Unit Integrative Structural Biology, Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, Graz, Austria
| | | | - Ulrich Stelzl
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
| | - Markus H Hoffmann
- Department of Dermatology, Allergy and Venerology, University of Lübeck, Lübeck, Germany
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Tobias Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece.
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Équipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France.
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria.
- Field of Excellence BioHealth, University of Graz, Graz, Austria.
- BioTechMed Graz, Graz, Austria.
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13
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Mustor EM, Wohlfahrt J, Guergues J, Stevens SM, Shaw LN. A Simplified Method for Comprehensive Capture of the Staphylococcus aureus Proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.07.607079. [PMID: 39149396 PMCID: PMC11326305 DOI: 10.1101/2024.08.07.607079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Staphylococcus aureus is a major human pathogen causing myriad infections in both community and healthcare settings. Although well studied, a comprehensive exploration of its dynamic and adaptive proteome is still somewhat lacking. Herein, we employed streamlined liquid- and gas-phase fractionation with PASEF analysis on a TIMS-TOF instrument to expand coverage and explore the S. aureus dark proteome. In so doing, we captured the most comprehensive S. aureus proteome to date, totaling 2,231 proteins (85.6% coverage), using a significantly simplified process that demonstrated high reproducibility with minimal input material. We then showcase application of this library for differential expression profiling by investigating temporal dynamics of the S. aureus proteome. This revealed alterations in metabolic processes, ATP production, RNA processing, and stress-response proteins as cultures progressed to stationary growth. Notably, a significant portion of the library (94%) and proteome (80.5%) was identified by this single-shot, DIA-based analysis. Overall, our study shines new light on the hidden S. aureus proteome, generating a valuable new resource to facilitate further study of this dangerous pathogen.
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Affiliation(s)
- Emilee M Mustor
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
- Center for Antimicrobial Resistance, University of South Florida, Tampa, FL, USA
| | - Jessica Wohlfahrt
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Jennifer Guergues
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Stanley M Stevens
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Lindsey Neil Shaw
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
- Center for Antimicrobial Resistance, University of South Florida, Tampa, FL, USA
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14
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Bayne EF, Buck KM, Towler AG, Zhu Y, Pergande MR, Zhou T, Price S, Rossler KJ, Morales-Tirado V, Lloyd S, Wang F, He Y, Tian Y, Ge Y. High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. J Proteome Res 2024; 23:2908-2918. [PMID: 38315831 DOI: 10.1021/acs.jproteome.3c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins.
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Affiliation(s)
- Elizabeth F Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Anna G Towler
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Melissa R Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Tianhua Zhou
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Scott Price
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kalina J Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Vanessa Morales-Tirado
- Discovery Immunology, Pharmacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sarah Lloyd
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Fei Wang
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Yupeng He
- Discovery Immunology, Pharmacology and Pathology, AbbVie, Inc., North Chicago, Illinois 60064, United States
| | - Yu Tian
- Quantitative Translational & ADME Science, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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15
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Reis-de-Oliveira G, Carregari VC, Sousa GRDRD, Martins-de-Souza D. OmicScope unravels systems-level insights from quantitative proteomics data. Nat Commun 2024; 15:6510. [PMID: 39095347 PMCID: PMC11297029 DOI: 10.1038/s41467-024-50875-z] [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: 02/13/2024] [Accepted: 07/13/2024] [Indexed: 08/04/2024] Open
Abstract
Shotgun proteomics analysis presents multifaceted challenges, demanding diverse tool integration for insights. Addressing this complexity, OmicScope emerges as an innovative solution for quantitative proteomics data analysis. Engineered to handle various data formats, it performs data pre-processing - including joining replicates, normalization, data imputation - and conducts differential proteomics analysis for both static and longitudinal experimental designs. Empowered by Enrichr with over 224 databases, OmicScope performs Over Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA). Additionally, its Nebula module facilitates meta-analysis from independent datasets, providing a systems biology approach for enriched insights. Complete with a data visualization toolkit and accessible as Python package and a web application, OmicScope democratizes proteomics analysis, offering an efficient and high-quality pipeline for researchers.
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Affiliation(s)
- Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Research Center, Boldrini Children's Hospital, Campinas, SP, Brazil.
| | - Victor Corasolla Carregari
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
- University of Campinas (UNICAMP), Campinas, SP, Brazil.
- Instituto Nacional de Biomarcadores Em Neuropsiquiatria (INBION) Conselho Nacional de Desenvolvimento Científico E Tecnológico, São Paulo, Brazil.
- Experimental Medicine Research Cluster (EMRC), University of Campinas, Campinas, SP, Brazil.
- D'Or Institute for Research and Education (IDOR), São Paulo, Brazil.
- INCT in Modelling Human Complex Diseases with 3D Platforms (Model3D), São Paulo, Brazil.
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16
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Říhová K, Lapčík P, Veselá B, Knopfová L, Potěšil D, Pokludová J, Šmarda J, Matalová E, Bouchal P, Beneš P. Caspase-9 Is a Positive Regulator of Osteoblastic Cell Migration Identified by diaPASEF Proteomics. J Proteome Res 2024; 23:2999-3011. [PMID: 38498986 PMCID: PMC11301665 DOI: 10.1021/acs.jproteome.3c00641] [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: 10/03/2023] [Revised: 02/21/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Caspase-9 is traditionally considered the initiator caspase of the intrinsic apoptotic pathway. In the past decade, however, other functions beyond initiation/execution of cell death have been described including cell type-dependent regulation of proliferation, differentiation/maturation, mitochondrial, and endosomal/lysosomal homeostasis. As previous studies revealed nonapoptotic functions of caspases in osteogenesis and bone homeostasis, this study was performed to identify proteins and pathways deregulated by knockout of caspase-9 in mouse MC3T3-E1 osteoblasts. Data-independent acquisition-parallel accumulation serial fragmentation (diaPASEF) proteomics was used to compare protein profiles of control and caspase-9 knockout cells. A total of 7669 protein groups were quantified, and 283 upregulated/141 downregulated protein groups were associated with the caspase-9 knockout phenotype. The deregulated proteins were mainly enriched for those associated with cell migration and motility and DNA replication/repair. Altered migration was confirmed in MC3T3-E1 cells with the genetic and pharmacological inhibition of caspase-9. ABHD2, an established regulator of cell migration, was identified as a possible substrate of caspase-9. We conclude that caspase-9 acts as a modulator of osteoblastic MC3T3-E1 cell migration and, therefore, may be involved in bone remodeling and fracture repair.
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Affiliation(s)
- Kamila Říhová
- Department
of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, Brno 602 00, Czech Republic
| | - Petr Lapčík
- Department
of Biochemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Barbora Veselá
- Laboratory
of Odontogenesis and Osteogenesis, Institute of Animal Physiology
and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
| | - Lucia Knopfová
- Department
of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, Brno 602 00, Czech Republic
| | - David Potěšil
- Proteomics
Core Facility, Central European Institute for Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Jana Pokludová
- Department
of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, Brno 602 00, Czech Republic
| | - Jan Šmarda
- Department
of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Eva Matalová
- Laboratory
of Odontogenesis and Osteogenesis, Institute of Animal Physiology
and Genetics, Czech Academy of Sciences, Brno 602 00, Czech Republic
- Department
of Physiology, Faculty of Veterinary Medicine, University of Veterinary Sciences, Brno 612 42, Czech Republic
| | - Pavel Bouchal
- Department
of Biochemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Petr Beneš
- Department
of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Center, St. Anne’s
University Hospital, Brno 602 00, Czech Republic
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17
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Oliinyk D, Will A, Schneidmadel FR, Böhme M, Rinke J, Hochhaus A, Ernst T, Hahn N, Geis C, Lubeck M, Raether O, Humphrey SJ, Meier F. µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Mol Syst Biol 2024; 20:972-995. [PMID: 38907068 PMCID: PMC11297287 DOI: 10.1038/s44320-024-00050-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation.
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Affiliation(s)
- Denys Oliinyk
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Andreas Will
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Felix R Schneidmadel
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Maximilian Böhme
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Jenny Rinke
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Andreas Hochhaus
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Thomas Ernst
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Markus Lubeck
- Bruker Daltonics GmbH & Co. KG, 28359, Bremen, Germany
| | | | - Sean J Humphrey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Victoria, Australia.
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany.
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany.
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18
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Zhang S, Ghalandari B, Chen Y, Wang Q, Liu K, Sun X, Ding X, Song S, Jiang L, Ding X. Boronic Acid-Rich Lanthanide Metal-Organic Frameworks Enable Deep Proteomics with Ultratrace Biological Samples. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2401559. [PMID: 38958107 DOI: 10.1002/adma.202401559] [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: 01/30/2024] [Revised: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Label-free proteomics is widely used to identify disease mechanism and potential therapeutic targets. However, deep proteomics with ultratrace clinical specimen remains a major technical challenge due to extensive contact loss during complex sample pretreatment. Here, a hybrid of four boronic acid-rich lanthanide metal-organic frameworks (MOFs) with high protein affinity is introduced to capture proteins in ultratrace samples jointly by nitrogen-boronate complexation, cation-π and ionic interactions. A MOFs Aided Sample Preparation (MASP) workflow that shrinks sample volume and integrates lysis, protein capture, protein digestion and peptide collection steps into a single PCR tube to minimize sample loss caused by non-specific absorption, is proposed further. MASP is validated to quantify ≈1800 proteins in 10 HEK-293T cells. MASP is applied to profile cerebrospinal fluid (CSF) proteome from cerebral stroke and brain damaged patients, and identified ≈3700 proteins in 1 µL CSF. MASP is further demonstrated to detect ≈9600 proteins in as few as 50 µg mouse brain tissues. MASP thus enables deep, scalable, and reproducible proteome on precious clinical samples with low abundant proteins.
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Affiliation(s)
- Shuang Zhang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Behafarid Ghalandari
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Youming Chen
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Qingwen Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Kun Liu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xinyi Sun
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xinwen Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Sunfengda Song
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
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19
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Tonry C, Linden K, Collier P, Ledwidge M, McDonald K, Collins BC, Watson CJ. Proteomic Characterisation of Heart Failure Reveals a Unique Molecular Phenotype for Hypertrophic Cardiomyopathy. Biomedicines 2024; 12:1712. [PMID: 39200175 PMCID: PMC11351942 DOI: 10.3390/biomedicines12081712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 09/02/2024] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a disease, which is difficult to diagnose at an early stage and for which there is a pressing need for more effective treatment options. The purpose of this study was to compare the molecular profile of HCM to that of ischaemic cardiomyopathy (ISCM) and dilated cardiomyopathy (DCM) for identification of protein and pathway targets that could support the development of better diagnostic and treatment options for HCM. A high-throughput mass spectrometry workflow was applied to achieve deep quantitative coverage of left ventricular tissue from HCM, DCM, ISCM and non-heart-failure control patients. HCM had a diverse proteomic profile compared to that of DCM and ISCM. Differentially expressed proteins unique to HCM were identified based on an observed fold change of ≥1.5 or ≤0.67 and q-value ≤ 0.05. Candidate proteins of interest were found to be significantly associated with clinical features of HCM. The significant association between these proteins and HCM was validated in an independent dataset. This represents one of the largest and deepest proteomic datasets for myocardial tissue reported to date. The dataset highlights the diverse proteomic profile of HCM, relative to other cardiomyopathies, and reveals disease-relevant pathways and promising biomarker candidates that are uniquely associated with HCM.
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Affiliation(s)
- Claire Tonry
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (C.T.)
| | - Katie Linden
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (C.T.)
| | - Patrick Collier
- Department of Cardiovascular Medicine, Cleveland Clinic, OH 44195, USA
| | - Mark Ledwidge
- STOP-HF Unit, Department of Cardiology, St. Vincent’s University Hospital Healthcare Group, D04 T6F4 Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ken McDonald
- STOP-HF Unit, Department of Cardiology, St. Vincent’s University Hospital Healthcare Group, D04 T6F4 Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Ben C. Collins
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5DL, UK
| | - Chris J. Watson
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (C.T.)
- STOP-HF Unit, Department of Cardiology, St. Vincent’s University Hospital Healthcare Group, D04 T6F4 Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, D04 V1W8 Dublin, Ireland
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20
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Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Rutter JC, Lumpkin RJ, Sandoval B, Jin CY, Schmoker AM, Ficarro SB, Cheong H, Metivier RJ, Wang MY, Xu S, Byun WS, Groendyke BJ, You I, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Sperling HT, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL. Template-assisted covalent modification underlies activity of covalent molecular glues. Nat Chem Biol 2024:10.1038/s41589-024-01668-4. [PMID: 39075252 DOI: 10.1038/s41589-024-01668-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/05/2024] [Indexed: 07/31/2024]
Abstract
Molecular glues are proximity-inducing small molecules that have emerged as an attractive therapeutic approach. However, developing molecular glues remains challenging, requiring innovative mechanistic strategies to stabilize neoprotein interfaces and expedite discovery. Here we unveil a trans-labeling covalent molecular glue mechanism, termed 'template-assisted covalent modification'. We identified a new series of BRD4 molecular glue degraders that recruit CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). Through comprehensive biochemical, structural and mutagenesis analyses, we elucidated how pre-existing structural complementarity between DCAF16 and BRD4BD2 serves as a template to optimally orient the degrader for covalent modification of DCAF16Cys58. This process stabilizes the formation of BRD4-degrader-DCAF16 ternary complex and facilitates BRD4 degradation. Supporting generalizability, we found that a subset of degraders also induces GAK-BRD4BD2 interaction through trans-labeling of GAK. Together, our work establishes 'template-assisted covalent modification' as a mechanism for covalent molecular glues, which opens a new path to proximity-driven pharmacology.
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Affiliation(s)
- Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle W Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Justine C Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anna M Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hakyung Cheong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebecca J Metivier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michelle Y Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Brian J Groendyke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Logan H Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan M Tsai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felix C Majewski
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Haniya T Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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21
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Romero-Pérez PS, Moran HM, Horani A, Truong A, Manriquez-Sandoval E, Ramirez JF, Martinez A, Gollub E, Hunter K, Lotthammer JM, Emenecker RJ, Boothby TC, Holehouse AS, Fried SD, Sukenik S. Protein surface chemistry encodes an adaptive resistance to desiccation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.28.604841. [PMID: 39131385 PMCID: PMC11312438 DOI: 10.1101/2024.07.28.604841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Cellular desiccation - the loss of nearly all water from the cell - is a recurring stress in an increasing number of ecosystems that can drive proteome-wide protein unfolding and aggregation. For cells to survive this stress, at least some of the proteome must disaggregate and resume function upon rehydration. The molecular determinants that underlie the ability of proteins to do this remain largely unknown. Here, we apply quantitative and structural proteomic mass spectrometry to desiccated and rehydrated yeast extracts to show that some proteins possess an innate capacity to survive extreme water loss. Structural analysis correlates the ability of proteins to resist desiccation with their surface chemistry. Remarkably, highly resistant proteins are responsible for the production of the cell's building blocks - amino acids, metabolites, and sugars. Conversely, those proteins that are most desiccation-sensitive are involved in ribosome biogenesis and other energy consuming processes. As a result, the rehydrated proteome is preferentially enriched with metabolite and small molecule producers and depleted of some of the cell's heaviest consumers. We propose this functional bias enables cells to kickstart their metabolism and promote cell survival following desiccation and rehydration.
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Affiliation(s)
| | - Haley M. Moran
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Azeem Horani
- Quantitative and Systems Biology Program, University of California Merced, Merced, CA 95343, USA
| | - Alexander Truong
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Edgar Manriquez-Sandoval
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - John F. Ramirez
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Alec Martinez
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Edith Gollub
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Kara Hunter
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Jeffrey M. Lotthammer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Thomas C. Boothby
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Shahar Sukenik
- Dept of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
- Quantitative and Systems Biology Program, University of California Merced, Merced, CA 95343, USA
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22
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Tsukidate T, Stiving AQ, Rivera S, Sahoo A, Madabhushi S, Li X. diaPASEF Enables High-Throughput Proteomic Analysis of Host Cell Proteins for Biopharmaceutical Process Development. Anal Chem 2024. [PMID: 39060242 DOI: 10.1021/acs.analchem.4c00977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Monitoring and quantifying host cell proteins (HCPs) in biotherapeutic production processes is crucial to ensure product quality, stability, and safety. Liquid chromatography-mass spectrometry (LC-MS) analysis has emerged as an important tool for identifying and quantifying individual HCPs. However, LC-MS-based approaches face challenges due to the wide dynamic range between HCPs and the therapeutic protein as well as laborious sample preparation and long instrument time. To address these limitations, we evaluated the application of parallel accumulation-serial fragmentation combined with data-independent acquisition (diaPASEF) to HCP analysis for biopharmaceutical process development applications. We evaluated different library generation strategies and LC methods, demonstrating the suitability of these workflows for various HCP analysis needs, such as in-depth characterization and high-throughput analysis of process intermediates. Remarkably, the diaPASEF approach enabled the quantification of hundreds of HCPs that were undetectable by a standard data-dependent acquisition mode while considerably improving sample requirement, throughput, coverage, quantitative precision, and data completeness.
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Affiliation(s)
- Taku Tsukidate
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Alyssa Q Stiving
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Shannon Rivera
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ansuman Sahoo
- Biologics Process Research & Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Sri Madabhushi
- Biologics Process Research & Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Xuanwen Li
- Analytical Research & Development Mass Spectrometry, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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23
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Lai Y, Koelmel JP, Walker DI, Price EJ, Papazian S, Manz KE, Castilla-Fernández D, Bowden JA, Nikiforov V, David A, Bessonneau V, Amer B, Seethapathy S, Hu X, Lin EZ, Jbebli A, McNeil BR, Barupal D, Cerasa M, Xie H, Kalia V, Nandakumar R, Singh R, Tian Z, Gao P, Zhao Y, Froment J, Rostkowski P, Dubey S, Coufalíková K, Seličová H, Hecht H, Liu S, Udhani HH, Restituito S, Tchou-Wong KM, Lu K, Martin JW, Warth B, Godri Pollitt KJ, Klánová J, Fiehn O, Metz TO, Pennell KD, Jones DP, Miller GW. High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:12784-12822. [PMID: 38984754 PMCID: PMC11271014 DOI: 10.1021/acs.est.4c01156] [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: 02/01/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
In the modern "omics" era, measurement of the human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics and metabolomics, has emerged as a leading technology to broadly profile chemical exposure agents and related biomolecules for accurate mass measurement, high sensitivity, rapid data acquisition, and increased resolution of chemical space. Non-targeted approaches are increasingly accessible, supporting a shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating chemical exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical and computational infrastructures are needed to expand the analysis coverage through streamlined, scalable, and harmonized workflows and data pipelines that permit longitudinal chemical exposome tracking, retrospective validation, and multi-omics integration for meaningful health-oriented inferences. In this article, we survey the literature on state-of-the-art HRMS-based technologies, review current analytical workflows and informatic pipelines, and provide an up-to-date reference on exposomic approaches for chemists, toxicologists, epidemiologists, care providers, and stakeholders in health sciences and medicine. We propose efforts to benchmark fit-for-purpose platforms for expanding coverage of chemical space, including gas/liquid chromatography-HRMS (GC-HRMS and LC-HRMS), and discuss opportunities, challenges, and strategies to advance the burgeoning field of the exposome.
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Affiliation(s)
- Yunjia Lai
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Jeremy P. Koelmel
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Douglas I. Walker
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Elliott J. Price
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Stefano Papazian
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Katherine E. Manz
- Department
of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Delia Castilla-Fernández
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1010 Vienna, Austria
| | - John A. Bowden
- Center for
Environmental and Human Toxicology, Department of Physiological Sciences,
College of Veterinary Medicine, University
of Florida, Gainesville, Florida 32611, United States
| | | | - Arthur David
- Univ Rennes,
Inserm, EHESP, Irset (Institut de recherche en santé, environnement
et travail) − UMR_S, 1085 Rennes, France
| | - Vincent Bessonneau
- Univ Rennes,
Inserm, EHESP, Irset (Institut de recherche en santé, environnement
et travail) − UMR_S, 1085 Rennes, France
| | - Bashar Amer
- Thermo
Fisher Scientific, San Jose, California 95134, United States
| | | | - Xin Hu
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Elizabeth Z. Lin
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Akrem Jbebli
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Brooklynn R. McNeil
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Dinesh Barupal
- Department
of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Marina Cerasa
- Institute
of Atmospheric Pollution Research, Italian National Research Council, 00015 Monterotondo, Rome, Italy
| | - Hongyu Xie
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Vrinda Kalia
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Renu Nandakumar
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Randolph Singh
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Zhenyu Tian
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Peng Gao
- Department
of Environmental and Occupational Health, and Department of Civil
and Environmental Engineering, University
of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- UPMC Hillman
Cancer Center, Pittsburgh, Pennsylvania 15232, United States
| | - Yujia Zhao
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584CM, The Netherlands
| | | | | | - Saurabh Dubey
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kateřina Coufalíková
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hana Seličová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Helge Hecht
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Sheng Liu
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Hanisha H. Udhani
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sophie Restituito
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Kam-Meng Tchou-Wong
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Kun Lu
- Department
of Environmental Sciences and Engineering, Gillings School of Global
Public Health, The University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jonathan W. Martin
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Benedikt Warth
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1010 Vienna, Austria
| | - Krystal J. Godri Pollitt
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Jana Klánová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Oliver Fiehn
- West Coast
Metabolomics Center, University of California−Davis, Davis, California 95616, United States
| | - Thomas O. Metz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Kurt D. Pennell
- School
of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Dean P. Jones
- Department
of Medicine, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Gary W. Miller
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
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24
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Chang MEK, Lange J, Cartier JM, Moore TW, Soriano SM, Albracht B, Krawitzky M, Guturu H, Alavi A, Stukalov A, Zhou X, Elgierari EM, Chu J, Benz R, Cuevas JC, Ferdosi S, Hornburg D, Farokhzad O, Siddiqui A, Batzoglou S, Leach RJ, Liss MA, Kopp RP, Flory MR. A Scaled Proteomic Discovery Study for Prostate Cancer Diagnostic Markers Using Proteograph TM and Trapped Ion Mobility Mass Spectrometry. Int J Mol Sci 2024; 25:8010. [PMID: 39125581 PMCID: PMC11311733 DOI: 10.3390/ijms25158010] [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: 06/12/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024] Open
Abstract
There is a significant unmet need for clinical reflex tests that increase the specificity of prostate-specific antigen blood testing, the longstanding but imperfect tool for prostate cancer diagnosis. Towards this endpoint, we present the results from a discovery study that identifies new prostate-specific antigen reflex markers in a large-scale patient serum cohort using differentiating technologies for deep proteomic interrogation. We detect known prostate cancer blood markers as well as novel candidates. Through bioinformatic pathway enrichment and network analysis, we reveal associations of differentially abundant proteins with cytoskeletal, metabolic, and ribosomal activities, all of which have been previously associated with prostate cancer progression. Additionally, optimized machine learning classifier analysis reveals proteomic signatures capable of detecting the disease prior to biopsy, performing on par with an accepted clinical risk calculator benchmark.
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Affiliation(s)
- Matthew E. K. Chang
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Jane Lange
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Jessie May Cartier
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Travis W. Moore
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Sophia M. Soriano
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Brenna Albracht
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | | | | | | | | | | | | | | | - Ryan Benz
- Seer Inc., Redwood City, CA 94065, USA
| | | | | | | | | | | | | | - Robin J. Leach
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Michael A. Liss
- Roger L. & Laura D. Zeller Charitable Foundation in Urologic Oncology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Ryan P. Kopp
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Mark R. Flory
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
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25
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Lapcik P, Synkova K, Janacova L, Bouchalova P, Potesil D, Nenutil R, Bouchal P. A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer. Sci Data 2024; 11:794. [PMID: 39025866 PMCID: PMC11258311 DOI: 10.1038/s41597-024-03632-2] [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: 02/14/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, and deeper proteome coverage is needed for its molecular characterization. We present comprehensive library of targeted mass spectrometry assays specific for TNBC and demonstrate its applicability. Proteins were extracted from 105 TNBC tissues and digested. Aliquots were pooled, fractionated using hydrophilic chromatography and analyzed by LC-MS/MS in data-dependent acquisition (DDA) parallel accumulation-serial fragmentation (PASEF) mode on timsTOF Pro LC-MS system. 16 individual lysates were analyzed in data-independent acquisition (DIA)-PASEF mode. Hybrid library was generated in Spectronaut software and covers 244,464 precursors, 168,006 peptides and 11,564 protein groups (FDR = 1%). Application of our library for pilot quantitative analysis of 16 tissues increased identification numbers in Spectronaut 18.5 and DIA-NN 1.8.1 software compared to library-free setting, with Spectronaut achieving the best results represented by 190,310 precursors, 140,566 peptides, and 10,463 protein groups. In conclusion, we introduce assay library that offers the deepest coverage of TNBC proteome to date. The TNBC library is available via PRIDE repository (PXD047793).
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Grants
- NU22-08-00230 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- NU22-08-00230 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- NU22-08-00230 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- NU22-08-00230 Ministerstvo Zdravotnictví Ceské Republiky (Ministry of Health of the Czech Republic)
- LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- LX22NPO5102 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- CZ.02.1.01/0.0/0.0/18_046/0015974 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
- LM2023033 Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)
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Affiliation(s)
- Petr Lapcik
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Klara Synkova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lucia Janacova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Pavla Bouchalova
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - David Potesil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Rudolf Nenutil
- Department of Oncological Pathology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Pavel Bouchal
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.
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26
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Shi J, Liu Y, Xu YJ. MS based foodomics: An edge tool integrated metabolomics and proteomics for food science. Food Chem 2024; 446:138852. [PMID: 38428078 DOI: 10.1016/j.foodchem.2024.138852] [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: 11/29/2023] [Revised: 02/05/2024] [Accepted: 02/24/2024] [Indexed: 03/03/2024]
Abstract
Foodomics has become a popular methodology in food science studies. Mass spectrometry (MS) based metabolomics and proteomics analysis played indispensable roles in foodomics research. So far, several methodologies have been developed to detect the metabolites and proteins in diets and consumers, including sample preparation, MS data acquisition, annotation and interpretation. Moreover, multiomics analysis integrated metabolomics and proteomics have received considerable attentions in the field of food safety and nutrition, because of more comprehensive and deeply. In this context, we intended to review the emerging strategies and their applications in MS-based foodomics, as well as future challenges and trends. The principle and application of multiomics were also discussed, such as the optimization of data acquisition, development of analysis algorithm and exploration of systems biology.
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Affiliation(s)
- Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, People's Republic of China.
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27
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Wang Q, Ding X, Xu Z, Wang B, Wang A, Wang L, Ding Y, Song S, Chen Y, Zhang S, Jiang L, Ding X. The mouse multi-organ proteome from infancy to adulthood. Nat Commun 2024; 15:5752. [PMID: 38982135 PMCID: PMC11233712 DOI: 10.1038/s41467-024-50183-6] [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: 04/21/2023] [Accepted: 07/03/2024] [Indexed: 07/11/2024] Open
Abstract
The early-life organ development and maturation shape the fundamental blueprint for later-life phenotype. However, a multi-organ proteome atlas from infancy to adulthood is currently not available. Herein, we present a comprehensive proteomic analysis of ten mouse organs (brain, heart, lung, liver, kidney, spleen, stomach, intestine, muscle and skin) at three crucial developmental stages (1-, 4- and 8-weeks after birth) acquired using data-independent acquisition mass spectrometry. We detect and quantify 11,533 protein groups across the ten organs and obtain 115 age-related differentially expressed protein groups that are co-expressed in all organs from infancy to adulthood. We find that spliceosome proteins prevalently play crucial regulatory roles in the early-life development of multiple organs, and detect organ-specific expression patterns and sexual dimorphism. This multi-organ proteome atlas provides a fundamental resource for understanding the molecular mechanisms underlying early-life organ development and maturation.
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Affiliation(s)
- Qingwen Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xinwen Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhixiao Xu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Boqian Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Aiting Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sunfengda Song
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Youming Chen
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuang Zhang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China.
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28
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Ctortecka C, Clark NM, Boyle BW, Seth A, Mani DR, Udeshi ND, Carr SA. Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications. Nat Commun 2024; 15:5707. [PMID: 38977691 PMCID: PMC11231172 DOI: 10.1038/s41467-024-49651-w] [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: 01/24/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
The recent technological and computational advances in mass spectrometry-based single-cell proteomics have pushed the boundaries of sensitivity and throughput. However, reproducible quantification of thousands of proteins within a single cell remains challenging. To address some of those limitations, we present a dedicated sample preparation chip, the proteoCHIP EVO 96 that directly interfaces with the Evosep One. This, in combination with the Bruker timsTOF demonstrates double the identifications without manual sample handling and the newest generation timsTOF Ultra identifies up to 4000 with an average of 3500 protein groups per single HEK-293T without a carrier or match-between runs. Our workflow spans 4 orders of magnitude, identifies over 50 E3 ubiquitin-protein ligases, and profiles key regulatory proteins upon small molecule stimulation. This study demonstrates that the proteoCHIP EVO 96-based sample preparation with the timsTOF Ultra provides sufficient proteome depth to study complex biology beyond cell-type classifications.
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Affiliation(s)
| | | | - Brian W Boyle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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29
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Wang Y, Lih TM, Lee JW, Ohtsuka T, Hozaka Y, Mino-Kenudson M, Adsay NV, Luchini C, Scarpa A, Maker AV, Kim GE, Paulino J, Chen L, Jiao L, Sun Z, Goodman D, Pflüger MJ, Roberts NJ, Matthaei H, Wood LD, Furukawa T, Zhang H, Hruban RH. Multi-omic profiling of intraductal papillary neoplasms of the pancreas reveals distinct expression patterns and potential markers of progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.07.602385. [PMID: 39005476 PMCID: PMC11245086 DOI: 10.1101/2024.07.07.602385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In order to advance our understanding of precancers in the pancreas, 69 pancreatic intraductal papillary neoplasms (IPNs), including 64 intraductal papillary mucinous neoplasms (IPMNs) and 5 intraductal oncocytic papillary neoplasms (IOPNs), 32 pancreatic cyst fluid samples, 104 invasive pancreatic ductal adenocarcinomas (PDACs), 43 normal adjacent tissues (NATs), and 76 macro-dissected normal pancreatic ducts (NDs) were analyzed by mass spectrometry. A total of 10,246 proteins and 22,284 glycopeptides were identified in all tissue samples, and 756 proteins with more than 1.5-fold increase in abundance in IPMNs relative to NDs were identified, 45% of which were also identified in cyst fluids. The over-expression of selected proteins was validated by immunolabeling. Proteins and glycoproteins overexpressed in IPMNs included those involved in glycan biosynthesis and the immune system. In addition, multiomics clustering identified two subtypes of IPMNs. This study provides a foundation for understanding tumor progression and targets for earlier detection and therapies. Significance This multilevel characterization of intraductal papillary neoplasms of the pancreas provides a foundation for understanding the changes in protein and glycoprotein expression during the progression from normal duct to intraductal papillary neoplasm, and to invasive pancreatic carcinoma, providing a foundation for informed approaches to earlier detection and treatment.
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30
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Shen HP, Dong X, Li ZB, Wu JZ, Zheng CM, Hu XJ, Qian C, Wang SP, Zhao YL, Li JC. Protein Profiles and Novel Molecular Biomarkers of Schizophrenia Based on 4D-DIA Proteomics. J Proteome Res 2024; 23:2376-2385. [PMID: 38856018 DOI: 10.1021/acs.jproteome.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Schizophrenia is a severe psychological disorder. The current diagnosis mainly relies on clinical symptoms and lacks laboratory evidence, which makes it very difficult to make an accurate diagnosis especially at an early stage. Plasma protein profiles of schizophrenia patients were obtained and compared with healthy controls using 4D-DIA proteomics technology. Furthermore, 79 DEPs were identified between schizophrenia and healthy controls. GO functional analysis indicated that DEPs were predominantly associated with responses to toxic substances and platelet aggregation, suggesting the presence of metabolic and immune dysregulation in patients with schizophrenia. KEGG pathway enrichment analysis revealed that DEPs were primarily enriched in the chemokine signaling pathway and cytokine receptor interactions. A diagnostic model was ultimately established, comprising three proteins, namely, PFN1, GAPDH and ACTBL2. This model demonstrated an AUC value of 0.972, indicating its effectiveness in accurately identifying schizophrenia. PFN1, GAPDH and ACTBL2 exhibit potential as biomarkers for the early detection of schizophrenia. The findings of our studies provide novel insights into the laboratory-based diagnosis of schizophrenia.
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Affiliation(s)
- Hui-Ping Shen
- Department of Psychiatry, Shaoxing Seventh People's Hospital, Shaoxing 312000, China
| | - Xiaotao Dong
- Major Disease Biomarker Research Laboratory, School of Basic Medical Science, Henan University, Kaifeng 475004, China
| | - Zhi-Bin Li
- Major Disease Biomarker Research Laboratory, School of Basic Medical Science, Henan University, Kaifeng 475004, China
| | - Jing-Zhu Wu
- Department of Psychiatry, Shaoxing Seventh People's Hospital, Shaoxing 312000, China
| | - Chun-Mei Zheng
- Department of Psychiatry, Shaoxing Seventh People's Hospital, Shaoxing 312000, China
| | - Xie-Jun Hu
- Department of Psychiatry, Shaoxing Seventh People's Hospital, Shaoxing 312000, China
| | - Chao Qian
- Department of Psychiatry, Shaoxing Seventh People's Hospital, Shaoxing 312000, China
| | - Sheng-Pang Wang
- Department of Psychiatry, Shaoxing Seventh People's Hospital, Shaoxing 312000, China
| | - Yu-Long Zhao
- Department of Psychiatry, Shaoxing Seventh People's Hospital, Shaoxing 312000, China
| | - Ji-Cheng Li
- Major Disease Biomarker Research Laboratory, School of Basic Medical Science, Henan University, Kaifeng 475004, China
- Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
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31
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Deguchi S, Kosugi K, Takeishi N, Watanabe Y, Morimoto S, Negoro R, Yokoi F, Futatsusako H, Nakajima-Koyama M, Iwasaki M, Yamamoto T, Kawaguchi Y, Torisawa YS, Takayama K. Construction of multilayered small intestine-like tissue by reproducing interstitial flow. Cell Stem Cell 2024:S1934-5909(24)00220-0. [PMID: 38996472 DOI: 10.1016/j.stem.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/18/2024] [Accepted: 06/18/2024] [Indexed: 07/14/2024]
Abstract
Recent advances have made modeling human small intestines in vitro possible, but it remains a challenge to recapitulate fully their structural and functional characteristics. We suspected interstitial flow within the intestine, powered by circulating blood plasma during embryonic organogenesis, to be a vital factor. We aimed to construct an in vivo-like multilayered small intestinal tissue by incorporating interstitial flow into the system and, in turn, developed the micro-small intestine system by differentiating definitive endoderm and mesoderm cells from human pluripotent stem cells simultaneously on a microfluidic device capable of replicating interstitial flow. This approach enhanced cell maturation and led to the development of a three-dimensional small intestine-like tissue with villi-like epithelium and an aligned mesenchymal layer. Our micro-small intestine system not only overcomes the limitations of conventional intestine models but also offers a unique opportunity to gain insights into the detailed mechanisms underlying intestinal tissue development.
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Affiliation(s)
- Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
| | - Kaori Kosugi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Naoki Takeishi
- Faculty of Mechanical Engineering, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Yukio Watanabe
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Shiho Morimoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Ryosuke Negoro
- Laboratory of Molecular Pharmacokinetics, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Fuki Yokoi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroki Futatsusako
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Department of Human Health Sciences, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - May Nakajima-Koyama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Mio Iwasaki
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan; Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Yoshiya Kawaguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Yu-Suke Torisawa
- Department of Micro Engineering, Kyoto University, Kyoto 615-8540, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo 100-0004, Japan.
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32
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Jenke R, Oliinyk D, Zenz T, Körfer J, Schäker-Hübner L, Hansen FK, Lordick F, Meier-Rosar F, Aigner A, Büch T. HDAC inhibitors activate lipid peroxidation and ferroptosis in gastric cancer. Biochem Pharmacol 2024; 225:116257. [PMID: 38705532 DOI: 10.1016/j.bcp.2024.116257] [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: 01/18/2024] [Revised: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Gastric cancer remains among the deadliest neoplasms worldwide, with limited therapeutic options. Since efficacies of targeted therapies are unsatisfactory, drugs with broader mechanisms of action rather than a single oncogene inhibition are needed. Preclinical studies have identified histone deacetylases (HDAC) as potential therapeutic targets in gastric cancer. However, the mechanism(s) of action of HDAC inhibitors (HDACi) are only partially understood. This is particularly true with regard to ferroptosis as an emerging concept of cell death. In a panel of gastric cancer cell lines with different molecular characteristics, tumor cell inhibitory effects of different HDACi were studied. Lipid peroxidation levels were measured and proteome analysis was performed for the in-depth characterization of molecular alterations upon HDAC inhibition. HDACi effects on important ferroptosis genes were validated on the mRNA and protein level. Upon HDACi treatment, lipid peroxidation was found increased in all cell lines. Class I HDACi (VK1, entinostat) showed the same toxicity profile as the pan-HDACi vorinostat. Proteome analysis revealed significant and concordant alterations in the expression of proteins related to ferroptosis induction. Key enzymes like ACSL4, POR or SLC7A11 showed distinct alterations in their expression patterns, providing an explanation for the increased lipid peroxidation. Results were also confirmed in primary human gastric cancer tissue cultures as a relevant ex vivo model. We identify the induction of ferroptosis as new mechanism of action of class I HDACi in gastric cancer. Notably, these findings were independent of the genetic background of the cell lines, thus introducing HDAC inhibition as a more general therapeutic principle.
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Affiliation(s)
- Robert Jenke
- University Cancer Center Leipzig (UCCL), University Hospital Leipzig, Leipzig, Germany; Leipzig University, Medical Faculty, Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig, Germany; Comprehensive Cancer Center Central Germany (CCCG), Leipzig and Jena, Germany
| | - Denys Oliinyk
- Jena University Hospital, Functional Proteomics, Research Center Lobeda, Jena, Germany
| | - Tamara Zenz
- Leipzig University, Medical Faculty, Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig, Germany
| | - Justus Körfer
- University Cancer Center Leipzig (UCCL), University Hospital Leipzig, Leipzig, Germany; University Hospital Leipzig, Institute for Anatomy, Leipzig, Germany
| | - Linda Schäker-Hübner
- University of Bonn, Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, Bonn, Germany
| | - Finn K Hansen
- University of Bonn, Pharmaceutical Institute, Department of Pharmaceutical and Cell Biological Chemistry, Bonn, Germany
| | - Florian Lordick
- University Cancer Center Leipzig (UCCL), University Hospital Leipzig, Leipzig, Germany; Comprehensive Cancer Center Central Germany (CCCG), Leipzig and Jena, Germany
| | - Florian Meier-Rosar
- Jena University Hospital, Functional Proteomics, Research Center Lobeda, Jena, Germany; Comprehensive Cancer Center Central Germany (CCCG), Leipzig and Jena, Germany
| | - Achim Aigner
- Leipzig University, Medical Faculty, Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig, Germany; Comprehensive Cancer Center Central Germany (CCCG), Leipzig and Jena, Germany.
| | - Thomas Büch
- Leipzig University, Medical Faculty, Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig, Germany; Comprehensive Cancer Center Central Germany (CCCG), Leipzig and Jena, Germany
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33
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Ning J, Yang M, Zhu Q, Liu X, Li M, Luo X, Yue X. Revealing the diversity of endogenous peptides and parent proteins in human colostrum and mature milk through peptidomics analysis. Food Chem 2024; 445:138651. [PMID: 38359565 DOI: 10.1016/j.foodchem.2024.138651] [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: 10/26/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
Endogenous peptides and their parent proteins are important nutritional components with diverse biological functions. The objective of this study was to analyze and compare endogenous peptides and parent proteins found in human colostrum (HC) and human mature milk (HM) using a 4D label-free technique. In total, 5162 and 940 endogenous peptides derived from 258 parent proteins were identified in human milk by database (DB) search and de novo, respectively. Among these peptides, 2446 differentially expressed endogenous peptides with various bioactivities were identified. The Gene Ontology analysis unveiled the cellular components, biological processes, and molecular functions associated with these parent proteins. Metabolic pathway analysis suggested that neutrophil extracellular trap formation had the greatest significance with 24 parent proteins. These findings will offer a fresh perspective on the development of infant formula powder, highlighting the potential for incorporating these changes to enhance its nutritional composition and benefits.
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Affiliation(s)
- Jianting Ning
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Mei Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Qing Zhu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyu Liu
- Department of Obstetrics and Gynaecology, General Hospital of Northern Theater Command, Shenyang 110016, China
| | - Mohan Li
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Xue Luo
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, China.
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34
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Mangiavacchi A, Morelli G, Reppe S, Saera-Vila A, Liu P, Eggerschwiler B, Zhang H, Bensaddek D, Casanova EA, Medina Gomez C, Prijatelj V, Della Valle F, Atinbayeva N, Izpisua Belmonte JC, Rivadeneira F, Cinelli P, Gautvik KM, Orlando V. LINE-1 RNA triggers matrix formation in bone cells via a PKR-mediated inflammatory response. EMBO J 2024:10.1038/s44318-024-00143-z. [PMID: 38951609 DOI: 10.1038/s44318-024-00143-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 07/03/2024] Open
Abstract
Transposable elements (TEs) are mobile genetic modules of viral derivation that have been co-opted to become modulators of mammalian gene expression. TEs are a major source of endogenous dsRNAs, signaling molecules able to coordinate inflammatory responses in various physiological processes. Here, we provide evidence for a positive involvement of TEs in inflammation-driven bone repair and mineralization. In newly fractured mice bone, we observed an early transient upregulation of repeats occurring concurrently with the initiation of the inflammatory stage. In human bone biopsies, analysis revealed a significant correlation between repeats expression, mechanical stress and bone mineral density. We investigated a potential link between LINE-1 (L1) expression and bone mineralization by delivering a synthetic L1 RNA to osteoporotic patient-derived mesenchymal stem cells and observed a dsRNA-triggered protein kinase (PKR)-mediated stress response that led to strongly increased mineralization. This response was associated with a strong and transient inflammation, accompanied by a global translation attenuation induced by eIF2α phosphorylation. We demonstrated that L1 transfection reshaped the secretory profile of osteoblasts, triggering a paracrine activity that stimulated the mineralization of recipient cells.
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Affiliation(s)
- Arianna Mangiavacchi
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Science and Engineering Division, Thuwal, 23500-6900, Kingdom of Saudi Arabia.
| | - Gabriele Morelli
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Science and Engineering Division, Thuwal, 23500-6900, Kingdom of Saudi Arabia
| | - Sjur Reppe
- Oslo University Hospital, Department of Medical Biochemistry, Oslo, Norway
- Lovisenberg Diaconal Hospital, Unger-Vetlesen Institute, Oslo, Norway
- Oslo University Hospital, Department of Plastic and Reconstructive Surgery, Oslo, Norway
| | | | - Peng Liu
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Science and Engineering Division, Thuwal, 23500-6900, Kingdom of Saudi Arabia
| | - Benjamin Eggerschwiler
- Department of Trauma, University Hospital Zurich, Sternwartstrasse 14, 8091, Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Huoming Zhang
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, 23500-6900, Kingdom of Saudi Arabia
| | - Dalila Bensaddek
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal, 23500-6900, Kingdom of Saudi Arabia
| | - Elisa A Casanova
- Sequentia Biotech, Carrer Comte D'Urgell 240, Barcelona, 08036, Spain
| | | | - Vid Prijatelj
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Francesco Della Valle
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Science and Engineering Division, Thuwal, 23500-6900, Kingdom of Saudi Arabia
- Altos Labs, San Diego, CA, USA
| | - Nazerke Atinbayeva
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Science and Engineering Division, Thuwal, 23500-6900, Kingdom of Saudi Arabia
| | | | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Paolo Cinelli
- Sequentia Biotech, Carrer Comte D'Urgell 240, Barcelona, 08036, Spain
- Center for Applied Biotechnology and Molecular Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Valerio Orlando
- King Abdullah University of Science and Technology (KAUST), Biological Environmental Science and Engineering Division, Thuwal, 23500-6900, Kingdom of Saudi Arabia.
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Jiao X, Li X, Zhang N, Yan B, Huang J, Zhao J, Zhang H, Chen W, Fan D. Solubilization of fish myofibrillar proteins in NaCl and KCl solutions: A DIA-based proteomics analysis. Food Chem 2024; 445:138662. [PMID: 38354641 DOI: 10.1016/j.foodchem.2024.138662] [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: 12/05/2023] [Revised: 01/20/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Understanding the basic solubilization of fish myofibrillar proteins (MPs) in common monovalent chloride solutions is crucial for muscle food processing. In this study, the differential proteomic profiles of MPs during extraction and solubilization in NaCl and KCl solutions were investigated by using advanced four-dimensional data-independent acquisition (4D DIA) quantitative proteomics for the first time. Compared to routine biochemical analysis, this could provide insights into the solubilization of muscle proteins. We ensure the consistency of the effective ionic strength of NaCl and KCl buffers by adjusting the conductivity. The results showed that NaCl extractor mainly facilitated the solubilization of cytoskeletal proteins, biochemical enzymes, and stromal proteins compared to KCl, such as tubulin, myosin-9, collagen, plectin, protein phosphatase, and cathepsin D. However, no significant difference was observed in the extraction of major sarcomeric proteins, including myosin, actin, troponin C, myosin-binding protein C, M-Protein, α-actinin-3, and tropomyosin.
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Affiliation(s)
- Xidong Jiao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
| | - Xingying Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Nana Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China.
| | - Bowen Yan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China
| | - Jianlian Huang
- ANJOY FOODS GROUP CO., LTD., Xiamen 361022, China; Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China; Engineering Technology Research Center of Refrigeration and Conditioning Aquatic Food (Liaoning Anjoy Food Co., LTD), China National Light Industry Council, Anshan 114100, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Daming Fan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; Key Laboratory of Refrigeration and Conditioning Aquatic Products Processing, Ministry of Agriculture and Rural Affairs, Xiamen 361022, China; Engineering Technology Research Center of Refrigeration and Conditioning Aquatic Food (Liaoning Anjoy Food Co., LTD), China National Light Industry Council, Anshan 114100, China.
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36
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Ramsay E, Montaser AB, Niitsu K, Urtti A, Auriola S, Huttunen KM, Uchida Y, Kidron H, Terasaki T. Transporter Protein Expression of Corneal Epithelium in Rabbit and Porcine: Evaluation of Models for Ocular Drug Transport Study. Mol Pharm 2024; 21:3204-3217. [PMID: 38809137 DOI: 10.1021/acs.molpharmaceut.3c01210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The transcorneal route is the main entry route for drugs to the intraocular parts, after topical administration. The outer surface, the corneal epithelium (CE), forms the rate-limiting barrier for drug permeability. Information about the role and protein expression of drug and amino acid transporter proteins in the CE is sparse and lacking. The aim of our study was to characterize transporter protein expression in rabbit and porcine CE to better understand potential drug and nutrient absorption after topical administration. Proteins, mainly Abc and Slc transporters, were characterized with quantitative targeted absolute proteomics and global untargeted proteomics methods. In the rabbit CE, 24 of 48 proteins were detected in the targeted approach, and 21 of these were quantified. In the porcine CE, 26 of 58 proteins were detected in the targeted approach, and 20 of these were quantified. Among these, 15 proteins were quantified in both animals: 4f2hc (Slc3a2), Aqp0, Asct1 (Slc1a4), Asct2 (Slc1a5), Glut1 (Slc2a1), Hmit (Slc2a13), Insr, Lat1 (Slc7a5), Mct1 (Slc16a1), Mct2 (Slc16a7), Mct4 (Slc16a3), Mrp 4 (Abcc4), Na+/K+-ATPase, Oatp3a1 (Slco3a1), and Snat2 (Slc38a2). Overall, the global proteomics results supported the targeted proteomics results. Organic anion transporting polypeptide Oatp3a1 was detected and quantified for the first time in both rabbit (1.4 ± 0.4 fmol/cm2) and porcine (11.1 ± 5.3 fmol/cm2) CE. High expression levels were observed for L-type amino acid transporter, Lat1, which was quantified with newly selected extracellular domain peptides in rabbit (48.9 ± 11.8 fmol/cm2) and porcine (37.6 ± 11.5 fmol/cm2) CE. The knowledge of transporter protein expression in ocular barriers is a key factor in the successful design of new ocular drugs, pharmacokinetic modeling, understanding ocular diseases, and the translation to human.
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Affiliation(s)
- Eva Ramsay
- Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Ahmed B Montaser
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Kanako Niitsu
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Arto Urtti
- Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Seppo Auriola
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Kristiina M Huttunen
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
| | - Yasuo Uchida
- Department of Molecular Systems Pharmaceutics, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Heidi Kidron
- Drug Research Programme, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - Tetsuya Terasaki
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland
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37
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Eeltink S, De Vos J, Desmet G. Toward Unrivaled Chromatographic Resolving Power in Proteomics: Design and Development of Comprehensive Spatial Three-Dimensional Liquid-Phase Separation Technology. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:475-493. [PMID: 38424031 DOI: 10.1146/annurev-anchem-061522-044510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Spatial comprehensive three-dimensional chromatography (3D-LC) offers an innovative approach to achieve unprecedented resolving power in terms of peak capacity and sample throughput. This advanced technique separates components within a 3D separation space, where orthogonal retention mechanisms are incorporated. The parallel development of the second- and third-dimension stages effectively overcomes the inherent limitation of conventional multidimensional approaches, where sampled fractions are analyzed sequentially. This review focuses on the design aspects of the microchip for spatial 3D-LC and the selection of orthogonal separation modes to enable the analysis of intact proteins. The design considerations for the flow distributor and channel layout are discussed, along with various approaches to confine the flow during the subsequent development stages. Additionally, the integration of stationary phases into the microchip is addressed, and interfacing to mass spectrometry detection is discussed. According to Pareto optimality, the integration of isoelectric focusing, size-exclusion chromatography, and reversed-phase chromatography in a spatial 3D-LC approach is predicted to achieve an exceptional peak capacity of over 30,000 within a 1-h analysis, setting a new benchmark in chromatographic performance.
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Affiliation(s)
- Sebastiaan Eeltink
- 1Department of Chemical Engineering, Vrije Universiteit Brussel, Brussels, Belgium;
| | - Jelle De Vos
- 1Department of Chemical Engineering, Vrije Universiteit Brussel, Brussels, Belgium;
- 2Current affiliation: RIC Group, Kortrijk, Belgium
| | - Gert Desmet
- 1Department of Chemical Engineering, Vrije Universiteit Brussel, Brussels, Belgium;
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38
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Naimy S, Sølberg JBK, Kuczek DE, Løvendorf MB, Bzorek M, Litman T, Mund A, Rahbek Gjerdrum LM, Clark RA, Mann M, Dyring-Andersen B. Comparative Quantitative Proteomic Analysis of Melanoma Subtypes, Nevus-Associated Melanoma, and Corresponding Nevi. J Invest Dermatol 2024; 144:1608-1621.e4. [PMID: 38185415 DOI: 10.1016/j.jid.2023.12.011] [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: 07/04/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
Abstract
A substantial part of cutaneous malignant melanomas develops from benign nevi. However, the precise molecular events driving the transformation from benign to malignant melanoma are not well-understood. We used laser microdissection and mass spectrometry to analyze the proteomes of melanoma subtypes, including superficial spreading melanomas (n = 17), nodular melanomas (n = 17), and acral melanomas (n = 15). Furthermore, we compared the proteomes of nevi cells with those of melanoma cells within the same specimens (nevus-associated melanoma (n = 14)). In total, we quantified 7935 proteins. Despite the genomic and clinical differences of the melanoma subtypes, our analysis revealed relatively similar proteomes, except for the upregulation of proteins involved in immune activation in nodular melanomas versus acral melanomas. Examining nevus-associated melanoma versus nevi, we found 1725 differentially expressed proteins (false discovery rate < 0.05). Among these proteins were 140 that overlapped with cancer hallmarks, tumor suppressors, and regulators of metabolism and cell cycle. Pathway analysis indicated aberrant activation of the phosphoinositide 3-kinase-protein kinase B-mTOR pathways and the Hippo-YAP pathway. Using a classifier, we identified six proteins capable of distinguishing melanoma from nevi samples. Our study represents a comprehensive comparative analysis of the proteome in melanoma subtypes and associated nevi, offering insights into the biological behavior of these distinct entities.
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Affiliation(s)
- Soraya Naimy
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Julie B K Sølberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark
| | - Dorota E Kuczek
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Bengtson Løvendorf
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark; Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Bzorek
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Thomas Litman
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Mund
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Beatrice Dyring-Andersen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark; Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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39
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Yao D, Shen C, Yu J, Tang J, Zhang H, Xu X, Tu M, Cheong LZ. Proteomic analysis of milk fat globule membrane proteins in mature human milk of women with and without gestational diabetes mellitus. Food Chem 2024; 445:138691. [PMID: 38354646 DOI: 10.1016/j.foodchem.2024.138691] [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: 08/19/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Milk fat globule membrane proteins (MFGMP) in human milks have positive effects on infant's health. As gestational diabetes mellitus (GDM) causes variations in MFGMP, it is essential to understand the effects of GDMon MFGMP. This study aims to investigate and compare the MFGMP (>3 months postpartum) of GDM and non-GDM (NGDM) women using four-dimensional-data-independent-acquisition proteomics technology. Principal component analysis shows significant differences in the MFGMP of GDM and NGDM women. A total of 4747 MFGMP were identified in maturehuman milk of GDM and NGDM women. Among these proteins, 174 differentially expressed proteins (DEPs) were identified in MFGM of GDM and NGDM women. Albumin (FC = 7.96) and transthyretin (FC = 2.57) which are related to insulin resistance and involved in thyroid hormone synthesis, are significantly up-regulated in MFGMP of GDM mothers indicating insulin resistance, imbalance of glucose homeostasis and poor glucose metabolism might persist in postpartum period.
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Affiliation(s)
- Dan Yao
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo, 315211, China
| | - Cai Shen
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, University of Melbourne, 3010, Australia
| | - Jingwen Yu
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo, 315211, China
| | - Jiayue Tang
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo, 315211, China
| | - Hong Zhang
- Wilmar (Shanghai) Biotechnology Research and Development Center Co Ltd., No.118 Gaodong Rd., Pudong New District, Shanghai 200137, China
| | - Xuebing Xu
- Wilmar (Shanghai) Biotechnology Research and Development Center Co Ltd., No.118 Gaodong Rd., Pudong New District, Shanghai 200137, China
| | - Maolin Tu
- Zhejiang-Malaysia Joint Research Laboratory for Agricultural Product Processing and Nutrition, Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Science, Ningbo University, Ningbo, 315211, China
| | - Ling-Zhi Cheong
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, University of Melbourne, 3010, Australia.
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40
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He G, He Q, Cheng J, Yu R, Shuai J, Cao Y. ProPept-MT: A Multi-Task Learning Model for Peptide Feature Prediction. Int J Mol Sci 2024; 25:7237. [PMID: 39000344 PMCID: PMC11241495 DOI: 10.3390/ijms25137237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
In the realm of quantitative proteomics, data-independent acquisition (DIA) has emerged as a promising approach, offering enhanced reproducibility and quantitative accuracy compared to traditional data-dependent acquisition (DDA) methods. However, the analysis of DIA data is currently hindered by its reliance on project-specific spectral libraries derived from DDA analyses, which not only limits proteome coverage but also proves to be a time-intensive process. To overcome these challenges, we propose ProPept-MT, a novel deep learning-based multi-task prediction model designed to accurately forecast key features such as retention time (RT), ion intensity, and ion mobility (IM). Leveraging advanced techniques such as multi-head attention and BiLSTM for feature extraction, coupled with Nash-MTL for gradient coordination, ProPept-MT demonstrates superior prediction performance. Integrating ion mobility alongside RT, mass-to-charge ratio (m/z), and ion intensity forms 4D proteomics. Then, we outline a comprehensive workflow tailored for 4D DIA proteomics research, integrating the use of 4D in silico libraries predicted by ProPept-MT. Evaluation on a benchmark dataset showcases ProPept-MT's exceptional predictive capabilities, with impressive results including a 99.9% Pearson correlation coefficient (PCC) for RT prediction, a median dot product (DP) of 96.0% for fragment ion intensity prediction, and a 99.3% PCC for IM prediction on the test set. Notably, ProPept-MT manifests efficacy in predicting both unmodified and phosphorylated peptides, underscoring its potential as a valuable tool for constructing high-quality 4D DIA in silico libraries.
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Affiliation(s)
- Guoqiang He
- Postgraduate Training Base Alliance, Wenzhou Medical University, Wenzhou 325000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Qingzu He
- Department of Physics, and Fujian Provincial Key Laboratory for Soft Functional Materials Research, Xiamen University, Xiamen 361005, China
| | - Jinyan Cheng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Rongwen Yu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Jianwei Shuai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Yi Cao
- Postgraduate Training Base Alliance, Wenzhou Medical University, Wenzhou 325000, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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41
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Madsen S, Delgado AC, Cadilhac C, Maillard V, Battiston F, Igelbüscher CM, De Neck S, Magrinelli E, Jabaudon D, Telley L, Doetsch F, Knobloch M. A fluorescent perilipin 2 knock-in mouse model reveals a high abundance of lipid droplets in the developing and adult brain. Nat Commun 2024; 15:5489. [PMID: 38942786 PMCID: PMC11213871 DOI: 10.1038/s41467-024-49449-w] [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: 07/20/2022] [Accepted: 06/03/2024] [Indexed: 06/30/2024] Open
Abstract
Lipid droplets (LDs) are dynamic lipid storage organelles. They are tightly linked to metabolism and can exert protective functions, making them important players in health and disease. Most LD studies in vivo rely on staining methods, providing only a snapshot. We therefore developed a LD-reporter mouse by labelling the endogenous LD coat protein perilipin 2 (PLIN2) with tdTomato, enabling staining-free fluorescent LD visualisation in living and fixed tissues and cells. Here we validate this model under standard and high-fat diet conditions and demonstrate that LDs are highly abundant in various cell types in the healthy brain, including neurons, astrocytes, ependymal cells, neural stem/progenitor cells and microglia. Furthermore, we also show that LDs are abundant during brain development and can be visualized using live imaging of embryonic slices. Taken together, our tdTom-Plin2 mouse serves as a novel tool to study LDs and their dynamics under both physiological and diseased conditions in all tissues expressing Plin2.
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Affiliation(s)
- Sofia Madsen
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | | | - Christelle Cadilhac
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Vanille Maillard
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Fabrice Battiston
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | | | - Simon De Neck
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Elia Magrinelli
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Ludovic Telley
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | | | - Marlen Knobloch
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland.
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42
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Nanaware PP, Khan ZN, Clement CC, Shetty M, Mota I, Seltzer ES, Dzieciatkowska M, Gamboni F, D'Alessandro A, Ng C, Nagayama M, Lichti CF, Soni RK, Jacob B Geri, Matei I, Lyden D, Longman R, Lu TT, Wan X, Unanue ER, Stern LJ, Santambrogio L. Role of the afferent lymph as an immunological conduit to analyze tissue antigenic and inflammatory load. Cell Rep 2024; 43:114311. [PMID: 38848214 PMCID: PMC11233987 DOI: 10.1016/j.celrep.2024.114311] [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: 10/16/2023] [Revised: 04/03/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024] Open
Abstract
The lymphatic fluid is the conduit by which part of the tissue "omics" is transported to the draining lymph node for immunosurveillance. Following cannulation of the pre-nodal cervical and mesenteric afferent lymphatics, herein we investigate the lymph proteomic composition, uncovering that its composition varies according to the tissue of origin. Tissue specificity is also reflected in the dendritic cell-major histocompatibility complex class II-eluted immunopeptidome harvested from the cervical and mesenteric nodes. Following inflammatory disruption of the gut barrier, the lymph antigenic and inflammatory loads are analyzed in both mice and subjects with inflammatory bowel diseases. Gastrointestinal tissue damage reflects the lymph inflammatory and damage-associated molecular pattern signatures, microbiome-derived by-products, and immunomodulatory molecules, including metabolites of the gut-brain axis, mapped in the afferent mesenteric lymph. Our data point to the relevance of the lymphatic fluid to probe the tissue-specific antigenic and inflammatory load transported to the draining lymph node for immunosurveillance.
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Affiliation(s)
- Padma P Nanaware
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zohaib N Khan
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Cristina C Clement
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Madhur Shetty
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ines Mota
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ethan S Seltzer
- Pediatric Rheumatology and Autoimmunity and Inflammation Program, Hospital for Special Surgery Research Institute, New York NY 100021, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Fabia Gamboni
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Charles Ng
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital and Weill Cornell Medicine, New York, NY 10065, USA
| | - Manabu Nagayama
- Division of Gastroenterology and Hepatology, New York-Presbyterian Hospital and Weill Cornell Medicine, New York, NY 10065, USA
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York 10032, NY, USA
| | - Jacob B Geri
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA
| | - Irina Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, New York, NY 10065, USA
| | - David Lyden
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, New York, NY 10065, USA
| | - Randy Longman
- Division of Gastroenterology and Hepatology, New York-Presbyterian Hospital and Weill Cornell Medicine, New York, NY 10065, USA
| | - Theresa T Lu
- Pediatric Rheumatology and Autoimmunity and Inflammation Program, Hospital for Special Surgery Research Institute, New York NY 100021, USA
| | - Xiaoxiao Wan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Emil R Unanue
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Laura Santambrogio
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Sandra and Edward Meyer Cancer Center, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, New York, NY 10065, USA.
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43
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Zhang Y, Yang A, Zhao Z, Chen F, Yan X, Han Y, Wu D, Wu Y. Protein disulfide isomerase is essential for spermatogenesis in mice. JCI Insight 2024; 9:e177743. [PMID: 38912589 DOI: 10.1172/jci.insight.177743] [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: 11/20/2023] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
Spermatogenesis requires precise posttranslational control in the endoplasmic reticulum (ER), but the mechanism remains largely unknown. The protein disulfide isomerase (PDI) family is a group of thiol oxidoreductases responsible for catalyzing the disulfide bond formation of nascent proteins. In this study, we generated 14 strains of KO mice lacking the PDI family enzymes and found that only PDI deficiency caused spermatogenesis defects. Both inducible whole-body PDI-KO (UBC-Cre/Pdifl/fl) mice and premeiotic PDI-KO (Stra8-Cre/Pdifl/fl) mice experienced a significant decrease in germ cells, testicular atrophy, oligospermia, and complete male infertility. Stra8-Cre/Pdifl/fl spermatocytes had significantly upregulated ER stress-related proteins (GRP78 and XBP1) and apoptosis-related proteins (Cleaved caspase-3 and BAX), together with cell apoptosis. PDI deletion led to delayed DNA double-strand break repair and improper crossover at the pachytene spermatocytes. Quantitative mass spectrometry indicated that PDI deficiency downregulated vital proteins in spermatogenesis such as HSPA4L, SHCBP1L, and DDX4, consistent with the proteins' physical association with PDI in normal testes tissue. Furthermore, PDI served as a thiol oxidase for disulfide bond formation of SHCBP1L. Thus, PDI plays an essential role in protein quality control for spermatogenesis in mice.
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Affiliation(s)
- Yaqiong Zhang
- National Clinical Research Center for Hematologic Diseases, Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Aizhen Yang
- National Clinical Research Center for Hematologic Diseases, Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Zhenzhen Zhao
- National Clinical Research Center for Hematologic Diseases, Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Fengwu Chen
- National Clinical Research Center for Hematologic Diseases, Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Xiaofeng Yan
- National Clinical Research Center for Hematologic Diseases, Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Yue Han
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi Wu
- National Clinical Research Center for Hematologic Diseases, Cyrus Tang Medical Institute, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
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44
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Soni RK. Frontiers in plasma proteome profiling platforms: innovations and applications. Clin Proteomics 2024; 21:43. [PMID: 38902643 PMCID: PMC11191172 DOI: 10.1186/s12014-024-09497-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Biomarkers play a crucial role in advancing precision medicine by enabling more targeted and individualized approaches to diagnosis and treatment. Various biofluids, including serum, plasma, cerebrospinal fluid (CSF), saliva, tears, pancreatic cyst fluids, and urine, have been identified as rich sources of potential for the early detection of disease biomarkers in conditions such as cancer, cardiovascular diseases, and neurodegenerative disorders. The analysis of plasma and serum in proteomics research encounters challenges due to their high complexity and the wide dynamic range of protein abundance. These factors impede the sensitivity, coverage, and precision of protein detection when employing mass spectrometry, a widely utilized technology in discovery proteomics. Conventional approaches such as Neat Plasma workflow are inefficient in accurately quantifying low-abundant proteins, including those associated with tissue leakage, immune response molecules, interleukins, cytokines, and interferons. Moreover, the manual nature of the workflow poses a significant hurdle in conducting large cohort studies. In this study, our focus is on comparing workflows for plasma proteomic profiling to establish a methodology that is not only sensitive and reproducible but also applicable for large cohort studies in biomarker discovery. Our investigation revealed that the Proteograph XT workflow outperforms other workflows in terms of plasma proteome depth, quantitative accuracy, and reproducibility while offering complete automation of sample preparation. Notably, Proteograph XT demonstrates versatility by applying it to various types of biofluids. Additionally, the proteins quantified widely cover secretory proteins in peripheral blood, and the pathway analysis enriched with relevant components such as interleukins, tissue necrosis factors, chemokines, and B and T cell receptors provides valuable insights. These proteins, often challenging to quantify in complex biological samples, hold potential as early detection markers for various diseases, thereby contributing to the improvement of patient care quality.
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Affiliation(s)
- Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University Irving Medical Center, New York, USA.
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, USA.
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45
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Ma W, Sun Y, Zhang H. Protocol for identifying OXCT1-mediated LACTB succinylation sites in vitro. STAR Protoc 2024; 5:103088. [PMID: 38787728 PMCID: PMC11144799 DOI: 10.1016/j.xpro.2024.103088] [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: 01/10/2024] [Revised: 03/08/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
OXCT1 acts as a succinyltransferase to promote serine beta-lactamase-like protein (LACTB) K284 succinylation. Here, we present a protocol for detecting OXCT1-mediated LACTB succinylation levels and sites. We describe steps for using western blotting (WB) and mass spectrometry to determine OXCT1-mediated LACTB succinylation levels and sites in vitro. This protocol can be applied to detect and identify succinylation levels and sites on other proteins. For complete details on the use and execution of this protocol, please refer to Ma et al.1.
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Affiliation(s)
- Wenhao Ma
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Anhui Province Key Laboratory of Biomedical Aging Research, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Yuchen Sun
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Anhui Province Key Laboratory of Biomedical Aging Research, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Huafeng Zhang
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui 230601, China; Anhui Province Key Laboratory of Biomedical Aging Research, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China.
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46
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Fröhlich K, Fahrner M, Brombacher E, Seredynska A, Maldacker M, Kreutz C, Schmidt A, Schilling O. Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics. Mol Cell Proteomics 2024; 23:100800. [PMID: 38880244 DOI: 10.1016/j.mcpro.2024.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
Data-independent acquisition (DIA) has revolutionized the field of mass spectrometry (MS)-based proteomics over the past few years. DIA stands out for its ability to systematically sample all peptides in a given m/z range, allowing an unbiased acquisition of proteomics data. This greatly mitigates the issue of missing values and significantly enhances quantitative accuracy, precision, and reproducibility compared to many traditional methods. This review focuses on the critical role of DIA analysis software tools, primarily focusing on their capabilities and the challenges they address in proteomic research. Advances in MS technology, such as trapped ion mobility spectrometry, or high field asymmetric waveform ion mobility spectrometry require sophisticated analysis software capable of handling the increased data complexity and exploiting the full potential of DIA. We identify and critically evaluate leading software tools in the DIA landscape, discussing their unique features, and the reliability of their quantitative and qualitative outputs. We present the biological and clinical relevance of DIA-MS and discuss crucial publications that paved the way for in-depth proteomic characterization in patient-derived specimens. Furthermore, we provide a perspective on emerging trends in clinical applications and present upcoming challenges including standardization and certification of MS-based acquisition strategies in molecular diagnostics. While we emphasize the need for continuous development of software tools to keep pace with evolving technologies, we advise researchers against uncritically accepting the results from DIA software tools. Each tool may have its own biases, and some may not be as sensitive or reliable as others. Our overarching recommendation for both researchers and clinicians is to employ multiple DIA analysis tools, utilizing orthogonal analysis approaches to enhance the robustness and reliability of their findings.
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Affiliation(s)
- Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| | - Eva Brombacher
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Adrianna Seredynska
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maximilian Maldacker
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany.
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47
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Roberts DS, Loo JA, Tsybin YO, Liu X, Wu S, Chamot-Rooke J, Agar JN, Paša-Tolić L, Smith LM, Ge Y. Top-down proteomics. NATURE REVIEWS. METHODS PRIMERS 2024; 4:38. [PMID: 39006170 PMCID: PMC11242913 DOI: 10.1038/s43586-024-00318-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 07/16/2024]
Abstract
Proteoforms, which arise from post-translational modifications, genetic polymorphisms and RNA splice variants, play a pivotal role as drivers in biology. Understanding proteoforms is essential to unravel the intricacies of biological systems and bridge the gap between genotypes and phenotypes. By analysing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and can decipher protein function, uncover disease mechanisms and advance precision medicine. This Primer explores TDP, including the underlying principles, recent advances and an outlook on the future. The experimental section discusses instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques and data collection. The results section looks at how to decipher raw data, visualize intact protein spectra and unravel data analysis. Additionally, proteoform identification, characterization and quantification are summarized, alongside approaches for statistical analysis. Various applications are described, including the human proteoform project and biomedical, biopharmaceutical and clinical sciences. These are complemented by discussions on measurement reproducibility, limitations and a forward-looking perspective that outlines areas where the field can advance, including potential future applications.
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Affiliation(s)
- David S Roberts
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California - Los Angeles, Los Angeles, CA, USA
| | | | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
| | | | - Jeffrey N Agar
- Departments of Chemistry and Chemical Biology and Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Ljiljana Paša-Tolić
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
- Department of Cell and Regenerative Biology, Human Proteomics Program, University of Wisconsin - Madison, Madison, WI, USA
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48
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Eberhard CD, Orsburn BC. Acetic acid is a superior ion pairing modifier for sub-nanogram and single cell proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.01.551522. [PMID: 37577694 PMCID: PMC10418182 DOI: 10.1101/2023.08.01.551522] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
A recent study demonstrated a substantial increase in peptide signal and corresponding proteome coverage when employing 0.5% acetic acid (AA) as the ion pairing modifier in place of the 0.1% formic acid traditionally used in shotgun proteomics. In this study, we investigated the effect of modifier in the context of sub-nanogram and single cell proteomics (SCP). We first evaluated a tryptic digest standard down to 20 picograms total load on column on a TIMSTOF SCP system. In line with the previous results, we observed a signal increase when using AA, leading to increased proteome coverage at every peptide load assessed. Relative improvements were more apparent at lower concentrations, with a 20 picogram peptide digest demonstrating a striking 1.8-fold increase to over 2,000 protein groups identified in a 30 minute analysis. Furthermore, we find that this increase in signal can be leveraged to reduce ramp times, leading to 1.7x more scans across each peak and improvements in quantification as measured by %CVs. When evaluating single cancer cells, approximately 13% more peptide groups were identified on average when employing AA in the place of FA. All vendor raw and processed data are available through ProteomeXchange as PXD046002 and PXD051590.
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49
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Wu Z, Chai Z, Cai X, Wang J, Wang H, Yue B, Zhang M, Wang J, Wang H, Zhong J, Xin J. Protein Lactylation Profiles Provide Insights into Molecular Mechanisms Underlying Metabolism in Yak. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38850252 DOI: 10.1021/acs.jafc.4c01800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
Protein lysine lactylation, a recently discovered post-translational modification (PTM), is prevalent across tissues and cells of diverse species, serving as a regulator of glycolytic flux and biological metabolism. The yak (Bos grunniens), a species that has inhabited the Qinghai-Tibetan Plateau for millennia, has evolved intricate adaptive mechanisms to cope with the region's unique geographical and climatic conditions, exhibiting remarkable energy utilization and metabolic efficiency. Nonetheless, the specific landscape of lysine lactylation in yaks remains poorly understood. Herein, we present the first comprehensive lactylome profile of the yak, effectively identifying 421, 308, and 650 lactylated proteins in the heart, muscles, and liver, respectively. These lactylated proteins are involved in glycolysis/gluconeogenesis, the tricarboxylic acid cycle, oxidative phosphorylation, and metabolic process encompassing carbohydrates, lipids, and proteins during both anaerobic and aerobic glucose bio-oxidation, implying their crucial role in material and energy metabolism, as well as in maintaining homeostasis in yaks.
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Affiliation(s)
- Zhijuan Wu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Xin Cai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Binglin Yue
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Ming Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Haibo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, Chengdu, Sichuan 610225, China
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, Sichuan 610225, China
| | - Jinwei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850000, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Institute of Animal Science and Veterinary, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850009, China
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50
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Tang N, Tang L, Lyu J, Jiang X, Li Y, Ding C, Xiang S. Effect of Acupuncture on Tear Proteomics in Patients with Video Display Terminal-Related Dry Eye. J Proteome Res 2024; 23:2206-2218. [PMID: 38723043 PMCID: PMC11165574 DOI: 10.1021/acs.jproteome.4c00134] [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: 03/01/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 06/13/2024]
Abstract
Acupuncture is widely used to treat dry eye disease (DED), but its effect has not been reported in treating video display terminal (VDT)-related dry eye, and the mechanism of acupuncture on VDT-related dry eye is also unknown. In our study, the tear proteome was compared with identifying possible mechanisms and biomarkers for predicting acupuncture effectiveness in VDT-related dry eye. The results showed that the ocular surface disease index scores were significantly different between the acupuncture group (AC group) and artificial tears group (AT group) at the end of the study, whereas tear film breakup time (TFBUT) and Schirmer I test (SIT) were not significantly different between the groups. Proteome changes pre- and post-treatment in the AC group were associated with B cell-related immune processes, inflammation, glycolysis, and actin cytoskeleton. Furthermore, the proteins hexosaminidase A and mannose-binding lectin 1 could prospectively predict whether acupuncture treatment was effective. Therefore, we believe that acupuncture can provide greater improvement in the clinical symptoms of VDT-related dry eye than artificial tears. The mechanism of acupuncture in VDT-related dry eye treatment may be associated with glycolysis- and actin cytoskeleton remodeling-mediated inflammatory and immune processes. Additionally, hexosaminidase A and mannose-binding lectin 1 are biomarkers for predicting the efficacy of acupuncture for VDT-related dry eye.
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Affiliation(s)
- Na Tang
- National
Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Lewei Tang
- National
Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Jiacheng Lyu
- State
Key Laboratory of Genetic Engineering and Collaborative Innovation
Center for Genetics and Development, School of Life Sciences, Institutes
of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Xiaohan Jiang
- National
Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yan Li
- National
Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Chen Ding
- State
Key Laboratory of Genetic Engineering and Collaborative Innovation
Center for Genetics and Development, School of Life Sciences, Institutes
of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Shengjin Xiang
- National
Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
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