1
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Deinhardt-Emmer S, Deshpande S, Kitazawa K, Herman AB, Bons J, Rose JP, Kumar PA, Anerillas C, Neri F, Ciotlos S, Perez K, Köse-Vogel N, Häder A, Abdelmohsen K, Löffler B, Gorospe M, Desprez PY, Melov S, Furman D, Schilling B, Campisi J. Role of the Senescence-Associated Factor Dipeptidyl Peptidase 4 in the Pathogenesis of SARS-CoV-2 Infection. Aging Dis 2024; 15:1398-1415. [PMID: 37728586 PMCID: PMC11081172 DOI: 10.14336/ad.2023.0812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/12/2023] [Indexed: 09/21/2023] Open
Abstract
During cellular senescence, persistent growth arrest and changes in protein expression programs are accompanied by a senescence-associated secretory phenotype (SASP). In this study, we detected the upregulation of the SASP-related protein dipeptidyl peptidase 4 (DDP4) in human primary lung cells rendered senescent by exposure to ionizing radiation. DPP4 is an exopeptidase that plays a crucial role in the cleavage of various proteins, resulting in the loss of N-terminal dipeptides and proinflammatory effects. Interestingly, our data revealed an association between severe coronavirus disease 2019 (COVID-19) and DDP4, namely that DPP4 levels increased in the plasma of patients with COVID-19 and were correlated with age and disease progression. Although we could not determine the direct effect of DDP4 on viral replication, mechanistic studies in cell culture revealed a negative impact on the expression of the tight junction protein zonula occludens-1 (ZO-1), which contributes to epithelial barrier function. Mass spectrometry analysis indicated that DPP4 overexpressing cells exhibited a decrease in ZO-1 and increased expression of pro-inflammatory cytokines and chemokines. By investigating the effect of DPP4 on the barrier function of human primary cells, we detected an increase in ZO-1 using DPP4 inhibitors. These results provide an important contribution to our understanding of DPP4 in the context of senescence, suggesting that DPP4 plays a major role as part of the SASP. Our results provide evidence that cellular senescence, a hallmark of aging, has an important impact on respiratory infections.
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Affiliation(s)
- Stefanie Deinhardt-Emmer
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | | | - Koji Kitazawa
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Allison B. Herman
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Jacob P. Rose
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | | | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Francesco Neri
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Serban Ciotlos
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Kevin Perez
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - Nilay Köse-Vogel
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Antje Häder
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Germany.
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | | | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | - David Furman
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA 94305, USA.
- Buck Artificial Intelligence Platform, Buck Institute for Research on Aging, Novato, CA 94945, USA.
| | | | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
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2
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Menon T, Illing PT, Chaurasia P, McQuilten HA, Shepherd C, Rowntree LC, Petersen J, Littler DR, Khuu G, Huang Z, Allen LF, Rockman S, Crowe J, Flanagan KL, Wakim LM, Nguyen THO, Mifsud NA, Rossjohn J, Purcell AW, van de Sandt CE, Kedzierska K. CD8 + T-cell responses towards conserved influenza B virus epitopes across anatomical sites and age. Nat Commun 2024; 15:3387. [PMID: 38684663 PMCID: PMC11059233 DOI: 10.1038/s41467-024-47576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/03/2024] [Indexed: 05/02/2024] Open
Abstract
Influenza B viruses (IBVs) cause substantive morbidity and mortality, and yet immunity towards IBVs remains understudied. CD8+ T-cells provide broadly cross-reactive immunity and alleviate disease severity by recognizing conserved epitopes. Despite the IBV burden, only 18 IBV-specific T-cell epitopes restricted by 5 HLAs have been identified currently. A broader array of conserved IBV T-cell epitopes is needed to develop effective cross-reactive T-cell based IBV vaccines. Here we identify 9 highly conserved IBV CD8+ T-cell epitopes restricted to HLA-B*07:02, HLA-B*08:01 and HLA-B*35:01. Memory IBV-specific tetramer+CD8+ T-cells are present within blood and tissues. Frequencies of IBV-specific CD8+ T-cells decline with age, but maintain a central memory phenotype. HLA-B*07:02 and HLA-B*08:01-restricted NP30-38 epitope-specific T-cells have distinct T-cell receptor repertoires. We provide structural basis for the IBV HLA-B*07:02-restricted NS1196-206 (11-mer) and HLA-B*07:02-restricted NP30-38 epitope presentation. Our study increases the number of IBV CD8+ T-cell epitopes, and defines IBV-specific CD8+ T-cells at cellular and molecular levels, across tissues and age.
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Affiliation(s)
- Tejas Menon
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T Illing
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Priyanka Chaurasia
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Chloe Shepherd
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jan Petersen
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Grace Khuu
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ziyi Huang
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Lilith F Allen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Steve Rockman
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- CSL Seqirus Ltd, Parkville, VIC, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, VIC, Australia
| | - Katie L Flanagan
- Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
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3
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Numa K, Patel SK, Zhang ZA, Burton JB, Matsumoto A, Hughes JWB, Sotozono C, Schilling B, Desprez PY, Campisi J, Kitazawa K. Senescent characteristics of human corneal endothelial cells upon ultraviolet-A exposure. Aging (Albany NY) 2024; 16:6673-6693. [PMID: 38683123 PMCID: PMC11087119 DOI: 10.18632/aging.205761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/28/2024] [Indexed: 05/01/2024]
Abstract
PURPOSE The objective of this study was to investigate the senescent phenotypes of human corneal endothelial cells (hCEnCs) upon treatment with ultraviolet (UV)-A. METHODS We assessed cell morphology, senescence-associated β-galactosidase (SA-β-gal) activity, cell proliferation and expression of senescence markers (p16 and p21) in hCEnCs exposed to UV-A radiation, and senescent hCEnCs induced by ionizing radiation (IR) were used as positive controls. We performed RNA sequencing and proteomics analyses to compare gene and protein expression profiles between UV-A- and IR-induced senescent hCEnCs, and we also compared the results to non-senescent hCEnCs. RESULTS Cells exposed to 5 J/cm2 of UV-A or to IR exhibited typical senescent phenotypes, including enlargement, increased SA-β-gal activity, decreased cell proliferation and elevated expression of p16 and p21. RNA-Seq analysis revealed that 83.9% of the genes significantly upregulated and 82.6% of the genes significantly downregulated in UV-A-induced senescent hCEnCs overlapped with the genes regulated in IR-induced senescent hCEnCs. Proteomics also revealed that 93.8% of the proteins significantly upregulated in UV-A-induced senescent hCEnCs overlapped with those induced by IR. In proteomics analyses, senescent hCEnCs induced by UV-A exhibited elevated expression levels of several factors part of the senescence-associated secretory phenotype. CONCLUSIONS In this study, where senescence was induced by UV-A, a more physiological stress for hCEnCs compared to IR, we determined that UV-A modulated the expression of many genes and proteins typically altered upon IR treatment, a more conventional method of senescence induction, even though UV-A also modulated specific pathways unrelated to IR.
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Affiliation(s)
- Kohsaku Numa
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Kyoto Prefectural University of Medicine, Department of Ophthalmology, Kyoto 6020841, Japan
| | - Sandip Kumar Patel
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QR, UK
| | | | | | - Akifumi Matsumoto
- Kyoto Prefectural University of Medicine, Department of Ophthalmology, Kyoto 6020841, Japan
| | | | - Chie Sotozono
- Kyoto Prefectural University of Medicine, Department of Ophthalmology, Kyoto 6020841, Japan
| | | | - Pierre-Yves Desprez
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- California Pacific Medical Center, Research Institute, San Francisco, CA 94107, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Koji Kitazawa
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Kyoto Prefectural University of Medicine, Department of Ophthalmology, Kyoto 6020841, Japan
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4
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Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. A framework for quality control in quantitative proteomics. bioRxiv 2024:2024.04.12.589318. [PMID: 38645098 PMCID: PMC11030400 DOI: 10.1101/2024.04.12.589318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share real-world case studies applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis using Skyline, longitudinal QC metrics using AutoQC, and server-based data deposition using PanoramaWeb. We propose that this integrated approach to QC be used as a starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible.
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Affiliation(s)
- Kristine A. Tsantilas
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Julia E. Robbins
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Jea Park
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Deanna L. Plubell
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Washington 98195, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Brendan X. MacLean
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Josh Eckels
- LabKey, 500 Union St #1000, Seattle, Washington 98101, United States
| | - Christine C. Wu
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael S. Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607
| | - Sandra E. Spencer
- Canada’s Michael Smith Genome Sciences Centre (BC Cancer Research Institute), University of British Columbia, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew N. Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Washington 98195, United States
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5
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Freestone J, Noble WS, Keich U. Analysis of Tandem Mass Spectrometry Data with CONGA: Combining Open and Narrow Searches with Group-Wise Analysis. J Proteome Res 2024. [PMID: 38652578 DOI: 10.1021/acs.jproteome.3c00399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Searching for tandem mass spectrometry proteomics data against a database is a well-established method for assigning peptide sequences to observed spectra but typically cannot identify peptides harboring unexpected post-translational modifications (PTMs). Open modification searching aims to address this problem by allowing a spectrum to match a peptide even if the spectrum's precursor mass differs from the peptide mass. However, expanding the search space in this way can lead to a loss of statistical power to detect peptides. We therefore developed a method, called CONGA (combining open and narrow searches with group-wise analysis), that takes into account results from both types of searches─a traditional "narrow window" search and an open modification search─while carrying out rigorous false discovery rate control. The result is an algorithm that provides the best of both worlds: the ability to detect unexpected PTMs without a concomitant loss of power to detect unmodified peptides.
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Affiliation(s)
- Jack Freestone
- School of Mathematics and Statistics F07, University of Sydney, NSW 2006, Australia
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Uri Keich
- School of Mathematics and Statistics F07, University of Sydney, NSW 2006, Australia
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6
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Burns AR, Wiedrick J, Feryn A, Maes M, Midha MK, Baxter DH, Morrone SR, Prokop TJ, Kapil C, Hoopmann MR, Kusebauch U, Deutsch EW, Rappaport N, Watanabe K, Moritz RL, Miller RA, Lapidus JA, Orwoll ES. Proteomic changes induced by longevity-promoting interventions in mice. GeroScience 2024; 46:1543-1560. [PMID: 37653270 PMCID: PMC10828338 DOI: 10.1007/s11357-023-00917-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023] Open
Abstract
Using mouse models and high-throughput proteomics, we conducted an in-depth analysis of the proteome changes induced in response to seven interventions known to increase mouse lifespan. This included two genetic mutations, a growth hormone receptor knockout (GHRKO mice) and a mutation in the Pit-1 locus (Snell dwarf mice), four drug treatments (rapamycin, acarbose, canagliflozin, and 17α-estradiol), and caloric restriction. Each of the interventions studied induced variable changes in the concentrations of proteins across liver, kidney, and gastrocnemius muscle tissue samples, with the strongest responses in the liver and limited concordance in protein responses across tissues. To the extent that these interventions promote longevity through common biological mechanisms, we anticipated that proteins associated with longevity could be identified by characterizing shared responses across all or multiple interventions. Many of the proteome alterations induced by each intervention were distinct, potentially implicating a variety of biological pathways as being related to lifespan extension. While we found no protein that was affected similarly by every intervention, we identified a set of proteins that responded to multiple interventions. These proteins were functionally diverse but tended to be involved in peroxisomal oxidation and metabolism of fatty acids. These results provide candidate proteins and biological mechanisms related to enhancing longevity that can inform research on therapeutic approaches to promote healthy aging.
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Affiliation(s)
- Adam R Burns
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA.
| | - Jack Wiedrick
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA
| | - Alicia Feryn
- Biostatistics & Design Program, Oregon Health & Science University, Portland, OR, USA
| | - Michal Maes
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | - Charu Kapil
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | | | | | | | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Jodi A Lapidus
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, OR, USA
| | - Eric S Orwoll
- Department of Endocrinology, Oregon Health & Science University, Portland, OR, USA
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7
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Frommelt F, Fossati A, Uliana F, Wendt F, Xue P, Heusel M, Wollscheid B, Aebersold R, Ciuffa R, Gstaiger M. DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes. Nat Methods 2024; 21:635-647. [PMID: 38532014 PMCID: PMC11009110 DOI: 10.1038/s41592-024-02211-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.
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Affiliation(s)
- Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
| | - Andrea Fossati
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Fabian Wendt
- Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland
| | - Peng Xue
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Guangzhou National Laboratory, Guang Zhou, China
| | - Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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8
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Veth TS, Nouwen LV, Zwaagstra M, Lyoo H, Wierenga KA, Westendorp B, Altelaar MAFM, Berkers C, van Kuppeveld FJM, Heck AJR. Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection. Mol Cell Proteomics 2024; 23:100757. [PMID: 38556169 PMCID: PMC11067349 DOI: 10.1016/j.mcpro.2024.100757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/16/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Picornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a proteome-wide overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the kinase activity landscape during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays covering ∼40% of the human kinome. Our data show that upon infection, kinases of the MAPK pathways become activated (e.g., ERK1/2, RSK1/2, JNK1/2/3, and p38), while kinases involved in regulating the cell cycle (e.g., CDK1/2, GWL, and DYRK3) become inactivated. Additionally, we observed the activation of CHK2, an important kinase involved in the DNA damage response. Using pharmacological kinase inhibitors, we demonstrate that several of these activated kinases are essential for the replication of encephalomyocarditis virus. Altogether, the data provide a quantitative understanding of the regulation of kinome activity induced by picornavirus infection, providing a resource important for developing novel antiviral therapeutic interventions.
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Affiliation(s)
- Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Lonneke V Nouwen
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Marleen Zwaagstra
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Heyrhyoung Lyoo
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Kathryn A Wierenga
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Bart Westendorp
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Celia Berkers
- Faculty of Veterinary Medicine, Division of Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank J M van Kuppeveld
- Faculty of Veterinary Medicine, Virology Division, Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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9
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Torres-Sangiao E, Happonen L, Heusel M, Palm F, Gueto-Tettay C, Malmström L, Shannon O, Malmström J. Quantification of Adaptive Immune Responses Against Protein-Binding Interfaces in the Streptococcal M1 Protein. Mol Cell Proteomics 2024; 23:100753. [PMID: 38527648 PMCID: PMC11059317 DOI: 10.1016/j.mcpro.2024.100753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 02/28/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024] Open
Abstract
Bacterial or viral antigens can contain subdominant protein regions that elicit weak antibody responses upon vaccination or infection although there is accumulating evidence that antibody responses against subdominant regions can enhance the protective immune response. One proposed mechanism for subdominant protein regions is the binding of host proteins that prevent antibody production against epitopes hidden within the protein binding interfaces. Here, we used affinity purification combined with quantitative mass spectrometry (AP-MS) to examine the level of competition between antigen-specific antibodies and host-pathogen protein interaction networks using the M1 protein from Streptococcus pyogenes as a model system. As most humans have circulating antibodies against the M1 protein, we first used AP-MS to show that the M1 protein interspecies protein network formed with human plasma proteins is largely conserved in naïve mice. Immunizing mice with the M1 protein generated a time-dependent increase of anti-M1 antibodies. AP-MS analysis comparing the composition of the M1-plasma protein network from naïve and immunized mice showed significant enrichment of 292 IgG peptides associated with 56 IgG chains in the immune mice. Despite the significant increase of bound IgGs, the levels of interacting plasma proteins were not significantly reduced in the immune mice. The results indicate that the antigen-specific polyclonal IgG against the M1 protein primarily targets epitopes outside the other plasma protein binding interfaces. In conclusion, this study demonstrates that AP-MS is a promising strategy to determine the relationship between antigen-specific antibodies and host-pathogen interaction networks that could be used to define subdominant protein regions of relevance for vaccine development.
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Affiliation(s)
- Eva Torres-Sangiao
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Escherichia coli Group, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Clinical Microbiology Lab, University Hospital Complex of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Lotta Happonen
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Morizt Heusel
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Evosep ApS, Odense, Denmark
| | - Frida Palm
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Carlos Gueto-Tettay
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Lars Malmström
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Onna Shannon
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden; Faculty of Odontology, Section for Oral Biology and Pathology, Malmö University, Malmö, Sweden
| | - Johan Malmström
- Faculty of Medicine, Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden.
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10
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Kirk AM, Crawford JC, Chou CH, Guy C, Pandey K, Kozlik T, Shah RK, Chung S, Nguyen P, Zhang X, Wang J, Bell M, Mettelman RC, Allen EK, Pogorelyy MV, Kim H, Minervina AA, Awad W, Bajracharya R, White T, Long D, Gordon B, Morrison M, Glazer ES, Murphy AJ, Jiang Y, Fitzpatrick EA, Yarchoan M, Sethupathy P, Croft NP, Purcell AW, Federico SM, Stewart E, Gottschalk S, Zamora AE, DeRenzo C, Strome SE, Thomas PG. DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma. Cell Rep Med 2024; 5:101469. [PMID: 38508137 PMCID: PMC10983114 DOI: 10.1016/j.xcrm.2024.101469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/29/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Fibrolamellar carcinoma (FLC) is a liver tumor with a high mortality burden and few treatment options. A promising therapeutic vulnerability in FLC is its driver mutation, a conserved DNAJB1-PRKACA gene fusion that could be an ideal target neoantigen for immunotherapy. In this study, we aim to define endogenous CD8 T cell responses to this fusion in FLC patients and evaluate fusion-specific T cell receptors (TCRs) for use in cellular immunotherapies. We observe that fusion-specific CD8 T cells are rare and that FLC patient TCR repertoires lack large clusters of related TCR sequences characteristic of potent antigen-specific responses, potentially explaining why endogenous immune responses are insufficient to clear FLC tumors. Nevertheless, we define two functional fusion-specific TCRs, one of which has strong anti-tumor activity in vivo. Together, our results provide insights into the fragmented nature of neoantigen-specific repertoires in humans and indicate routes for clinical development of successful immunotherapies for FLC.
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Affiliation(s)
- Allison M Kirk
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ching-Heng Chou
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ravi K Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shanzou Chung
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaoyu Zhang
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jin Wang
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hyunjin Kim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Resha Bajracharya
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Toni White
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald Long
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Brittney Gordon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michelle Morrison
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan S Glazer
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Andrew J Murphy
- Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yixing Jiang
- Department of Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Elizabeth A Fitzpatrick
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Sara M Federico
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anthony E Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Scott E Strome
- College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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11
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Paramasivan S, Ashick M, Dudley KJ, Satake N, Mills PC, Sadowski P, Nagaraj SH. VPBrowse: Genome-based representation of MS/MS spectra to quantify 10,000 bovine proteins. Proteomics 2024:e2300431. [PMID: 38468111 DOI: 10.1002/pmic.202300431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/11/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
SWATH is a data acquisition strategy acclaimed for generating quantitatively accurate and consistent measurements of proteins across multiple samples. Its utility for proteomics studies in nonlaboratory animals, however, is currently compromised by the lack of sufficiently comprehensive and reliable public libraries, either experimental or predicted, and relevant platforms that support their sharing and utilization in an intuitive manner. Here we describe the development of the Veterinary Proteome Browser, VPBrowse (http://browser.proteo.cloud/), an on-line platform for genome-based representation of the Bos taurus proteome, which is equipped with an interactive database and tools for searching, visualization, and building quantitative mass spectrometry assays. In its current version (VPBrowse 1.0), it contains high-quality fragmentation spectra acquired on QToF instrument for over 36,000 proteotypic peptides, the experimental evidence for over 10,000 proteins. Data can be downloaded in different formats to enable analysis using popular software packages for SWATH data processing whilst normalization to iRT scale ensures compatibility with diverse chromatography systems. When applied to published blood plasma dataset from the biomarker discovery study, the resource supported label-free quantification of additional proteins not reported by the authors previously including PSMA4, a tissue leakage protein and a promising candidate biomarker of animal's response to dehorning-related injury.
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Affiliation(s)
- Selvam Paramasivan
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Mohamed Ashick
- LifeBytes India Private Limited, Bengaluru, Karnataka, India
| | - Kevin J Dudley
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Nana Satake
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Paul C Mills
- School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
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12
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Creus-Muncunill J, Haure-Mirande JV, Mattei D, Bons J, Ramirez AV, Hamilton BW, Corwin C, Chowdhury S, Schilling B, Ellerby LM, Ehrlich ME. TYROBP/DAP12 knockout in Huntington's disease Q175 mice cell-autonomously decreases microglial expression of disease-associated genes and non-cell-autonomously mitigates astrogliosis and motor deterioration. J Neuroinflammation 2024; 21:66. [PMID: 38459557 PMCID: PMC10924371 DOI: 10.1186/s12974-024-03052-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
INTRODUCTION Huntington's disease (HD) is a fatal neurodegenerative disorder caused by an expansion of the CAG trinucleotide repeat in the Huntingtin gene (HTT). Immune activation is abundant in the striatum of HD patients. Detection of active microglia at presymptomatic stages suggests that microgliosis is a key early driver of neuronal dysfunction and degeneration. Recent studies showed that deletion of Tyrobp, a microglial protein, ameliorates neuronal dysfunction in Alzheimer's disease amyloidopathy and tauopathy mouse models while decreasing components of the complement subnetwork. OBJECTIVE While TYROBP/DAP12-mediated microglial activation is detrimental for some diseases such as peripheral nerve injury, it is beneficial for other diseases. We sought to determine whether the TYROBP network is implicated in HD and whether Tyrobp deletion impacts HD striatal function and transcriptomics. METHODS To test the hypothesis that Tyrobp deficiency would be beneficial in an HD model, we placed the Q175 HD mouse model on a Tyrobp-null background. We characterized these mice with a combination of behavioral testing, immunohistochemistry, transcriptomic and proteomic profiling. Further, we evaluated the gene signature in isolated Q175 striatal microglia, with and without Tyrobp. RESULTS Comprehensive analysis of publicly available human HD transcriptomic data revealed that the TYROBP network is overactivated in the HD putamen. The Q175 mice showed morphologic microglial activation, reduced levels of post-synaptic density-95 protein and motor deficits at 6 and 9 months of age, all of which were ameliorated on the Tyrobp-null background. Gene expression analysis revealed that lack of Tyrobp in the Q175 model does not prevent the decrease in the expression of striatal neuronal genes but reduces pro-inflammatory pathways that are specifically active in HD human brain, including genes identified as detrimental in neurodegenerative diseases, e.g. C1q and members of the Ccr5 signaling pathway. Integration of transcriptomic and proteomic data revealed that astrogliosis and complement system pathway were reduced after Tyrobp deletion, which was further validated by immunofluorescence analysis. CONCLUSIONS Our data provide molecular and functional support demonstrating that Tyrobp deletion prevents many of the abnormalities in the HD Q175 mouse model, suggesting that the Tyrobp pathway is a potential therapeutic candidate for Huntington's disease.
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Affiliation(s)
| | | | - Daniele Mattei
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Angie V Ramirez
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - B Wade Hamilton
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Chuhyon Corwin
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Sarah Chowdhury
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | | | | | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA.
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13
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Burton JB, Silva-Barbosa A, Bons J, Rose J, Pfister K, Simona F, Gandhi T, Reiter L, Bernhardt O, Hunter CL, Goetzman ES, Sims-Lucas S, Schilling B. Substantial downregulation of mitochondrial and peroxisomal proteins during acute kidney injury revealed by data-independent acquisition proteomics. Proteomics 2024; 24:e2300162. [PMID: 37775337 DOI: 10.1002/pmic.202300162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 10/01/2023]
Abstract
Acute kidney injury (AKI) manifests as a major health concern, particularly for the elderly. Understanding AKI-related proteome changes is critical for prevention and development of novel therapeutics to recover kidney function and to mitigate the susceptibility for recurrent AKI or development of chronic kidney disease. In this study, mouse kidneys were subjected to ischemia-reperfusion injury, and the contralateral kidneys remained uninjured to enable comparison and assess injury-induced changes in the kidney proteome. A ZenoTOF 7600 mass spectrometer was optimized for data-independent acquisition (DIA) to achieve comprehensive protein identification and quantification. Short microflow gradients and the generation of a deep kidney-specific spectral library allowed for high-throughput, comprehensive protein quantification. Upon AKI, the kidney proteome was completely remodeled, and over half of the 3945 quantified protein groups changed significantly. Downregulated proteins in the injured kidney were involved in energy production, including numerous peroxisomal matrix proteins that function in fatty acid oxidation, such as ACOX1, CAT, EHHADH, ACOT4, ACOT8, and Scp2. Injured kidneys exhibited severely damaged tissues and injury markers. The comprehensive and sensitive kidney-specific DIA-MS assays feature high-throughput analytical capabilities to achieve deep coverage of the kidney proteome, and will serve as useful tools for developing novel therapeutics to remediate kidney function.
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Affiliation(s)
- Jordan B Burton
- Buck Institute for Research on Aging, Novato, California, USA
| | - Anne Silva-Barbosa
- Department of Pediatrics, School of Medicine, Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, California, USA
| | - Katherine Pfister
- Department of Pediatrics, School of Medicine, Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | | | | | | | - Eric S Goetzman
- Department of Pediatrics, School of Medicine, Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sunder Sims-Lucas
- Department of Pediatrics, School of Medicine, Medical Center Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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14
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Hou J, Deng Q, Qiu X, Liu S, Li Y, Huang C, Wang X, Zhang Q, Deng X, Zhong Z, Zhong W. Proteomic analysis of plasma proteins from patients with cardiac rupture after acute myocardial infarction using TMT-based quantitative proteomics approach. Clin Proteomics 2024; 21:18. [PMID: 38429673 PMCID: PMC10908035 DOI: 10.1186/s12014-024-09474-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 02/23/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Cardiac rupture (CR) is a rare but catastrophic mechanical complication of acute myocardial infarction (AMI) that seriously threatens human health. However, the reliable biomarkers for clinical diagnosis and the underlying signaling pathways insights of CR has yet to be elucidated. METHODS In the present study, a quantitative approach with tandem mass tag (TMT) labeling and liquid chromatography-tandem mass spectrometry was used to characterize the differential protein expression profiles of patients with CR. Plasma samples were collected from patients with CR (n = 37), patients with AMI (n = 47), and healthy controls (n = 47). Candidate proteins were selected for validation by multiple reaction monitoring (MRM) and enzyme-linked immunosorbent assay (ELISA). RESULTS In total, 1208 proteins were quantified and 958 differentially expressed proteins (DEPs) were identified. The difference in the expression levels of the DEPs was more noticeable between the CR and Con groups than between the AMI and Con groups. Bioinformatics analysis showed most of the DEPs to be involved in numerous crucial biological processes and signaling pathways, such as RNA transport, ribosome, proteasome, and protein processing in the endoplasmic reticulum, as well as necroptosis and leukocyte transendothelial migration, which might play essential roles in the complex pathological processes associated with CR. MRM analysis confirmed the accuracy of the proteomic analysis results. Four proteins i.e., C-reactive protein (CRP), heat shock protein beta-1 (HSPB1), vinculin (VINC) and growth/differentiation factor 15 (GDF15), were further validated via ELISA. By receiver operating characteristic (ROC) analysis, combinations of these four proteins distinguished CR patients from AMI patients with a high area under the curve (AUC) value (0.895, 95% CI, 0.802-0.988, p < 0.001). CONCLUSIONS Our study highlights the value of comprehensive proteomic characterization for identifying plasma proteome changes in patients with CR. This pilot study could serve as a valid foundation and initiation point for elucidation of the mechanisms of CR, which might aid in identifying effective diagnostic biomarkers in the future.
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Affiliation(s)
- Jingyuan Hou
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
- GuangDong Engineering Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, Guangdong, 514031, China
| | - Qiaoting Deng
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
| | - Xiaohong Qiu
- Meizhou clinical Medical School, Guangdong Medical University, Meizhou, Guangdong, 514031, China
| | - Sudong Liu
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
| | - Youqian Li
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Changjing Huang
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Xianfang Wang
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China
| | - Qunji Zhang
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
| | - Xunwei Deng
- Research Experimental Center, Meizhou Clinical Institute of Shantou University Medical College, Meizhou, Guangdong, 514031, China
| | - Zhixiong Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China.
| | - Wei Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital, Meizhou, Guangdong, 514031, China.
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15
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Zang T, Fear MW, Parker TJ, Holland AJA, Martin L, Langley D, Kimble R, Wood FM, Cuttle L. Inflammatory proteins and neutrophil extracellular traps increase in burn blister fluid 24h after burn. Burns 2024:S0305-4179(24)00064-0. [PMID: 38490838 DOI: 10.1016/j.burns.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024]
Abstract
Burn wound blister fluid is a valuable matrix for understanding the biological pathways associated with burn injury. In this study, 152 blister fluid samples collected from paediatric burn wounds at three different hospitals were analysed using mass spectrometry proteomic techniques. The protein abundance profile at different days after burn indicated more proteins were associated with cellular damage/repair in the first 24 h, whereas after this point more proteins were associated with antimicrobial defence. The inflammatory proteins persisted at a high level in the blister fluid for more than 7 days. This may indicate that removal of burn blisters prior to two days after burn is optimal to prevent excessive or prolonged inflammation in the wound environment. Additionally, many proteins associated with the neutrophil extracellular trap (NET) pathway were increased after burn, further implicating NETs in the post-burn inflammatory response. NET inhibitors may therefore be a potential treatment to reduce post-burn inflammation and coagulation pathology and enhance burn wound healing outcomes.
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Affiliation(s)
- Tuo Zang
- Queensland University of Technology (QUT), Faculty of Health, School of Biomedical Sciences, Centre for Children's Health Research, South Brisbane, Queensland, Australia
| | - Mark W Fear
- Burn Injury Research Unit, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Tony J Parker
- Queensland University of Technology (QUT), School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland, Australia
| | - Andrew J A Holland
- The Children's Hospital at Westmead Burns Unit, Kids Research Institute, Department of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, New South Wales, Australia
| | - Lisa Martin
- Burn Injury Research Unit, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Donna Langley
- Queensland University of Technology (QUT), Faculty of Health, School of Biomedical Sciences, Centre for Children's Health Research, South Brisbane, Queensland, Australia
| | - Roy Kimble
- Children's Health Queensland, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Fiona M Wood
- Burn Injury Research Unit, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia; Burns Service of Western Australia, Perth Children's Hospital and Fiona Stanley Hospital, Perth, WA, Australia
| | - Leila Cuttle
- Queensland University of Technology (QUT), Faculty of Health, School of Biomedical Sciences, Centre for Children's Health Research, South Brisbane, Queensland, Australia.
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16
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Jiang L, Qin J, Dai Y, Zhao S, Zhan Q, Cui P, Ren L, Wang X, Zhang R, Gao C, Zhou Y, Cai S, Wang G, Xie W, Tang X, Shi M, Ma F, Liu J, Wang T, Wang C, Svrcek M, Bardier-Dupas A, Emile JF, de Mestier L, Bachet JB, Nicolle R, Cros J, Laurent-Puig P, Wei M, Song B, Jing W, Guo S, Zheng K, Jiang H, Wang H, Deng X, Chen H, Tian Q, Wang S, Shi S, Jin G, Yin T, Fang H, Chen S, Shen B. Prospective observational study on biomarkers of response in pancreatic ductal adenocarcinoma. Nat Med 2024; 30:749-761. [PMID: 38287168 DOI: 10.1038/s41591-023-02790-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024]
Abstract
Adjuvant chemotherapy benefits patients with resected pancreatic ductal adenocarcinoma (PDAC), but the compromised physical state of post-operative patients can hinder compliance. Biomarkers that identify candidates for prompt adjuvant therapy are needed. In this prospective observational study, 1,171 patients with PDAC who underwent pancreatectomy were enrolled and extensively followed-up. Proteomic profiling of 191 patient samples unveiled clinically relevant functional protein modules. A proteomics-level prognostic risk model was established for PDAC, with its utility further validated using a publicly available external cohort. More importantly, through an interaction effect regression analysis leveraging both clinical and proteomic datasets, we discovered two biomarkers (NDUFB8 and CEMIP2), indicative of the overall sensitivity of patients with PDAC to adjuvant chemotherapy. The biomarkers were validated through immunohistochemistry on an internal cohort of 386 patients. Rigorous validation extended to two external multicentic cohorts-a French multicentric cohort (230 patients) and a cohort from two grade-A tertiary hospitals in China (466 patients)-enhancing the robustness and generalizability of our findings. Moreover, experimental validation through functional assays was conducted on PDAC cell lines and patient-derived organoids. In summary, our cohort-scale integration of clinical and proteomic data demonstrates the potential of proteomics-guided prognosis and biomarker-aided adjuvant chemotherapy for PDAC.
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Affiliation(s)
- Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiejie Qin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shulin Zhao
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhan
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peng Cui
- Burning Rock Biotech, Guangzhou, China
| | - Lingjie Ren
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruihong Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenxu Gao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanting Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | | | - Xiaomei Tang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Minmin Shi
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfang Ma
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Magali Svrcek
- Department of Pathology, Saint-Antoine Hospital - Sorbonne Universités, Paris, France
| | - Armelle Bardier-Dupas
- Department of Pathology, Pitié-Salpêtrière Hospital - Sorbonne Universités, Paris, France
| | - Jean Francois Emile
- Department of Pathology, Ambroise Paré Hospital - Université Saint Quentin en Yvelines, Paris, France
| | - Louis de Mestier
- Department of Pancreatology, Université Paris Cité - FHU MOSAIC, Beaujon Hospital, Clichy, France
| | - Jean-Baptiste Bachet
- Department of Gastroenterology, Pitié-Salpêtrière Hospital - Sorbonne Universités, Paris, France
| | - Remy Nicolle
- Université Paris Cité, FHU MOSAIC, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, Paris, France
| | - Jerome Cros
- Department of Pathology, Université Paris Cité - FHU MOSAIC, Beaujon Hospital, Clichy, France
| | - Pierre Laurent-Puig
- Department of Biochemistry, Hôpital Européen Georges Pompidou, Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université Paris Cité, Equipe labellisée Ligue Nationale contre le cancer, CNRS, Paris, France
| | - Miaoyan Wei
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bin Song
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wei Jing
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Kailian Zheng
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hui Jiang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pathology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Huan Wang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Tian
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengyue Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
| | - Tong Yin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
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17
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Garralda E, Beaulieu ME, Moreno V, Casacuberta-Serra S, Martínez-Martín S, Foradada L, Alonso G, Massó-Vallés D, López-Estévez S, Jauset T, Corral de la Fuente E, Doger B, Hernández T, Perez-Lopez R, Arqués O, Castillo Cano V, Morales J, Whitfield JR, Niewel M, Soucek L, Calvo E. MYC targeting by OMO-103 in solid tumors: a phase 1 trial. Nat Med 2024; 30:762-771. [PMID: 38321218 PMCID: PMC10957469 DOI: 10.1038/s41591-024-02805-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024]
Abstract
Among the 'most wanted' targets in cancer therapy is the oncogene MYC, which coordinates key transcriptional programs in tumor development and maintenance. It has, however, long been considered undruggable. OMO-103 is a MYC inhibitor consisting of a 91-amino acid miniprotein. Here we present results from a phase 1 study of OMO-103 in advanced solid tumors, established to examine safety and tolerability as primary outcomes and pharmacokinetics, recommended phase 2 dose and preliminary signs of activity as secondary ones. A classical 3 + 3 design was used for dose escalation of weekly intravenous, single-agent OMO-103 administration in 21-day cycles, encompassing six dose levels (DLs). A total of 22 patients were enrolled, with treatment maintained until disease progression. The most common adverse events were grade 1 infusion-related reactions, occurring in ten patients. One dose-limiting toxicity occurred at DL5. Pharmacokinetics showed nonlinearity, with tissue saturation signs at DL5 and a terminal half-life in serum of 40 h. Of the 19 patients evaluable for response, 12 reached the predefined 9-week time point for assessment of drug antitumor activity, eight of those showing stable disease by computed tomography. One patient defined as stable disease by response evaluation criteria in solid tumors showed a 49% reduction in total tumor volume at best response. Transcriptomic analysis supported target engagement in tumor biopsies. In addition, we identified soluble factors that are potential pharmacodynamic and predictive response markers. Based on all these data, the recommended phase 2 dose was determined as DL5 (6.48 mg kg-1).ClinicalTrials.gov identifier: NCT04808362 .
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Affiliation(s)
| | | | - Víctor Moreno
- START Madrid-FJD-Hospital Fundación Jiménez Díaz, Madrid, Spain
| | | | | | | | - Guzman Alonso
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | | | | | - Bernard Doger
- START Madrid-FJD-Hospital Fundación Jiménez Díaz, Madrid, Spain
| | | | | | - Oriol Arqués
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | | | | | | | - Laura Soucek
- Vall d'Hebron Institute of Oncology, Barcelona, Spain.
- Peptomyc S.L., Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - Emiliano Calvo
- START Madrid-CIOCC-Centro Integral Oncológico Clara Campal, Madrid, Spain
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18
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Schurman CA, Kaya S, Dole N, Luna NMM, Castillo N, Potter R, Rose JP, Bons J, King CD, Burton JB, Schilling B, Melov S, Tang S, Schaible E, Alliston T. Aging impairs the osteocytic regulation of collagen integrity and bone quality. Bone Res 2024; 12:13. [PMID: 38409111 PMCID: PMC10897167 DOI: 10.1038/s41413-023-00303-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 02/28/2024] Open
Abstract
Poor bone quality is a major factor in skeletal fragility in elderly individuals. The molecular mechanisms that establish and maintain bone quality, independent of bone mass, are unknown but are thought to be primarily determined by osteocytes. We hypothesize that the age-related decline in bone quality results from the suppression of osteocyte perilacunar/canalicular remodeling (PLR), which maintains bone material properties. We examined bones from young and aged mice with osteocyte-intrinsic repression of TGFβ signaling (TβRIIocy-/-) that suppresses PLR. The control aged bone displayed decreased TGFβ signaling and PLR, but aging did not worsen the existing PLR suppression in male TβRIIocy-/- bone. This relationship impacted the behavior of collagen material at the nanoscale and tissue scale in macromechanical tests. The effects of age on bone mass, density, and mineral material behavior were independent of osteocytic TGFβ. We determined that the decline in bone quality with age arises from the loss of osteocyte function and the loss of TGFβ-dependent maintenance of collagen integrity.
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Affiliation(s)
- Charles A Schurman
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Serra Kaya
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Neha Dole
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Nadja M Maldonado Luna
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA
| | - Natalia Castillo
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA
| | - Ryan Potter
- Washington University in St Louis, Department of Orthopedics, St. Louis, MO, 63130, USA
| | - Jacob P Rose
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Jordan B Burton
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Simon Tang
- Washington University in St Louis, Department of Orthopedics, St. Louis, MO, 63130, USA
| | - Eric Schaible
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA.
- UC Berkeley/UCSF Graduate Program in Bioengineering, San Francisco, CA, 94143, USA.
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19
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Silva Barbosa AC, Pfister KE, Chiba T, Bons J, Rose JP, Burton JB, King CD, O'Broin A, Young V, Zhang B, Sivakama B, Schmidt AV, Uhlean R, Oda A, Schilling B, Goetzman ES, Sims-Lucas S. Dicarboxylic Acid Dietary Supplementation Protects against AKI. J Am Soc Nephrol 2024; 35:135-148. [PMID: 38044490 PMCID: PMC10843194 DOI: 10.1681/asn.0000000000000266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/20/2023] [Indexed: 12/05/2023] Open
Abstract
SIGNIFICANCE STATEMENT In this study, we demonstrate that a common, low-cost compound known as octanedioic acid (DC 8 ) can protect mice from kidney damage typically caused by ischemia-reperfusion injury or the chemotherapy drug cisplatin. This compound seems to enhance peroxisomal activity, which is responsible for breaking down fats, without adversely affecting mitochondrial function. DC 8 is not only affordable and easy to administer but also effective. These encouraging findings suggest that DC 8 could potentially be used to assist patients who are at risk of experiencing this type of kidney damage. BACKGROUND Proximal tubules are rich in peroxisomes, which are damaged during AKI. Previous studies demonstrated that increasing peroxisomal fatty acid oxidation (FAO) is renoprotective, but no therapy has emerged to leverage this mechanism. METHODS Mice were fed with either a control diet or a diet enriched with dicarboxylic acids, which are peroxisome-specific FAO substrates, then subjected to either ischemia-reperfusion injury-AKI or cisplatin-AKI models. Biochemical, histologic, genetic, and proteomic analyses were performed. RESULTS Both octanedioic acid (DC 8 ) and dodecanedioic acid (DC 12 ) prevented the rise of AKI markers in mice that were exposed to renal injury. Proteomics analysis demonstrated that DC 8 preserved the peroxisomal and mitochondrial proteomes while inducing extensive remodeling of the lysine succinylome. This latter finding indicates that DC 8 is chain shortened to the anaplerotic substrate succinate and that peroxisomal FAO was increased by DC 8 . CONCLUSIONS DC 8 supplementation protects kidney mitochondria and peroxisomes and increases peroxisomal FAO, thereby protecting against AKI.
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Affiliation(s)
- Anne C Silva Barbosa
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Katherine E Pfister
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Takuto Chiba
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California
| | - Jacob P Rose
- Buck Institute for Research on Aging, Novato, California
| | | | | | - Amy O'Broin
- Buck Institute for Research on Aging, Novato, California
| | - Victoria Young
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Bob Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Bharathi Sivakama
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alexandra V Schmidt
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rebecca Uhlean
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Akira Oda
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Eric S Goetzman
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sunder Sims-Lucas
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania
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20
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Lou R, Shui W. Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023. Mol Cell Proteomics 2024; 23:100712. [PMID: 38182042 PMCID: PMC10847697 DOI: 10.1016/j.mcpro.2024.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024] Open
Abstract
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful technology for high-throughput, accurate, and reproducible quantitative proteomics. This review provides a comprehensive overview of recent advances in both the experimental and computational methods for DIA proteomics, from data acquisition schemes to analysis strategies and software tools. DIA acquisition schemes are categorized based on the design of precursor isolation windows, highlighting wide-window, overlapping-window, narrow-window, scanning quadrupole-based, and parallel accumulation-serial fragmentation-enhanced DIA methods. For DIA data analysis, major strategies are classified into spectrum reconstruction, sequence-based search, library-based search, de novo sequencing, and sequencing-independent approaches. A wide array of software tools implementing these strategies are reviewed, with details on their overall workflows and scoring approaches at different steps. The generation and optimization of spectral libraries, which are critical resources for DIA analysis, are also discussed. Publicly available benchmark datasets covering global proteomics and phosphoproteomics are summarized to facilitate performance evaluation of various software tools and analysis workflows. Continued advances and synergistic developments of versatile components in DIA workflows are expected to further enhance the power of DIA-based proteomics.
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Affiliation(s)
- Ronghui Lou
- iHuman Institute, ShanghaiTech University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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21
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Wei D, Sun J, Luo Z, Zhang G, Liu Y, Zhang H, Xie Z, Gu Z, Tao WA. Targeted Phosphoproteomics of Human Saliva Extracellular Vesicles via Multiple Reaction Monitoring Cubed (MRM 3). Anal Chem 2024; 96:1223-1231. [PMID: 38205554 DOI: 10.1021/acs.analchem.3c04464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Oral squamous cell carcinoma (OSCC) has become a global health problem due to its increasing incidence and high mortality rate. Early intervention through monitoring of the diagnostic biomarker levels during OSCC treatment is critical. Extracellular vesicles (EVs) are emerging surrogates in intercellular communication through transporting biomolecule cargo and have recently been identified as a potential source of biomarkers such as phosphoproteins for many diseases. Here, we developed a multiple reaction monitoring cubed (MRM3) method coupled with a novel sample preparation strategy, extracellular vesicles to phosphoproteins (EVTOP), to quantify phosphoproteins using a minimal amount of saliva (50 μL) samples from OSCC patients with high specificity and sensitivity. Our results established differential patterns in the phosphopeptide content of healthy, presurgery, and postsurgery OSCC patient groups. Notably, we discovered significantly increased salivary phosphorylated alpha-amylase (AMY) in the postsurgery group compared to the presurgery group. We hereby present the first targeted MS method with extremely high sensitivity for measuring endogenous phosphoproteins in human saliva EVs.
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Affiliation(s)
- Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Jie Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhuojun Luo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Guiyuan Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Yufeng Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Hao Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhuoying Xie
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - W Andy Tao
- Department of Chemistry and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
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22
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Sakson R, Beedgen L, Bernhard P, Alp KM, Lübbehusen N, Röth R, Niesler B, Luzarowski M, Shevchuk O, Mayer MP, Thiel C, Ruppert T. Targeted Proteomics Reveals Quantitative Differences in Low-Abundance Glycosyltransferases of Patients with Congenital Disorders of Glycosylation. Int J Mol Sci 2024; 25:1191. [PMID: 38256263 PMCID: PMC10816918 DOI: 10.3390/ijms25021191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Protein glycosylation is an essential post-translational modification in all domains of life. Its impairment in humans can result in severe diseases named congenital disorders of glycosylation (CDGs). Most of the glycosyltransferases (GTs) responsible for proper glycosylation are polytopic membrane proteins that represent challenging targets in proteomics. We established a multiple reaction monitoring (MRM) assay to comprehensively quantify GTs involved in the processes of N-glycosylation and O- and C-mannosylation in the endoplasmic reticulum. High robustness was achieved by using an enriched membrane protein fraction of isotopically labeled HEK 293T cells as an internal protein standard. The analysis of primary skin fibroblasts from eight CDG type I patients with impaired ALG1, ALG2, and ALG11 genes, respectively, revealed a substantial reduction in the corresponding protein levels. The abundance of the other GTs, however, remained unchanged at the transcript and protein levels, indicating that there is no fail-safe mechanism for the early steps of glycosylation in the endoplasmic reticulum. The established MRM assay was shared with the scientific community via the commonly used open source Skyline software environment, including Skyline Batch for automated data analysis. We demonstrate that another research group could easily reproduce all analysis steps, even while using different LC-MS hardware.
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Affiliation(s)
- Roman Sakson
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg University, 69120 Heidelberg, Germany
| | - Lars Beedgen
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Patrick Bernhard
- Institute for Surgical Pathology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - K. Merve Alp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Nicole Lübbehusen
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Ralph Röth
- nCounter Core Facility, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Beate Niesler
- nCounter Core Facility, Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Marcin Luzarowski
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Olga Shevchuk
- Department of Immunodynamics, Institute of Experimental Immunology and Imaging, University Hospital Essen, 45147 Essen, Germany
| | - Matthias P. Mayer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department Pediatrics I, Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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23
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Wilson KA, Bar S, Dammer EB, Carrera EM, Hodge BA, Hilsabeck TAU, Bons J, Brownridge GW, Beck JN, Rose J, Granath-Panelo M, Nelson CS, Qi G, Gerencser AA, Lan J, Afenjar A, Chawla G, Brem RB, Campeau PM, Bellen HJ, Schilling B, Seyfried NT, Ellerby LM, Kapahi P. OXR1 maintains the retromer to delay brain aging under dietary restriction. Nat Commun 2024; 15:467. [PMID: 38212606 PMCID: PMC10784588 DOI: 10.1038/s41467-023-44343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Dietary restriction (DR) delays aging, but the mechanism remains unclear. We identified polymorphisms in mtd, the fly homolog of OXR1, which influenced lifespan and mtd expression in response to DR. Knockdown in adulthood inhibited DR-mediated lifespan extension in female flies. We found that mtd/OXR1 expression declines with age and it interacts with the retromer, which regulates trafficking of proteins and lipids. Loss of mtd/OXR1 destabilized the retromer, causing improper protein trafficking and endolysosomal defects. Overexpression of retromer genes or pharmacological restabilization with R55 rescued lifespan and neurodegeneration in mtd-deficient flies and endolysosomal defects in fibroblasts from patients with lethal loss-of-function of OXR1 variants. Multi-omic analyses in flies and humans showed that decreased Mtd/OXR1 is associated with aging and neurological diseases. mtd/OXR1 overexpression rescued age-related visual decline and tauopathy in a fly model. Hence, OXR1 plays a conserved role in preserving retromer function and is critical for neuronal health and longevity.
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Affiliation(s)
- Kenneth A Wilson
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sudipta Bar
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Eric B Dammer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Brian A Hodge
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Tyler A U Hilsabeck
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Jennifer N Beck
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | | | - Grace Qi
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | | | - Jianfeng Lan
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Guanxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, The Afilliated Hospital of Guilin Medican University, Guilin, 541001, Guanxi, China
| | - Alexandra Afenjar
- Assistance Publique des Hôpitaux de Paris, Unité de Génétique Clinique, Hôpital Armand Trousseau, Groupe Hospitalier Universitaire, Paris, 75012, France
- Département de Génétique et Embryologie Médicale, CRMR des Malformations et Maladies Congénitales du Cervelet, GRC ConCer-LD, Sorbonne Universités, Hôpital Trousseau, Paris, 75012, France
| | - Geetanjali Chawla
- RNA Biology Laboratory, Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institute of Eminence, NH91, Tehsil Dadri, G. B. Nagar, 201314, Uttar Pradesh, India
| | - Rachel B Brem
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA, 94720, USA
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC, H3T 1J4, Canada
| | - Hugo J Bellen
- Departments of Molecular and Human Genetics and Neuroscience, Neurological Research Institute, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lisa M Ellerby
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
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24
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Moutin EB, Bons J, Giavara G, Lourenco F, Pan D, Burton JB, Shah S, Colombé M, Gascard P, Tlsty T, Schilling B, Winton DJ. Extracellular Matrix Orchestration of Tissue Remodeling in the Chronically Inflamed Mouse Colon. Cell Mol Gastroenterol Hepatol 2024; 17:639-656. [PMID: 38199279 PMCID: PMC10905044 DOI: 10.1016/j.jcmgh.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
BACKGROUND & AIMS Chronic inflammatory illnesses are debilitating and recurrent conditions associated with significant comorbidities, including an increased risk of developing cancer. Extensive tissue remodeling is a hallmark of such illnesses, and is both a consequence and a mediator of disease progression. Despite previous characterization of epithelial and stromal remodeling during inflammatory bowel disease, a complete understanding of its impact on disease progression is lacking. METHODS A comprehensive proteomic pipeline using data-independent acquisition was applied to decellularized colon samples from the Muc2 knockout (Muc2KO) mouse model of colitis for an in-depth characterization of extracellular matrix remodeling. Unique proteomic profiles of the matrisomal landscape were extracted from prepathologic and overt colitis. Integration of proteomics and transcriptomics data sets extracted from the same murine model produced network maps describing the orchestrating role of matrisomal proteins in tissue remodeling during the progression of colitis. RESULTS The in-depth proteomic workflow used here allowed the addition of 34 proteins to the known colon matrisomal signature. Protein signatures of prepathologic and pathologic colitic states were extracted, differentiating the 2 states by expression of small leucine-rich proteoglycans. We outlined the role of this class and other matrisomal proteins in tissue remodeling during colitis, as well as the potential for coordinated regulation of cell types by matrisomal ligands. CONCLUSIONS Our work highlights a central role for matrisomal proteins in tissue remodeling during colitis and defines orchestrating nodes that can be exploited in the selection of therapeutic targets.
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Affiliation(s)
- Elisa B Moutin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, California
| | - Giada Giavara
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Filipe Lourenco
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Deng Pan
- Department of Pathology, University of California, San Francisco, California
| | | | - Samah Shah
- Buck Institute for Research on Aging, Novato, California
| | - Mathilde Colombé
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Philippe Gascard
- Department of Pathology, University of California, San Francisco, California
| | - Thea Tlsty
- Department of Pathology, University of California, San Francisco, California
| | | | - Douglas J Winton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom.
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25
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Jadeja S, Kupcik R, Fabrik I, Sklenářová H, Lenčo J. A stationary phase with a positively charged surface allows for minimizing formic acid concentration in the mobile phase, enhancing electrospray ionization in LC-MS proteomic experiments. Analyst 2023; 148:5980-5990. [PMID: 37870390 DOI: 10.1039/d3an01508d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The default choice of mobile phase acidifier for bottom-up LC-MS proteomic analyses is 0.10% formic acid because of its decent acidity, decent ion pairing ability, and low suppression of electrospray ionization. In recent years, state-of-the-art columns have been designed specifically to provide efficient separation even when using an MS-friendly mobile phase of low ionic strength. Despite this, no attempts have been made to improve the sensitivity of the MS-based analytical methods by reducing the amount of formic acid in the mobile phase. In this study, we evaluated the effect of reduced formic acid concentration in the mobile phase on the chromatographic behavior and MS response of peptides when separated using columns packed with a C18 stationary phase with a positively charged surface. Using 0.01% formic acid in the mobile phase maintained excellent chromatographic performance and increased MS signal response compared to the standard of 0.10%. The enhanced MS response translated to about 50% improved peptide identifications depending on the complexity and amount of sample injected. The increased retention of peptides at a reduced formic acid concentration was directly proportional to the number of acidic residues in the peptide sequence. The study was carried out by covering a spectrum of protein samples with varied complexity using analytical flow, micro-, and nanoflow regimes to expand the applicability in routine practice.
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Affiliation(s)
- Siddharth Jadeja
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| | - Rudolf Kupcik
- Biomedical Research Centre, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Hana Sklenářová
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
| | - Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 03 Hradec Králové, Czech Republic.
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26
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Will A, Oliinyk D, Bleiholder C, Meier F. Peptide collision cross sections of 22 post-translational modifications. Anal Bioanal Chem 2023; 415:6633-6645. [PMID: 37758903 PMCID: PMC10598134 DOI: 10.1007/s00216-023-04957-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Recent advances have rekindled the interest in ion mobility as an additional dimension of separation in mass spectrometry (MS)-based proteomics. Ion mobility separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed ~4300 pairs of matching modified and unmodified peptide ion species by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.26%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between -1.4% (arginine citrullination) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM and is partially correlated with the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.
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Affiliation(s)
- Andreas Will
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Denys Oliinyk
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32304, USA
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany.
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27
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. Mass Spectrom Rev 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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28
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Gupta S, Sing JC, Röst HL. Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment. Commun Biol 2023; 6:1101. [PMID: 37903988 PMCID: PMC10616189 DOI: 10.1038/s42003-023-05437-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 10/10/2023] [Indexed: 11/01/2023] Open
Abstract
DIA is a mainstream method for quantitative proteomics, but consistent quantification across multiple LC-MS/MS instruments remains a bottleneck in parallelizing data acquisition. One reason for this inconsistency and missing quantification is the retention time shift which current software does not adequately address for runs from multiple sites. We present multirun chromatogram alignment strategies to map peaks across columns, including the traditional reference-based Star method, and two novel approaches: MST and Progressive alignment. These reference-free strategies produce a quantitatively accurate data-matrix, even from heterogeneous multi-column studies. Progressive alignment also generates merged chromatograms from all runs which has not been previously achieved for LC-MS/MS data. First, we demonstrate the effectiveness of multirun alignment strategies on a gold-standard annotated dataset, resulting in a threefold reduction in quantitation error-rate compared to non-aligned DIA results. Subsequently, on a multi-species dataset that DIAlignR effectively controls the quantitative error rate, improves precision in protein measurements, and exhibits conservative peak alignment. We next show that the MST alignment reduces cross-site CV by 50% for highly abundant proteins when applied to a dataset from 11 different LC-MS/MS setups. Finally, the reanalysis of 949 plasma runs with multirun alignment revealed a more than 50% increase in insulin resistance (IR) and respiratory viral infection (RVI) proteins, identifying 11 and 13 proteins respectively, compared to prior analysis without it. The three strategies are implemented in our DIAlignR workflow (>2.3) and can be combined with linear, non-linear, or hybrid pairwise alignment.
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Affiliation(s)
- Shubham Gupta
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Justin C Sing
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hannes L Röst
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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29
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Dipali SS, King CD, Rose JP, Burdette JE, Campisi J, Schilling B, Duncan FE. Proteomic quantification of native and ECM-enriched mouse ovaries reveals an age-dependent fibro-inflammatory signature. Aging (Albany NY) 2023; 15:10821-10855. [PMID: 37899138 PMCID: PMC10637783 DOI: 10.18632/aging.205190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023]
Abstract
The ovarian microenvironment becomes fibrotic and stiff with age, in part due to increased collagen and decreased hyaluronan. However, the extracellular matrix (ECM) is a complex network of hundreds of proteins, glycoproteins, and glycans which are highly tissue specific and undergo pronounced changes with age. To obtain an unbiased and comprehensive profile of age-associated alterations to the murine ovarian proteome and ECM, we used a label-free quantitative proteomic methodology. We validated conditions to enrich for the ECM prior to proteomic analysis. Following analysis by data-independent acquisition (DIA) and quantitative data processing, we observed that both native and ECM-enriched ovaries clustered separately based on age, indicating distinct age-dependent proteomic signatures. We identified a total of 4,721 proteins from both native and ECM-enriched ovaries, of which 383 proteins were significantly altered with advanced age, including 58 ECM proteins. Several ECM proteins upregulated with age have been associated with fibrosis in other organs, but to date their roles in ovarian fibrosis are unknown. Pathways regulating DNA metabolism and translation were downregulated with age, whereas pathways involved in ECM remodeling and immune response were upregulated. Interestingly, immune-related pathways were upregulated with age even in ECM-enriched ovaries, suggesting a novel interplay between the ECM and the immune system. Moreover, we identified putative markers of unique immune cell populations present in the ovary with age. These findings provide evidence from a proteomic perspective that the aging ovary provides a fibroinflammatory milieu, and our study suggests target proteins which may drive these age-associated phenotypes for future investigation.
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Affiliation(s)
- Shweta S. Dipali
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Jacob P. Rose
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Joanna E. Burdette
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | | | - Francesca E. Duncan
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Buck Institute for Research on Aging, Novato, CA 94945, USA
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30
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Rose JP, Schurman CA, King CD, Bons J, Patel SK, Burton JB, O’Broin A, Alliston T, Schilling B. Deep coverage and quantification of the bone proteome provides enhanced opportunities for new discoveries in skeletal biology and disease. PLoS One 2023; 18:e0292268. [PMID: 37816044 PMCID: PMC10564166 DOI: 10.1371/journal.pone.0292268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/15/2023] [Indexed: 10/12/2023] Open
Abstract
Dysregulation of cell signaling in chondrocytes and in bone cells, such as osteocytes, osteoblasts, osteoclasts, and an elevated burden of senescent cells in cartilage and bone, are implicated in osteoarthritis (OA). Mass spectrometric analyses provides a crucial molecular tool-kit to understand complex signaling relationships in age-related diseases, such as OA. Here we introduce a novel mass spectrometric workflow to promote proteomic studies of bone. This workflow uses highly specialized steps, including extensive overnight demineralization, pulverization, and incubation for 72 h in 6 M guanidine hydrochloride and EDTA, followed by proteolytic digestion. Analysis on a high-resolution Orbitrap Eclipse and Orbitrap Exploris 480 mass spectrometer using Data-Independent Acquisition (DIA) provides deep coverage of the bone proteome, and preserves post-translational modifications, such as hydroxyproline. A spectral library-free quantification strategy, directDIA, identified and quantified over 2,000 protein groups (with ≥ 2 unique peptides) from calcium-rich bone matrices. Key components identified were proteins of the extracellular matrix (ECM), bone-specific proteins (e.g., secreted protein acidic and cysteine rich, SPARC, and bone sialoprotein 2, IBSP), and signaling proteins (e.g., transforming growth factor beta-2, TGFB2), and lysyl oxidase homolog 2 (LOXL2), an important protein in collagen crosslinking. Post-translational modifications (PTMs) were identified without the need for specific enrichment. This includes collagen hydroxyproline modifications, chemical modifications for collagen self-assembly and network formation. Multiple senescence factors were identified, such as complement component 3 (C3) protein of the complement system and many matrix metalloproteinases, that might be monitored during age-related bone disease progression. Our innovative workflow yields in-depth protein coverage and quantification strategies to discover underlying biological mechanisms of bone aging and to provide tools to monitor therapeutic interventions. These novel tools to monitor the bone proteome open novel horizons to investigate bone-specific diseases, many of which are age-related.
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Affiliation(s)
- Jacob P. Rose
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | | | - Christina D. King
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Sandip K. Patel
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Jordan B. Burton
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Amy O’Broin
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Tamara Alliston
- Department of Orthopaedic Surgery, University of California, San Francisco, CA, Unted States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, United States of America
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, CA, United States of America
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31
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Neale Q, Prefontaine A, Battellino T, Mizero B, Yeung D, Spicer V, Budisa N, Perreault H, Zahedi RP, Krokhin OV. Compendium of Chromatographic Behavior of Post-translationally and Chemically Modified Peptides in Bottom-Up Proteomic Experiments. Anal Chem 2023; 95:14634-14642. [PMID: 37739932 DOI: 10.1021/acs.analchem.3c02412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
We have systematically evaluated the chromatographic behavior of post-translationally/chemically modified peptides using data spanning over 70 of the most relevant modifications. These retention properties were measured for standard bottom-up proteomic settings (fully porous C18 separation media, 0.1% formic acid as ion-pairing modifier) using collections of modified/nonmodified peptide pairs. These pairs were generated by spontaneous degradation, chemical or enzymatic treatment, analysis of synthetic peptides, or the cotranslational incorporation of noncanonical proline analogues. In addition, these measurements were validated using external data acquired for synthetic peptides and enzymatically induced citrullination. Working in units of hydrophobicity index (HI, % ACN) and evaluating the average retention shifts (ΔHI) represent the simplest approach to describe the effect of modifications from a didactic point of view. Plotting HI values for modified (y-axis) vs nonmodified (x-axis) counterparts generates unique slope and intercept values for each modification defined by the chemistry of the modifying moiety: its hydrophobicity, size, pKa of ionizable groups, and position of the altered residue. These composition-dependent correlations can be used for coarse incorporation of PTMs into models for prediction of peptide retention. More accurate predictions would require the development of specific sequence-dependent algorithms to predict ΔHI values.
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Affiliation(s)
- Quinn Neale
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Alexandre Prefontaine
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Taylor Battellino
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Benilde Mizero
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Darien Yeung
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Helene Perreault
- Department of Chemistry, University of Manitoba, 360 Parker Building, Winnipeg R3T 2N2, Manitoba, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- CancerCare Manitoba Research Institute, 675 McDermot Avenue, Winnipeg R3E 0 V9, Manitoba, Canada
| | - Oleg V Krokhin
- Department of Biochemistry and Medical Genetics, University of Manitoba, 336 Basic Medical Sciences Building, 745 Bannatyne Avenue, Winnipeg R3E 0J9, Manitoba, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, 799 JBRC, 715 McDermot Avenue, Winnipeg R3E 3P4, Manitoba, Canada
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Boileau C, Deforges S, Peret A, Scavarda D, Bartolomei F, Giles A, Partouche N, Gautron J, Viotti J, Janowitz H, Penchet G, Marchal C, Lagarde S, Trebuchon A, Villeneuve N, Rumi J, Marissal T, Khazipov R, Khalilov I, Martineau F, Maréchal M, Lepine A, Milh M, Figarella-Branger D, Dougy E, Tong S, Appay R, Baudouin S, Mercer A, Smith JB, Danos O, Porter R, Mulle C, Crépel V. GluK2 Is a Target for Gene Therapy in Drug-Resistant Temporal Lobe Epilepsy. Ann Neurol 2023; 94:745-761. [PMID: 37341588 DOI: 10.1002/ana.26723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
OBJECTIVE Temporal lobe epilepsy (TLE) is characterized by recurrent seizures generated in the limbic system, particularly in the hippocampus. In TLE, recurrent mossy fiber sprouting from dentate gyrus granule cells (DGCs) crea an aberrant epileptogenic network between DGCs which operates via ectopically expressed GluK2/GluK5-containing kainate receptors (KARs). TLE patients are often resistant to anti-seizure medications and suffer significant comorbidities; hence, there is an urgent need for novel therapies. Previously, we have shown that GluK2 knockout mice are protected from seizures. This study aims at providing evidence that downregulating KARs in the hippocampus using gene therapy reduces chronic epileptic discharges in TLE. METHODS We combined molecular biology and electrophysiology in rodent models of TLE and in hippocampal slices surgically resected from patients with drug-resistant TLE. RESULTS Here, we confirmed the translational potential of KAR suppression using a non-selective KAR antagonist that markedly attenuated interictal-like epileptiform discharges (IEDs) in TLE patient-derived hippocampal slices. An adeno-associated virus (AAV) serotype-9 vector expressing anti-grik2 miRNA was engineered to specifically downregulate GluK2 expression. Direct delivery of AAV9-anti grik2 miRNA into the hippocampus of TLE mice led to a marked reduction in seizure activity. Transduction of TLE patient hippocampal slices reduced levels of GluK2 protein and, most importantly, significantly reduced IEDs. INTERPRETATION Our gene silencing strategy to knock down aberrant GluK2 expression demonstrates inhibition of chronic seizure in a mouse TLE model and IEDs in cultured slices derived from TLE patients. These results provide proof-of-concept for a gene therapy approach targeting GluK2 KARs for drug-resistant TLE patients. ANN NEUROL 2023;94:745-761.
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Affiliation(s)
| | - Severine Deforges
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | - Didier Scavarda
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Pediatric Neurosurgery, Marseille, France
| | - Fabrice Bartolomei
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | | | - Nicolas Partouche
- Aix-Marseille Univ. INSERM, Marseille, France
- Corlieve Therapeutics SAS, uniQure NV, Paris, France
| | - Justine Gautron
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
- Corlieve Therapeutics SAS, uniQure NV, Paris, France
| | - Julio Viotti
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | | | - Cécile Marchal
- Pellegrin Hospital, Neurosurgery Department, Bordeaux, France
| | - Stanislas Lagarde
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Agnès Trebuchon
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Nathalie Villeneuve
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Julie Rumi
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | | | | | | | | | - Marine Maréchal
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
| | - Anne Lepine
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Mathieu Milh
- APHM, INSERM, Aix Marseille Univ, INS, Timone Hospital, Epileptology Department, Marseille, France
| | - Dominique Figarella-Branger
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Etienne Dougy
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Soutsakhone Tong
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | - Romain Appay
- APHM, CNRS, INP, Inst Neurophysiopathol, CHU Timone, Service d'Anatomie Pathologique et de Neuropathologie, Aix-Marseille Univ, Marseille, France
| | | | | | | | | | | | - Christophe Mulle
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience IINS, UMR 5297, Bordeaux, France
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Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim Kim J, Lee KA, Leib RD, Nelson AJ, Patel P, Ren JM, Stemmer PM, Zhu Y, Neely BA, Patel B. A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development. Mol Cell Proteomics 2023; 22:100639. [PMID: 37657519 PMCID: PMC10561125 DOI: 10.1016/j.mcpro.2023.100639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Recent advances in methodology have made phosphopeptide analysis a tractable problem for many proteomics researchers. There are now a wide variety of robust and accessible enrichment strategies to generate phosphoproteomes while free or inexpensive software tools for quantitation and site localization have simplified phosphoproteome analysis workflow tremendously. As a research group under the Association for Biomolecular Resource Facilities umbrella, the Proteomics Standards Research Group has worked to develop a multipathway phosphopeptide standard based on a mixture of heavy-labeled phosphopeptides designed to enable researchers to rapidly develop assays. This mixture contains 131 mass spectrometry vetted phosphopeptides specifically chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling networks: AMPK signaling, death and apoptosis signaling, ErbB signaling, insulin/insulin-like growth factor-1 signaling, mTOR signaling, PI3K/AKT signaling, and stress (p38/SAPK/JNK) signaling. Here, we describe a characterization of this mixture spiked into a HeLa tryptic digest stimulated with both epidermal growth factor and insulin-like growth factor-1 to activate the MAPK and PI3K/AKT/mTOR pathways. We further demonstrate a comparison of phosphoproteomic profiling of HeLa performed independently in five labs using this phosphopeptide mixture with data-independent acquisition. Despite different experimental and instrumentation processes, we found that labs could produce reproducible, harmonized datasets by reporting measurements as ratios to the standard, while intensity measurements showed lower consistency between labs even after normalization. Our results suggest that widely available, biologically relevant phosphopeptide standards can act as a quantitative "yardstick" across laboratories and sample preparations enabling experimental designs larger than a single laboratory can perform. Raw data files are publicly available in the MassIVE dataset MSV000090564.
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Affiliation(s)
- Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.
| | - Allis Chien
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | | | - Anthony W Herren
- UC Davis Genome Center, Proteomics Core, University of California Davis, Davis California, USA
| | - Jenny Kim Kim
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Kimberly A Lee
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Ryan D Leib
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | - Purvi Patel
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Jian Min Ren
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Paul M Stemmer
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Yiying Zhu
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Bhavin Patel
- Thermo Fisher Scientific, Rockford, Illinois, USA
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Müller Bark J, Trevisan França de Lima L, Zhang X, Broszczak D, Leo PJ, Jeffree RL, Chua B, Day BW, Punyadeera C. Proteome profiling of salivary small extracellular vesicles in glioblastoma patients. Cancer 2023; 129:2836-2847. [PMID: 37254878 PMCID: PMC10952188 DOI: 10.1002/cncr.34888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND Extracellular vesicles (EVs) play a critical role in intercellular communication under physiological and pathological conditions, including cancer. EVs cargo reflects their cell of origin, suggesting their utility as biomarkers. EVs are detected in several biofluids, and their ability to cross the blood-brain barrier has highlighted their potential as prognostic and diagnostic biomarkers in gliomas, including glioblastoma (GBM). Studies have demonstrated the potential clinical utility of plasma-derived EVs in glioma. However, little is known about the clinical utility of saliva-derived EVs in GBM. METHODS Small EVs were isolated from whole mouth saliva of GBM patients pre- and postoperatively. Isolation was performed using differential centrifugation and/or ultracentrifugation. EVs were characterized by concentration, size, morphology, and EVs cell-surface protein markers. Protein cargo in EVs was profiled using mass spectrometry. RESULTS There were no statistically significant differences in size and concentration of EVs derived from pre- and post GBM patients' saliva samples. A higher number of proteins were detected in preoperative samples compared to postoperative samples. The authors found four highly abundant proteins (aldolase A, 14-3-3 protein ε, enoyl CoA hydratase 1, and transmembrane protease serine 11B) in preoperative saliva samples from GBM patients with poor outcomes. Functional enrichment analysis of pre- and postoperative saliva samples showed significant enrichment of several pathways, including those related to the immune system, cell cycle and programmed cell death. CONCLUSIONS This study, for the first time, demonstrates the feasibility of isolating and characterizing small EVs from pre- and postoperative saliva samples from GBM patients. Preliminary findings encourage further large cohort validation studies on salivary small EVs to evaluate prognosis in GBM.
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Affiliation(s)
- Juliana Müller Bark
- Centre for Biomedical TechnologiesThe School of Biomedical SciencesFaculty of HealthQueensland University of TechnologyBrisbaneQueenslandAustralia
- Saliva and Liquid Biopsy Translational LaboratoryGriffith Institute for Drug Discovery Griffith UniversityBrisbaneQueenslandAustralia
- Translational Research InstituteBrisbaneQueenslandAustralia
| | - Lucas Trevisan França de Lima
- Centre for Biomedical TechnologiesThe School of Biomedical SciencesFaculty of HealthQueensland University of TechnologyBrisbaneQueenslandAustralia
- Saliva and Liquid Biopsy Translational LaboratoryGriffith Institute for Drug Discovery Griffith UniversityBrisbaneQueenslandAustralia
- Translational Research InstituteBrisbaneQueenslandAustralia
- Gallipoli Medical Research InstituteGreenslopes Private HospitalBrisbaneQueenslandAustralia
| | - Xi Zhang
- Centre for Biomedical TechnologiesThe School of Biomedical SciencesFaculty of HealthQueensland University of TechnologyBrisbaneQueenslandAustralia
- Saliva and Liquid Biopsy Translational LaboratoryGriffith Institute for Drug Discovery Griffith UniversityBrisbaneQueenslandAustralia
- Translational Research InstituteBrisbaneQueenslandAustralia
| | - Daniel Broszczak
- School of Biomedical SciencesFaculty of HealthQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Paul J. Leo
- Translational Research InstituteBrisbaneQueenslandAustralia
- Translational Genomics GroupQueensland University of TechnologyTranslational Research InstituteWoolloongabbaQueenslandAustralia
| | - Rosalind L. Jeffree
- Faculty of MedicineUniversity of QueenslandBrisbaneQueenslandAustralia
- Kenneth G. Jamieson Department of NeurosurgeryRoyal Brisbane and Women's HospitalHerstonQueenslandAustralia
| | - Benjamin Chua
- Faculty of MedicineUniversity of QueenslandBrisbaneQueenslandAustralia
- Cancer Care ServicesRoyal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
| | - Bryan W. Day
- Cell and Molecular Biology DepartmentSid Faithfull Brain Cancer LaboratoryQIMR Berghofer MRIBrisbaneQueenslandAustralia
| | - Chamindie Punyadeera
- Centre for Biomedical TechnologiesThe School of Biomedical SciencesFaculty of HealthQueensland University of TechnologyBrisbaneQueenslandAustralia
- Saliva and Liquid Biopsy Translational LaboratoryGriffith Institute for Drug Discovery Griffith UniversityBrisbaneQueenslandAustralia
- Menzies Health Institute (MHIQ)Griffith UniversityGold CoastQueenslandAustralia
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Cengiz Winter N, Karakaya M, Mosen P, Brusius I, Anlar B, Haliloglu G, Winter D, Wirth B. Proteomic Investigation of Differential Interactomes of Glypican 1 and a Putative Disease-Modifying Variant of Ataxia. J Proteome Res 2023; 22:3081-3095. [PMID: 37585105 PMCID: PMC10476613 DOI: 10.1021/acs.jproteome.3c00402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Indexed: 08/17/2023]
Abstract
In a currently 13-year-old girl of consanguineous Turkish parents, who developed unsteady gait and polyneuropathy at the ages of 3 and 6 years, respectively, we performed whole genome sequencing and identified a biallelic missense variant c.424C>T, p.R142W in glypican 1 (GPC1) as a putative disease-associated variant. Up to date, GPC1 has not been associated with a neuromuscular disorder, and we hypothesized that this variant, predicted as deleterious, may be causative for the disease. Using mass spectrometry-based proteomics, we investigated the interactome of GPC1 WT and the missense variant. We identified 198 proteins interacting with GPC1, of which 16 were altered for the missense variant. This included CANX as well as vacuolar ATPase (V-ATPase) and the mammalian target of rapamycin complex 1 (mTORC1) complex members, whose dysregulation could have a potential impact on disease severity in the patient. Importantly, these proteins are novel interaction partners of GPC1. At 10.5 years, the patient developed dilated cardiomyopathy and kyphoscoliosis, and Friedreich's ataxia (FRDA) was suspected. Given the unusually severe phenotype in a patient with FRDA carrying only 104 biallelic GAA repeat expansions in FXN, we currently speculate that disturbed GPC1 function may have exacerbated the disease phenotype. LC-MS/MS data are accessible in the ProteomeXchange Consortium (PXD040023).
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Affiliation(s)
- Nur Cengiz Winter
- Institute
of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
- Center
for Molecular Medicine Cologne, University
of Cologne, 50931 Cologne, Germany
| | - Mert Karakaya
- Institute
of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
- Center
for Molecular Medicine Cologne, University
of Cologne, 50931 Cologne, Germany
- Center
for Rare Diseases Cologne, University Hospital
of Cologne, 50931 Cologne, Germany
| | - Peter Mosen
- Institute
for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
| | - Isabell Brusius
- Institute
of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
| | - Banu Anlar
- Department
of Pediatrics, Division of Pediatric Neurology, Hacettepe University Faculty of Medicine, 06230 Ankara, Turkey
| | - Goknur Haliloglu
- Department
of Pediatrics, Division of Pediatric Neurology, Hacettepe University Faculty of Medicine, 06230 Ankara, Turkey
| | - Dominic Winter
- Institute
for Biochemistry and Molecular Biology, Medical Faculty, University of Bonn, 53115 Bonn, Germany
| | - Brunhilde Wirth
- Institute
of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
- Center
for Molecular Medicine Cologne, University
of Cologne, 50931 Cologne, Germany
- Center
for Rare Diseases Cologne, University Hospital
of Cologne, 50931 Cologne, Germany
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Lundeen RA, Kennedy JJ, Murillo OD, Ivey RG, Zhao L, Schoenherr RM, Hoofnagle AN, Wang P, Whiteaker JR, Paulovich AG. Monitoring Both Extended and Tryptic Forms of Stable Isotope-Labeled Standard Peptides Provides an Internal Quality Control of Proteolytic Digestion in Targeted Mass Spectrometry-Based Assays. Mol Cell Proteomics 2023; 22:100621. [PMID: 37478973 PMCID: PMC10458721 DOI: 10.1016/j.mcpro.2023.100621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted mass spectrometry (MS)-based proteomic assays, such as multiplexed multiple reaction monitoring (MRM)-MS assays, enable sensitive and specific quantification of proteotypic peptides as stoichiometric surrogates for proteins. Efforts are underway to expand the use of MRM-MS assays in clinical environments, which requires a reliable strategy to monitor proteolytic digestion efficiency within individual samples. Towards this goal, extended stable isotope-labeled standard (SIS) peptides (hE), which incorporate native proteolytic cleavage sites, can be spiked into protein lysates prior to proteolytic (trypsin) digestion, and release of the tryptic SIS peptide (hT) can be monitored. However, hT measurements alone cannot monitor the extent of digestion and may be confounded by matrix effects specific to individual patient samples; therefore, they are not sufficient to monitor sample-to-sample digestion variability. We hypothesized that measuring undigested hE, along with its paired hT, would improve detection of digestion issues compared to only measuring hT. We tested the ratio of the SIS pair measurements, or hE/hT, as a quality control (QC) metric of trypsin digestion for two MRM assays: a direct-MRM (398 targets) and an immuno-MRM (126 targets requiring immunoaffinity peptide enrichment) assay, with extended SIS peptides observable for 54% (216) and 62% (78) of the targets, respectively. We evaluated the quantitative bias for each target in a series of experiments that adversely affected proteolytic digestion (e.g., variable digestion times, pH, and temperature). We identified a subset of SIS pairs (36 for the direct-MRM, 7 for the immuno-MRM assay) for which the hE/hT ratio reliably detected inefficient digestion that resulted in decreased assay sensitivity and unreliable endogenous quantification. The hE/hT ratio was more responsive to a decrease in digestion efficiency than a metric based on hT measurements alone. For clinical-grade MRM-MS assays, this study describes a ready-to-use QC panel and also provides a road map for designing custom QC panels.
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Affiliation(s)
- Rachel A Lundeen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Regine M Schoenherr
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
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Pandey K, Wang SS, Mifsud NA, Faridi P, Davenport AJ, Webb AI, Sandow JJ, Ayala R, Monje M, Cross RS, Ramarathinam SH, Jenkins MR, Purcell AW. A combined immunopeptidomics, proteomics, and cell surface proteomics approach to identify immunotherapy targets for diffuse intrinsic pontine glioma. Front Oncol 2023; 13:1192448. [PMID: 37637064 PMCID: PMC10455951 DOI: 10.3389/fonc.2023.1192448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/19/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Diffuse intrinsic pontine glioma (DIPG), recently reclassified as a subtype of diffuse midline glioma, is a highly aggressive brainstem tumor affecting children and young adults, with no cure and a median survival of only 9 months. Conventional treatments are ineffective, highlighting the need for alternative therapeutic strategies such as cellular immunotherapy. However, identifying unique and tumor-specific cell surface antigens to target with chimeric antigen receptor (CAR) or T-cell receptor (TCR) therapies is challenging. Methods In this study, a multi-omics approach was used to interrogate patient-derived DIPG cell lines and to identify potential targets for immunotherapy. Results Through immunopeptidomics, a range of targetable peptide antigens from cancer testis and tumor-associated antigens as well as peptides derived from human endogenous retroviral elements were identified. Proteomics analysis also revealed upregulation of potential drug targets and cell surface proteins such as Cluster of differentiation 27 (CD276) B7 homolog 3 protein (B7H3), Interleukin 13 alpha receptor 2 (IL-13Rα2), Human Epidermal Growth Factor Receptor 3 (HER2), Ephrin Type-A Receptor 2 (EphA2), and Ephrin Type-A Receptor 3 (EphA3). Discussion The results of this study provide a valuable resource for the scientific community to accelerate immunotherapeutic approaches for DIPG. Identifying potential targets for CAR and TCR therapies could open up new avenues for treating this devastating disease.
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Affiliation(s)
- Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stacie S. Wang
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Children’s Cancer Centre, Royal Children’s Hospital, Parkville, VIC, Australia
| | - Nicole A. Mifsud
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pouya Faridi
- Monash Proteomics and Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Clinical Sciences, Department of Medicine, Monash University, Clayton, VIC, Australia
- Department of Medicine, Sub-Faculty of Clinical and Molecular Medicine, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Alexander J. Davenport
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Andrew I. Webb
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Jarrod J. Sandow
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michelle Monje
- Department of Neurology and Neurological Sciences and Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Ryan S. Cross
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Misty R. Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- LaTrobe Institute for Molecular Science, LaTrobe University, Bundoora, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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38
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Park SH, Helsley RN, Fadhul T, Willoughby JLS, Noetzli L, Tu HC, Solheim MH, Fujisaka S, Pan H, Dreyfuss JM, Bons J, Rose J, King CD, Schilling B, Lusis AJ, Pan C, Gupta M, Kulkarni RN, Fitzgerald K, Kern PA, Divanovic S, Kahn CR, Softic S. Fructose induced KHK-C can increase ER stress independent of its effect on lipogenesis to drive liver disease in diet-induced and genetic models of NAFLD. Metabolism 2023; 145:155591. [PMID: 37230214 PMCID: PMC10752375 DOI: 10.1016/j.metabol.2023.155591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a liver manifestation of metabolic syndrome, and is estimated to affect one billion individuals worldwide. An increased intake of a high-fat diet (HFD) and sugar-sweetened beverages are risk-factors for NAFLD development, but how their combined intake promotes progression to a more severe form of liver injury is unknown. Here we show that fructose metabolism via ketohexokinase (KHK) C isoform leads to unresolved endoplasmic reticulum (ER) stress when coupled with a HFD intake. Conversely, a liver-specific knockdown of KHK in mice consuming fructose on a HFD is adequate to improve the NAFLD activity score and exert a profound effect on the hepatic transcriptome. Overexpression of KHK-C in cultured hepatocytes is sufficient to induce ER stress in fructose free media. Upregulation of KHK-C is also observed in mice with genetically induced obesity or metabolic dysfunction, whereas KHK knockdown in these mice improves metabolic function. Additionally, in over 100 inbred strains of male or female mice hepatic KHK expression correlates positively with adiposity, insulin resistance, and liver triglycerides. Similarly, in 241 human subjects and their controls, hepatic Khk expression is upregulated in early, but not late stages of NAFLD. In summary, we describe a novel role of KHK-C in triggering ER stress, which offers a mechanistic understanding of how the combined intake of fructose and a HFD propagates the development of metabolic complications.
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Affiliation(s)
- Se-Hyung Park
- Department of Pediatrics, Division of Pediatric Gastroenterology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Robert N Helsley
- Department of Pediatrics, Division of Pediatric Gastroenterology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Taghreed Fadhul
- Department of Pediatrics, Division of Pediatric Gastroenterology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | | | - Leila Noetzli
- Alnylam Pharmaceuticals Inc., Cambridge, MA 02142, USA
| | - Ho-Chou Tu
- Alnylam Pharmaceuticals Inc., Cambridge, MA 02142, USA
| | - Marie H Solheim
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, 50931 Cologne, Germany
| | - Shiho Fujisaka
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; First Department of Internal Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Hui Pan
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Jonathan M Dreyfuss
- Bioinformatics and Biostatistics Core, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Joanna Bons
- Proteomics and Aging Center, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Jacob Rose
- Proteomics and Aging Center, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Christina D King
- Proteomics and Aging Center, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Birgit Schilling
- Proteomics and Aging Center, Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, Department of Human Genetics, A2-237 Center for the Health Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Calvin Pan
- Department of Medicine/Division of Cardiology, Department of Human Genetics, A2-237 Center for the Health Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Manoj Gupta
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Rohit N Kulkarni
- Section of Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02215, USA
| | | | - Philip A Kern
- Department of Medicine, Division of Endocrinology, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Senad Divanovic
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - C Ronald Kahn
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Samir Softic
- Department of Pediatrics, Division of Pediatric Gastroenterology, University of Kentucky College of Medicine, Lexington, KY 40536, USA; Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA; Department of Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY 40536, USA.
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39
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Sun R, Ge W, Zhu Y, Sayad A, Luna A, Lyu M, Liang S, Tobalina L, Rajapakse VN, Yu C, Zhang H, Fang J, Wu F, Xie H, Saez-Rodriguez J, Ying H, Reinhold WC, Sander C, Pommier Y, Neel BG, Aebersold R, Guo T. Proteomic Dynamics of Breast Cancer Cell Lines Identifies Potential Therapeutic Protein Targets. Mol Cell Proteomics 2023; 22:100602. [PMID: 37343696 PMCID: PMC10392136 DOI: 10.1016/j.mcpro.2023.100602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 04/18/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
Treatment and relevant targets for breast cancer (BC) remain limited, especially for triple-negative BC (TNBC). We identified 6091 proteins of 76 human BC cell lines using data-independent acquisition (DIA). Integrating our proteomic findings with prior multi-omics datasets, we found that including proteomics data improved drug sensitivity predictions and provided insights into the mechanisms of action. We subsequently profiled the proteomic changes in nine cell lines (five TNBC and four non-TNBC) treated with EGFR/AKT/mTOR inhibitors. In TNBC, metabolism pathways were dysregulated after EGFR/mTOR inhibitor treatment, while RNA modification and cell cycle pathways were affected by AKT inhibitor. This systematic multi-omics and in-depth analysis of the proteome of BC cells can help prioritize potential therapeutic targets and provide insights into adaptive resistance in TNBC.
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Affiliation(s)
- Rui Sun
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Bioinformatics Department, Westlake Omics (Hangzhou) Biotechnology Co, Ltd, Hangzhou, Zhejiang, China
| | - Yi Zhu
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Azin Sayad
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA
| | - Augustin Luna
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mengge Lyu
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Shuang Liang
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Luis Tobalina
- Bioinformatics and Data Science, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chenhuan Yu
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Huanhuan Zhang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Jie Fang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Fang Wu
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Hui Xie
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Huazhong Ying
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chris Sander
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Benjamin G Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA.
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Tiannan Guo
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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40
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Batavia AA, Rutishauser D, Sobottka B, Schraml P, Beerenwinkel N, Moch H. Biallelic ELOC-Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity. Mod Pathol 2023; 36:100194. [PMID: 37088333 DOI: 10.1016/j.modpat.2023.100194] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023]
Abstract
Approximately 70% of clear cell renal cell carcinoma (ccRCC) is characterized by the biallelic inactivation of von Hippel-Lindau (VHL) on chromosome 3p. ELOC-mutated (Elongin C-mutated) renal cell carcinoma containing biallelic ELOC inactivations with chromosome 8q deletions is considered a novel subtype of renal cancer possessing a morphologic overlap with ccRCC, renal cell carcinoma (RCC) with fibromyomatous stroma exhibiting Tuberous Sclerosis Complex (TSC)/mammalian Target of Rapamycin (mTOR) mutations, and clear cell papillary tumor. However, the frequency and consequences of ELOC alterations in wild-type VHL and mutated VHL RCC are unclear. In this study, we characterize 123 renal tumors with clear cell morphology and known VHL mutation status to assess the morphologic and molecular consequences of ELOC inactivation. Using OncoScan and whole-exome sequencing, we identify 18 ELOC-deleted RCCs, 3 of which contain ELOC mutations resulting in the biallelic inactivation of ELOC. Biallelic ELOC and biallelic VHL aberrations were mutually exclusive; however, 2 ELOC-mutated RCCs showed monoallelic VHL alterations. Furthermore, no mutations in TSC1, TSC2, or mTOR were identified in ELOC-mutated RCC with biallelic ELOC inactivation. Using High Ambiguity Driven biomolecular DOCKing, we report a novel ELOC variant containing a duplication event disrupting ELOC-VHL interaction alongside the frequently seen Y79C alteration. Using hyper reaction monitoring mass spectrometry, we show RCCs with biallelic ELOC alterations have significantly reduced ELOC expression but similar carbonic anhydrase 9 and vascular endothelial growth factor A expression compared with classical ccRCC with biallelic VHL inactivation. The absence of biallelic VHL and TSC1, TSC2, or mTOR inactivation in RCC with biallelic ELOC inactivation (ELOC mutation in combination with ELOC deletions on chromosome 8q) supports the notion of a novel, molecularly defined tumor entity.
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Affiliation(s)
- Aashil A Batavia
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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41
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Madhavan SS, Roa Diaz S, Peralta S, Nomura M, King CD, Lin A, Bhaumik D, Shah S, Blade T, Gray W, Chamoli M, Eap B, Panda O, Diaz D, Garcia TY, Stubbs BJ, Lithgow GJ, Schilling B, Verdin E, Chaudhuri AR, Newman JC. β-hydroxybutyrate is a metabolic regulator of proteostasis in the aged and Alzheimer disease brain. bioRxiv 2023:2023.07.03.547547. [PMID: 37461525 PMCID: PMC10349929 DOI: 10.1101/2023.07.03.547547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Loss of proteostasis is a hallmark of aging and Alzheimer disease (AD). Here, we identify β-hydroxybutyrate (βHB), a ketone body, as a regulator of protein solubility in the aging brain. βHB is a small molecule metabolite which primarily provides an oxidative substrate for ATP during hypoglycemic conditions, and also regulates other cellular processes through covalent and noncovalent protein interactions. We demonstrate βHB-induced protein insolubility across in vitro, ex vivo, and in vivo mouse systems. This activity is shared by select structurally similar metabolites, is not dependent on covalent protein modification, pH, or solute load, and is observable in mouse brain in vivo after delivery of a ketone ester. Furthermore, this phenotype is selective for pathological proteins such as amyloid-β, and exogenous βHB ameliorates pathology in nematode models of amyloid-β aggregation toxicity. We have generated a comprehensive atlas of the βHB-induced protein insolublome ex vivo and in vivo using mass spectrometry proteomics, and have identified common protein domains within βHB target sequences. Finally, we show enrichment of neurodegeneration-related proteins among βHB targets and the clearance of these targets from mouse brain, likely via βHB-induced autophagy. Overall, these data indicate a new metabolically regulated mechanism of proteostasis relevant to aging and AD.
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Affiliation(s)
- S S Madhavan
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Geriatrics, University of California San Francisco, San Francisco, CA, USA
| | - S Roa Diaz
- Buck Institute for Research on Aging, Novato, CA, USA
- Department of Geriatrics, University of California San Francisco, San Francisco, CA, USA
| | - S Peralta
- Buck Institute for Research on Aging, Novato, CA, USA
| | - M Nomura
- Buck Institute for Research on Aging, Novato, CA, USA
| | - C D King
- Buck Institute for Research on Aging, Novato, CA, USA
| | - A Lin
- Buck Institute for Research on Aging, Novato, CA, USA
| | - D Bhaumik
- Buck Institute for Research on Aging, Novato, CA, USA
| | - S Shah
- Buck Institute for Research on Aging, Novato, CA, USA
| | - T Blade
- Buck Institute for Research on Aging, Novato, CA, USA
| | - W Gray
- Buck Institute for Research on Aging, Novato, CA, USA
| | - M Chamoli
- Buck Institute for Research on Aging, Novato, CA, USA
| | - B Eap
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - O Panda
- Buck Institute for Research on Aging, Novato, CA, USA
| | - D Diaz
- Buck Institute for Research on Aging, Novato, CA, USA
| | - T Y Garcia
- Buck Institute for Research on Aging, Novato, CA, USA
- Department of Geriatrics, University of California San Francisco, San Francisco, CA, USA
| | - B J Stubbs
- Buck Institute for Research on Aging, Novato, CA, USA
| | - G J Lithgow
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - B Schilling
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - E Verdin
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - A R Chaudhuri
- Buck Institute for Research on Aging, Novato, CA, USA
| | - J C Newman
- Buck Institute for Research on Aging, Novato, CA, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Department of Geriatrics, University of California San Francisco, San Francisco, CA, USA
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42
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Wang F, Veth T, Kuipers M, Altelaar M, Stecker KE. Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation. Anal Chem 2023; 95:9471-9479. [PMID: 37319171 PMCID: PMC10308333 DOI: 10.1021/acs.analchem.3c00324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. Suspension trapping (S-Trap) is a novel, rapid, and universal method of sample preparation that is increasingly applied in bottom-up proteomics studies. However, the performance of the S-Trap protocol for phosphoproteomics studies is unclear. In the existing S-Trap protocol, the addition of phosphoric acid (PA) and methanol buffer creates a fine protein suspension to capture proteins on a filter and is a critical step for subsequent protein digestion. Herein, we demonstrate that this addition of PA is detrimental to downstream phosphopeptide enrichment, rendering the standard S-Trap protocol suboptimal for phosphoproteomics. In this study, the performance of the S-Trap digestion for proteomics and phosphoproteomics is systematically evaluated in large-scale and small-scale samples. The results of this comparative analysis show that an optimized S-Trap approach, where trifluoroacetic acid is substituted for PA, is a simple and effective method to prepare samples for phosphoproteomics. Our optimized S-Trap protocol is applied to extracellular vesicles to demonstrate superior sample preparation workflow for low-abundance, membrane-rich samples.
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Affiliation(s)
- Fujia Wang
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Tim Veth
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marije Kuipers
- Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584
CM Utrecht, the Netherlands
| | - Maarten Altelaar
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Kelly E. Stecker
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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43
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Strasser MK, Gibbs DL, Gascard P, Bons J, Hickey JW, Schürch CM, Tan Y, Black S, Chu P, Ozkan A, Basisty N, Sangwan V, Rose J, Shah S, Camilleri-Broet S, Fiset PO, Bertos N, Berube J, Djambazian H, Li R, Oikonomopoulos S, Fels-Elliott DR, Vernovsky S, Shimshoni E, Collyar D, Russell A, Ragoussis I, Stachler M, Goldenring JR, McDonald S, Ingber DE, Schilling B, Nolan GP, Tlsty TD, Huang S, Ferri LE. Concerted epithelial and stromal changes during progression of Barrett's Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis. bioRxiv 2023:2023.06.08.544265. [PMID: 37333362 PMCID: PMC10274886 DOI: 10.1101/2023.06.08.544265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Esophageal adenocarcinoma arises from Barrett's esophagus, a precancerous metaplastic replacement of squamous by columnar epithelium in response to chronic inflammation. Multi-omics profiling, integrating single-cell transcriptomics, extracellular matrix proteomics, tissue-mechanics and spatial proteomics of 64 samples from 12 patients' paths of progression from squamous epithelium through metaplasia, dysplasia to adenocarcinoma, revealed shared and patient-specific progression characteristics. The classic metaplastic replacement of epithelial cells was paralleled by metaplastic changes in stromal cells, ECM and tissue stiffness. Strikingly, this change in tissue state at metaplasia was already accompanied by appearance of fibroblasts with characteristics of carcinoma-associated fibroblasts and of an NK cell-associated immunosuppressive microenvironment. Thus, Barrett's esophagus progresses as a coordinated multi-component system, supporting treatment paradigms that go beyond targeting cancerous cells to incorporating stromal reprogramming.
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44
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Wilburn DB, Shannon AE, Spicer V, Richards AL, Yeung D, Swaney DL, Krokhin OV, Searle BC. Deep learning from harmonized peptide libraries enables retention time prediction of diverse post translational modifications. bioRxiv 2023:2023.05.30.542978. [PMID: 37398395 PMCID: PMC10312522 DOI: 10.1101/2023.05.30.542978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
In proteomics experiments, peptide retention time (RT) is an orthogonal property to fragmentation when assessing detection confidence. Advances in deep learning enable accurate RT prediction for any peptide from sequence alone, including those yet to be experimentally observed. Here we present Chronologer, an open-source software tool for rapid and accurate peptide RT prediction. Using new approaches to harmonize and false-discovery correct across independently collected datasets, Chronologer is built on a massive database with >2.2 million peptides including 10 common post-translational modification (PTM) types. By linking knowledge learned across diverse peptide chemistries, Chronologer predicts RTs with less than two-thirds the error of other deep learning tools. We show how RT for rare PTMs, such as OGlcNAc, can be learned with high accuracy using as few as 10-100 example peptides in newly harmonized datasets. This iteratively updatable workflow enables Chronologer to comprehensively predict RTs for PTM-marked peptides across entire proteomes.
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45
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Yang YY, Soh R, Vera-Colón M, Huang M, Zur Nieden NI, Wang Y. Targeted Proteomic Profiling Revealed Roles of Small GTPases during Osteogenic Differentiation. Anal Chem 2023; 95:6879-6887. [PMID: 37083350 PMCID: PMC10290900 DOI: 10.1021/acs.analchem.2c05781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The small GTPase superfamily of proteins are crucial for numerous cellular processes, including early development. The roles of these proteins in osteogenic differentiation, however, remained poorly explored. In this study, we employed a high-throughput targeted proteomic method, relying on scheduled liquid chromatography-multiple-reaction monitoring (LC-MRM) coupled with synthetic stable isotope-labeled peptides, to interrogate systematically the temporal responses of the entire small GTPase proteome during the course of osteogenic differentiation of H9 human embryonic stem cells. Our results demonstrated that the method offers high quantification accuracy, reproducibility, and throughput. In addition, the quantification results revealed altered expression of a large number of small GTPases accompanied with osteogenic differentiation, especially those involved with autophagy. We also documented a previously unrecognized role of KRAS in osteogenesis, where it regulates the accumulation of extracellular matrix for mineralization through attenuating the activity of secreted matrix metalloproteinase 9 (MMP9). Together, this study represents a novel application of a state-of-the-art analytical method, i.e., targeted quantitative proteomics, for revealing the progressive reprogramming of the small GTPase proteome during osteogenic differentiation of human embryonic stem cells, and our results revealed KRAS as a new regulator for osteogenesis.
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Affiliation(s)
- Yen-Yu Yang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Ruthia Soh
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Madeline Vera-Colón
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Ming Huang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Nicole I Zur Nieden
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, Riverside, California 92521-0403, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521-0403, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, California 92521-0403, United States
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46
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Chen M, Zhu P, Wan Q, Ruan X, Wu P, Hao Y, Zhang Z, Sun J, Nie W, Chen S. High-Coverage Four-Dimensional Data-Independent Acquisition Proteomics and Phosphoproteomics Enabled by Deep Learning-Driven Multidimensional Predictions. Anal Chem 2023; 95:7495-7502. [PMID: 37126374 DOI: 10.1021/acs.analchem.2c05414] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Four-dimensional (4D) data-independent acquisition (DIA)-based proteomics is a promising technology. However, its full performance is restricted by the time-consuming building and limited coverage of a project-specific experimental library. Herein, we developed a versatile multifunctional deep learning model Deep4D based on self-attention that could predict the collisional cross section, retention time, fragment ion intensity, and charge state with high accuracies for both the unmodified and phosphorylated peptides and thus established the complete workflows for high-coverage 4D DIA proteomics and phosphoproteomics based on multidimensional predictions. A 4D predicted library containing ∼2 million peptides was established that could realize experimental library-free DIA analysis, and 33% more proteins were identified than using an experimental library of single-shot measurement in the example of HeLa cells. These results show the great values of the convenient high-coverage 4D DIA proteomics methods.
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Affiliation(s)
- Moran Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Pujia Zhu
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Qiongqiong Wan
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Xianqin Ruan
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Pengfei Wu
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanhong Hao
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhourui Zhang
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Jian Sun
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Wenjing Nie
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
| | - Suming Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, China
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47
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Li X, Huang Y, Zheng K, Yu G, Wang Q, Gu L, Li J, Wang H, Zhang W, Sun Y, Li C. Integrated proteomic and phosphoproteomic data-independent acquisition data evaluate the personalized drug responses of primary and metastatic tumors in colorectal cancer. Biophys Rep 2023; 9:67-81. [PMID: 37753059 PMCID: PMC10518519 DOI: 10.52601/bpr.2022.210048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 11/18/2022] [Indexed: 02/19/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics and phosphoproteomics are powerful methods to study the biological mechanisms, diagnostic biomarkers, prognostic analysis, and drug therapy of tumors. Data-independent acquisition (DIA) mode is considered to perform better than data-dependent acquisition (DDA) mode in terms of quantitative reproducibility, specificity, accuracy, and identification of low-abundance proteins. Mini patient derived xenograft (MiniPDX) model is an effective model to assess the response to antineoplastic drugs in vivo and is helpful for the precise treatment of cancer patients. Kinases are favorable spots for tumor-targeted drugs, and their functional completion relies on signaling pathways through phosphorylating downstream substrates. Kinase-phosphorylation networks or edge interactions are considered more credible and permanent for characterizing complex diseases. Here, we provide a workflow for personalized drug response assessment in primary and metastatic colorectal cancer (CRC) tumors using DIA proteomic data, DIA phosphoproteomic data, and MiniPDX models. Three kinase inhibitors, afatinib, gefitinib, and regorafenib, are tested pharmacologically. The process mainly includes the following steps: clinical tissue collection, sample preparation, hybrid spectral libraries establishment, MS data acquisition, kinase-substrate network construction, in vivo drug test, and elastic regression modeling. Our protocol gives a more direct data basis for individual drug responses, and will improve the selection of treatment strategies for patients without the druggable mutation.
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Affiliation(s)
- Xumiao Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yiming Huang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kuo Zheng
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Guanyu Yu
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Qinqin Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lei Gu
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingquan Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hui Wang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Zhang
- Colorectal Surgery Department, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Yidi Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chen Li
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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48
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Kocsmár É, Schmid M, Cosenza-Contreras M, Kocsmár I, Föll M, Krey L, Barta BA, Rácz G, Kiss A, Werner M, Schilling O, Lotz G, Bronsert P. Proteome alterations in human autopsy tissues in relation to time after death. Cell Mol Life Sci 2023; 80:117. [PMID: 37020120 PMCID: PMC10075177 DOI: 10.1007/s00018-023-04754-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023]
Abstract
Protein expression is a primary area of interest for routine histological diagnostics and tissue-based research projects, but the limitations of its post-mortem applicability remain largely unclear. On the other hand, tissue specimens obtained during autopsies can provide unique insight into advanced disease states, especially in cancer research. Therefore, we aimed to identify the maximum post-mortem interval (PMI) which is still suitable for characterizing protein expression patterns, to explore organ-specific differences in protein degradation, and to investigate whether certain proteins follow specific degradation kinetics. Therefore, the proteome of human tissue samples obtained during routine autopsies of deceased patients with accurate PMI (6, 12, 18, 24, 48, 72, 96 h) and without specific diseases that significantly affect tissue preservation, from lungs, kidneys and livers, was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For the kidney and liver, significant protein degradation became apparent at 48 h. For the lung, the proteome composition was rather static for up to 48 h and substantial protein degradation was detected only at 72 h suggesting that degradation kinetics appear to be organ specific. More detailed analyses suggested that proteins with similar post-mortem kinetics are not primarily shared in their biological functions. The overrepresentation of protein families with analogous structural motifs in the kidney indicates that structural features may be a common factor in determining similar postmortem stability. Our study demonstrates that a longer post-mortem period may have a significant impact on proteome composition, but sampling within 24 h may be appropriate, as degradation is within acceptable limits even in organs with faster autolysis.
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Affiliation(s)
- Éva Kocsmár
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Marlene Schmid
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Miguel Cosenza-Contreras
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ildikó Kocsmár
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Melanie Föll
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
| | - Leah Krey
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bálint András Barta
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Gergely Rácz
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - András Kiss
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Martin Werner
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Gábor Lotz
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Peter Bronsert
- Institute of Surgical Pathology, University Medical Center Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Biobank Comprehensive Cancer Center Freiburg, University Medical Center, Freiburg, Germany.
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49
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Bons J, Pan D, Shah S, Bai R, Chen‐Tanyolac C, Wang X, Elliott DRF, Urisman A, O'Broin A, Basisty N, Rose J, Sangwan V, Camilleri‐Broët S, Tankel J, Gascard P, Ferri L, Tlsty TD, Schilling B. Data-independent acquisition and quantification of extracellular matrix from human lung in chronic inflammation-associated carcinomas. Proteomics 2023; 23:e2200021. [PMID: 36228107 PMCID: PMC10391693 DOI: 10.1002/pmic.202200021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
Abstract
Early events associated with chronic inflammation and cancer involve significant remodeling of the extracellular matrix (ECM), which greatly affects its composition and functional properties. Using lung squamous cell carcinoma (LSCC), a chronic inflammation-associated cancer (CIAC), we optimized a robust proteomic pipeline to discover potential biomarker signatures and protein changes specifically in the stroma. We combined ECM enrichment from fresh human tissues, data-independent acquisition (DIA) strategies, and stringent statistical processing to analyze "Tumor" and matched adjacent histologically normal ("Matched Normal") tissues from patients with LSCC. Overall, 1802 protein groups were quantified with at least two unique peptides, and 56% of those proteins were annotated as "extracellular." Confirming dramatic ECM remodeling during CIAC progression, 529 proteins were significantly altered in the "Tumor" compared to "Matched Normal" tissues. The signature was typified by a coordinated loss of basement membrane proteins and small leucine-rich proteins. The dramatic increase in the stromal levels of SERPINH1/heat shock protein 47, that was discovered using our ECM proteomic pipeline, was validated by immunohistochemistry (IHC) of "Tumor" and "Matched Normal" tissues, obtained from an independent cohort of LSCC patients. This integrated workflow provided novel insights into ECM remodeling during CIAC progression, and identified potential biomarker signatures and future therapeutic targets.
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Affiliation(s)
- Joanna Bons
- Buck Institute for Research on AgingNovatoCaliforniaUSA
| | - Deng Pan
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Samah Shah
- Buck Institute for Research on AgingNovatoCaliforniaUSA
| | - Rosemary Bai
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | | | - Xianhong Wang
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Daffolyn R. Fels Elliott
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Present address:
Pathology and Laboratory MedicineKansas University Medical Center, the University of KansasKansas CityKansasUSA
| | - Anatoly Urisman
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Amy O'Broin
- Buck Institute for Research on AgingNovatoCaliforniaUSA
| | | | - Jacob Rose
- Buck Institute for Research on AgingNovatoCaliforniaUSA
| | - Veena Sangwan
- Division of Thoracic and Upper Gastrointestinal SurgeryMontreal General HospitalMcGill University Health CentreMontrealQuebecCanada
| | | | - James Tankel
- Division of Thoracic and Upper Gastrointestinal SurgeryMontreal General HospitalMcGill University Health CentreMontrealQuebecCanada
| | - Philippe Gascard
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Lorenzo Ferri
- Division of Thoracic and Upper Gastrointestinal SurgeryMontreal General HospitalMcGill University Health CentreMontrealQuebecCanada
| | - Thea D. Tlsty
- Department of PathologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
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50
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Zhang R, Bons J, Scheidemantle G, Liu X, Bielska O, Carrico C, Rose J, Heckenbach I, Scheibye-Knudsen M, Schilling B, Verdin E. Histone malonylation is regulated by SIRT5 and KAT2A. iScience 2023; 26:106193. [PMID: 36879797 PMCID: PMC9985052 DOI: 10.1016/j.isci.2023.106193] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/18/2022] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
The posttranslational modification lysine malonylation is found in many proteins, including histones. However, it remains unclear whether histone malonylation is regulated or functionally relevant. Here, we report that availability of malonyl-co-enzyme A (malonyl-CoA), an endogenous malonyl donor, affects lysine malonylation, and that the deacylase SIRT5 selectively reduces malonylation of histones. To determine if histone malonylation is enzymatically catalyzed, we knocked down each of the 22 lysine acetyltransferases (KATs) to test their malonyltransferase potential. KAT2A knockdown in particular reduced histone malonylation levels. By mass spectrometry, H2B_K5 was highly malonylated and regulated by SIRT5 in mouse brain and liver. Acetyl-CoA carboxylase (ACC), the malonyl-CoA producing enzyme, was partly localized in the nucleolus, and histone malonylation increased nucleolar area and ribosomal RNA expression. Levels of global lysine malonylation and ACC expression were higher in older mouse brains than younger mice. These experiments highlight the role of histone malonylation in ribosomal gene expression.
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Affiliation(s)
- Ran Zhang
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Grace Scheidemantle
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Olga Bielska
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Chris Carrico
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Indra Heckenbach
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Nørregade 10, Copenhagen, Denmark
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Nørregade 10, Copenhagen, Denmark
| | - Birgit Schilling
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
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