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Devianto LA, Amarasiri M, Wang L, Iizuka T, Sano D. Identification of protein biomarkers in wastewater linked to the incidence of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175649. [PMID: 39168326 DOI: 10.1016/j.scitotenv.2024.175649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 07/19/2024] [Accepted: 08/17/2024] [Indexed: 08/23/2024]
Abstract
Wastewater-based epidemiological (WBE) surveillance is a viable disease surveillance technique capable of monitoring the spread of infectious disease agents in sewershed communities. In addition to detecting viral genomes in wastewater, WBE surveillance can identify other endogenous biomarkers that are significantly elevated and excreted in the saliva, urine, and/or stool of infected individuals. Human protein biomarkers allow the realization of real-time WBE surveillance using highly sensitive biosensors. In this study, we analyzed endogenous protein biomarkers present in wastewater influent through liquid chromatography-tandem mass spectrophotometry and scaffold data-independent acquisition to identify candidate target protein biomarkers for WBE surveillance of SARS-CoV-2. We found that out of the 1382 proteins observed in the wastewater samples, 44 were human proteins associated with infectious diseases. These included immune response substances such as immunoglobulins, cytokine-chemokines, and complements, as well as proteins belonging to antimicrobial and antiviral groups. A significant correlation was observed between the intensity of human infectious disease-related protein biomarkers in wastewater and COVID-19 case numbers. Real-time WBE surveillance using biosensors targeting immune response proteins, such as antibodies or immunoglobulins, in wastewater holds promise for expediting the implementation of relevant policies for the effective prevention of infectious diseases in the near future.
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Affiliation(s)
- Luhur Akbar Devianto
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan; Department of Environmental Engineering, Faculty of Agriculture Technology, Brawijaya University, Malang 65145, Indonesia
| | - Mohan Amarasiri
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Luyao Wang
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Takehito Iizuka
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Daisuke Sano
- Department of Frontier Science for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan; Wastewater Information Research Center, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan; New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi 980-8579, Japan.
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2
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Sze YH, Tse DYY, Zuo B, Li KK, Zhao Q, Jiang X, Kurihara T, Tsubota K, Lam TC. Deep Spectral Library of Mice Retina for Myopia Research: Proteomics Dataset generated by SWATH and DIA-NN. Sci Data 2024; 11:1115. [PMID: 39389962 PMCID: PMC11467338 DOI: 10.1038/s41597-024-03958-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 10/02/2024] [Indexed: 10/12/2024] Open
Abstract
The retina plays a crucial role in processing and decoding visual information, both in normal development and during myopia progression. Recent advancements have introduced a library-independent approach for data-independent acquisition (DIA) analyses. This study demonstrates deep proteome identification and quantification in individual mice retinas during myopia development, with an average of 6,263 ± 86 unique protein groups. We anticipate that the use of a predicted retinal-specific spectral library combined with the robust quantification achieved within this dataset will contribute to a better understanding of the proteome complexity. Furthermore, a comprehensive mice retinal-specific spectral library was generated, encompassing a total identification of 9,401 protein groups, 70,041 peptides, 95,339 precursors, and 761,868 transitions acquired using SWATH-MS acquisition on a ZenoTOF 7600 mass spectrometer. This dataset surpasses the spectral library generated through high-pH reversed-phase fractionation by data-dependent acquisition (DDA). The data is available via ProteomeXchange with the identifier PXD046983. It will also serve as an indispensable reference for investigations in myopia research and other retinal or neurological diseases.
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Affiliation(s)
- Ying Hon Sze
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hung Hom, Hong Kong
| | - Dennis Yan Yin Tse
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hung Hom, Hong Kong
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Bing Zuo
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - King Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Xiaoyan Jiang
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Toshihide Kurihara
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Kazuo Tsubota
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
- Tsubota Laboratory, Inc., Tokyo, Japan
| | - Thomas Cheun Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Hong Kong.
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hung Hom, Hong Kong.
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hung Hom, Hong Kong.
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen, 518052, China.
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Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, 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. J Proteome Res 2024; 23:4392-4408. [PMID: 39248652 DOI: 10.1021/acs.jproteome.4c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
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 vignettes 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 the protein and peptide levels 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 (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful 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. Data are available on Panorama Public and ProteomeXchange under the identifier PXD051318.
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Affiliation(s)
- Kristine A Tsantilas
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Gennifer E Merrihew
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Julia E Robbins
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Deanna L Plubell
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Jesse D Canterbury
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, 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, Seattle, Washington 98195, United States
| | - Michael S Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - 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, Seattle, Washington 98195, United States
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Verma A, Azhar G, Patyal P, Zhang W, Zhang X, Wei JY. Proteomic analysis of P. gingivalis-Lipopolysaccharide induced neuroinflammation in SH-SY5Y and HMC3 cells. GeroScience 2024; 46:4315-4332. [PMID: 38507186 PMCID: PMC11336124 DOI: 10.1007/s11357-024-01117-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Chronic periodontitis and its keystone pathogen, Porphyromonas gingivalis, have increasingly been linked with Alzheimer's disease (AD). However, P.gingivalis-lipopolysaccharide (LPS) mediated release of neuroinflammatory proteins contributes to AD remains underexplored. In this study, we utilized data-independent acquisition mass spectrometry to characterize P.gingivalis-LPS induced profile of differentially expressed proteins associated with the neuroinflammatory response in human neuroblastoma (SH-SY5Y) and human microglial (HMC3) cells. We reported a set of 124 proteins in SH-SY5Y cells and 96 proteins in HMC3 cells whose levels were significantly upregulated or downregulated by exposure to P. gingivalis-LPS. Our findings demonstrate that P. gingivalis-LPS contributed to the elevated expressions of dementia biomarkers and pro-inflammatory cytokines that include APP, Aβ1-42, Aβ1-40, T-Tau, p-Tau, VEGF, TGF-β, IL-1β, IL-6 and TNF-α through 2 distinct pathways of extracellular sensing by cell surface receptors and intracellular cytosolic receptors. Interestingly, intracellular signaling proteins activated with P. gingivalis-LPS transfection using Lipofectamine™ 2000 had significantly higher fold change protein expression compared to the extracellular signaling with P. gingivalis-LPS treatment. Additionally, we also explored P. gingivalis-LPS mediated activation of caspase-4 dependent non canonical inflammasome pathway in both SH-SY5Y and HMC3 cells. In summary, P. gingivalis-LPS induced neuroinflammatory protein expression in SH-SY5Y and HMC3 cells, provided insights into the specific inflammatory pathways underlying the potential link between P. gingivalis-LPS infection and the pathogenesis of Alzheimer's disease and related dementias.
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Affiliation(s)
- Ambika Verma
- Department of Geriatrics, Donald W. Reynolds Institute On Aging, University of Arkansas for Medical Sciences, 4301 West Markham, Little Rock, AR, 72205, USA
| | - Gohar Azhar
- Department of Geriatrics, Donald W. Reynolds Institute On Aging, University of Arkansas for Medical Sciences, 4301 West Markham, Little Rock, AR, 72205, USA
| | - Pankaj Patyal
- Department of Geriatrics, Donald W. Reynolds Institute On Aging, University of Arkansas for Medical Sciences, 4301 West Markham, Little Rock, AR, 72205, USA
| | - Wei Zhang
- Department of Mathematics and Statistics, University of Arkansas at Little Rock, Little Rock, AR, USA
| | - Xiaomin Zhang
- Department of Geriatrics, Donald W. Reynolds Institute On Aging, University of Arkansas for Medical Sciences, 4301 West Markham, Little Rock, AR, 72205, USA
| | - Jeanne Y Wei
- Department of Geriatrics, Donald W. Reynolds Institute On Aging, University of Arkansas for Medical Sciences, 4301 West Markham, Little Rock, AR, 72205, USA.
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Vaisar T, Babenko I, Horvath KV, Niisuke K, Asztalos BF. Relationships between HDL subpopulation proteome and HDL function in overweight/obese people with and without coronary heart disease. Atherosclerosis 2024; 397:118565. [PMID: 39260003 DOI: 10.1016/j.atherosclerosis.2024.118565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND AND AIMS The structure-function relationships of high-density lipoprotein (HDL) subpopulations are not well understood. Our aim was to examine the interrelationships between HDL particle proteome and HDL functionality in subjects with and without coronary heart disease (CHD). METHODS We isolated 5 different HDL subpopulations based on charge, size, and apolipoprotein A1 (APOA1) content from the plasma of 33 overweight/obese CHD patients and 33 age-and body mass index (BMI)-matched CHD-free subjects. We measured the relative molar concentration of HDL-associated proteins by liquid chromatography tandem mass spectrometry (LC-MS/MS) and assessed particle functionality. RESULTS We quantified 110 proteins associated with the 5 APOA1-containing HDL subpopulations. The relative molar concentration of these proteins spanned five orders of magnitude. Only 10 proteins were present in >1% while 73 were present in <0.1% concentration. Only 6 of the 10 most abundant proteins were apolipoproteins. Interestingly, the largest (α-1) and the smallest (preβ-1) HDL particles contained the most diverse proteomes. The protein composition of each HDL subpopulation was altered in CHD cases as compared to controls with the most prominent differences in preβ-1 and α-1 particles. APOA2 concentration was positively correlated with preβ-1 particle functionality (ABCA1-CEC/mg APOA1 in preβ-1) (R2 = 0.42, p = 0.005), while APOE concentration was inversely correlated with large-HDL particle functionality (SRBI-CEC/mg APOA1 in α-1+α-2) (R2 = 0.18, p = 0.01). CONCLUSIONS The protein composition of the different HDL subpopulations was altered differentially in CHD patients. The functionality of the small and large HDL particles correlated with the protein content of APOA2 and APOE, respectively. Our data indicate that distinct particle subspecies and specific particle associated proteins provide new information about the role of HDL in CHD.
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Affiliation(s)
- Tomas Vaisar
- UW Medicine Diabetes Institute, Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Ilona Babenko
- UW Medicine Diabetes Institute, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Katalin V Horvath
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Katrin Niisuke
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Bela F Asztalos
- Cardiovascular Nutrition Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
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6
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Akshintala VS, Moore MG, Cruz-Monserrate Z, Nathan JD, Searle BC, Abu-El-Haija M. Urine Proteomics Profiling Identifies Novel Acute Pancreatitis Diagnostic Biomarkers in a Pediatric Population. Gastroenterology 2024; 167:1019-1021.e2. [PMID: 38797238 PMCID: PMC11416306 DOI: 10.1053/j.gastro.2024.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 04/12/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Affiliation(s)
- Venkata S Akshintala
- Division of Gastroenterology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Madalyn G Moore
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Zobeida Cruz-Monserrate
- Division of Gastroenterology, Hepatology and Nutrition and, The James Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jaimie D Nathan
- Department of Pediatric Abdominal Transplant and Hepatopancreatobiliary Surgery, Nationwide Children's Hospital, Columbus, Ohio; Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Brian C Searle
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio; Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio.
| | - Maisam Abu-El-Haija
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.
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7
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Edgington RM, Wilburn DB. Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39332818 DOI: 10.1021/jasms.4c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/29/2024]
Abstract
Ubiquitylation is a structurally and functionally diverse post-translational modification that involves the covalent attachment of the small protein ubiquitin to other protein substrates. Trypsin-based proteomics is the most common approach for globally identifying ubiquitylation sites. However, we estimate that such methods are unable to detect ∼40% of ubiquitylation sites in the human proteome, i.e., "the dark ubiquitylome", including many important for human health and disease. In this meta-analysis of three large ubiquitylomic data sets, we performed a series of bioinformatic analyses to assess experimental features that could aid in uniquely identifying site-specific ubiquitylation events. Spectral predictions from Prosit were compared to experimental spectra of tryptic ubiquitylated peptides, revealing previously uncharacterized fragmentation of the diGly scar. Analysis of the LysC-derived ubiquitylated peptides reveals systematic, multidimensional peptide fragmentation, including diagnostic b-ions from fragmentation of the LysC ubiquitin scar. Comprehensively, these findings provide diagnostic spectral signatures of modification events that could be applied to new analysis methods for nontryptic ubiquitylomics.
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Affiliation(s)
- Regina M Edgington
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Damien B Wilburn
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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8
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Koenig C, Bortel P, Paterson RS, Rendl B, Madupe PP, Troché GB, Hermann NV, Martínez de Pinillos M, Martinón-Torres M, Mularczyk S, Schjellerup Jørkov ML, Gerner C, Kanz F, Martinez-Val A, Cappellini E, Olsen JV. Automated High-Throughput Biological Sex Identification from Archeological Human Dental Enamel Using Targeted Proteomics. J Proteome Res 2024. [PMID: 39324540 DOI: 10.1021/acs.jproteome.4c00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Biological sex is key information for archeological and forensic studies, which can be determined by proteomics. However, the lack of a standardized approach for fast and accurate sex identification currently limits the reach of proteomics applications. Here, we introduce a streamlined mass spectrometry (MS)-based workflow for the determination of biological sex using human dental enamel. Our approach builds on a minimally invasive sampling strategy by acid etching, a rapid online liquid chromatography (LC) gradient coupled to a high-resolution parallel reaction monitoring (PRM) assay allowing for a throughput of 200 samples per day (SPD) with high quantitative performance enabling confident identification of both males and females. Additionally, we developed a streamlined data analysis pipeline and integrated it into a Shiny interface for ease of use. The method was first developed and optimized using modern teeth and then validated in an independent set of deciduous teeth of known sex. Finally, the assay was successfully applied to archeological material, enabling the analysis of over 300 individuals. We demonstrate unprecedented performance and scalability, speeding up MS analysis by 10-fold compared to conventional proteomics-based sex identification methods. This work paves the way for large-scale archeological or forensic studies enabling the investigation of entire populations rather than focusing on individual high-profile specimens. Data are available via ProteomeXchange with the identifier PXD049326.
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Affiliation(s)
- Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Patricia Bortel
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str.38, 1090 Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria
| | - Ryan S Paterson
- Geogenetics Section, Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Barbara Rendl
- Center for Forensic Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Palesa P Madupe
- Geogenetics Section, Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Gaudry B Troché
- Geogenetics Section, Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Nuno Vibe Hermann
- Pediatric Dentistry and Clinical Genetics, Department of Odontology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marina Martínez de Pinillos
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Paseo Sierra de Atapuerca 3, Burgos 09002, Spain
| | - María Martinón-Torres
- Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Paseo Sierra de Atapuerca 3, Burgos 09002, Spain
- Department of Anthropology, University College London (UCL), 14 Taviton Street, London WC1H 0BW, United Kingdom
| | - Sandra Mularczyk
- Laboratory of Biological Anthropology, Globe Institute, University of Copenhagen, 1307 Copenhagen, Denmark
| | | | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str.38, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Waehringer Str.38, 1090 Vienna, Austria
| | - Fabian Kanz
- Center for Forensic Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Enrico Cappellini
- Geogenetics Section, Globe Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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Mao Y, Suryawanshi A, Patial S, Saini Y. Airspaces-derived exosomes contain disease-relevant protein signatures in a mouse model of cystic fibrosis (CF)-like mucoinflammatory lung disease. Front Pharmacol 2024; 15:1460692. [PMID: 39386033 PMCID: PMC11461968 DOI: 10.3389/fphar.2024.1460692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Accepted: 08/26/2024] [Indexed: 10/12/2024] Open
Abstract
Exosomes, membrane-bound extracellular vesicles, ranging from approximately 30-200 nm in diameter, are released by almost all cell types and play critical roles in intercellular communication. In response to the prevailing stress, the exosome-bound protein signatures vary in abundance and composition. To identify the bronchoalveolar lavage fluid (BALF) exosome-bound proteins associated with mucoinflammatory lung disease and to gain insights into their functional implications, we compared BALF exosomes-derived proteins from adult Scnn1b transgenic (Scnn1b-Tg+) and wild type (WT) mice. A total of 3,144 and 3,119 proteins were identified in BALF exosomes from Scnn1b-Tg+ and WT mice, respectively. Using cutoff criteria (Log2 fold-change > 1 and adjusted p-value < 0.05), the comparison of identified proteins revealed 127 and 30 proteins that were significantly upregulated and downregulated, respectively, in Scnn1b-Tg+ versus WT mice. In addition, 52 and 27 proteins were exclusively enriched in Scnn1b-Tg+ and WT mice, respectively. The identified exosome-bound proteins from the homeostatic airspaces of WT mice were mostly relevant to the normal physiological processes. The protein signatures enriched in the BALF exosomes of Scnn1b-Tg+ mice were relevant to macrophage activation and mucoinflammatory processes. Ingenuity pathway analyses revealed that the enriched proteins in Scnn1b-Tg+ mice contributed to the inflammatory responses and antimicrobial defense pathways. Selective proteins including, RETNLA/FIZZ1, LGALS3/Galectin-3, S100A8/MRP8, and CHIL3/YM1 were immunolocalized to specific cell types. The comparative analysis between enriched BALF exosome proteins and previously identified differentially upregulated genes in Scnn1b-Tg+ versus WT mice suggested that the compartment-/cell-specific upregulation in gene expression dictates the enrichment of their respective proteins in the lung airspaces. Taken together, this study demonstrates that the BALF exosome-bound protein signatures reflect disease-relevant disturbances. Our findings suggest that the exosomes carry disease-relevant protein signatures that can be used as a diagnostic as well as predictive biomarkers for mucoinflammatory lung disease.
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Affiliation(s)
- Yun Mao
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Amol Suryawanshi
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Sonika Patial
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
| | - Yogesh Saini
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
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10
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Zhang J, Donahue G, Gilbert MB, Lapidot T, Nicetto D, Zaret KS. Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613328. [PMID: 39345615 PMCID: PMC11429881 DOI: 10.1101/2024.09.16.613328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
H3K9me3-heterochromatin, established by lysine methyltransferases (KMTs) and compacted by HP1 isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3-heterochromatin stability is presently limited to individual domains and DNA repeats. We engineered Suv39h2 KO mouse embryonic stem cells to degrade remaining two H3K9me3-KMTs within one hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12-24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A "binary switch" governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMTs' depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening, and exit from pluripotency within 12 hr. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3-heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.
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Affiliation(s)
- Jingchao Zhang
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Dept. Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Greg Donahue
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Dept. Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael B. Gilbert
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tomer Lapidot
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Dario Nicetto
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Dept. Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Dept. Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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11
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Fries BD, Hummon AB. FAS Inhibited Proteomics and Phosphoproteomics Profiling of Colorectal Cancer Spheroids Shows Activation of Ferroptotic Death Mechanism. J Proteome Res 2024; 23:3904-3916. [PMID: 39079039 DOI: 10.1021/acs.jproteome.4c00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Colorectal cancer (CRC) is projected to become the third most diagnosed and third most fatal cancer in the United States by 2024, with early onset CRC on the rise. Research is constantly underway to discover novel therapeutics for the treatment of various cancers to improve patient outcomes and survival. Fatty acid synthase (FAS) has become a druggable target of interest for the treatment of many different cancers. One such inhibitor, TVB-2640, has gained popularity for its high specificity for FAS and has entered a phase 1 clinical trial for the treatment of solid tumors. However, the distinct molecular differences that occur upon inhibition of FAS have yet to be understood. Here, we conduct proteomics and phosphoproteomics analyses on HCT 116 and HT-29 CRC spheroids inhibited with either a generation 1 (cerulenin) or generation 2 (TVB-2640) FAS inhibitor. Proteins involved in lipid metabolism and cellular respiration were altered in abundance. It was also observed that proteins involved in ferroptosis─an iron mediated form of cell death─were altered. These results show that HT-29 spheroids exposed to cerulenin or TVB-2640 are undergoing a ferroptotic death mechanism. The data were deposited to the ProteomeXchange Consortium via the PRIDE repository with the identifier PXD050987.
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Affiliation(s)
- Brian D Fries
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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12
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Shi M, Huang C, Chen R, Chen DDY, Yan B. A New Evaluation Metric for Quantitative Accuracy of LC-MS/MS-Based Proteomics with Data-Independent Acquisition. J Proteome Res 2024; 23:3780-3790. [PMID: 39193824 DOI: 10.1021/acs.jproteome.4c00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Data-independent acquisition (DIA) has improved the identification and quantitation coverage of peptides and proteins in liquid chromatography-tandem mass spectrometry-based proteomics. However, different DIA data-processing tools can produce very different identification and quantitation results for the same data set. Currently, benchmarking studies of DIA tools are predominantly focused on comparing the identification results, while the quantitative accuracy of DIA measurements is acknowledged to be important but insufficiently investigated, and the absence of suitable metrics for comparing quantitative accuracy is one of the reasons. A new metric is proposed for the evaluation of quantitative accuracy to avoid the influence of differences in false discovery rate control stringency. The part of the quantitation results with high reliability was acquired from each DIA tool first, and the quantitative accuracy was evaluated by comparing quantification error rates at the same number of accurate ratios. From the results of four benchmark data sets, the proposed metric was shown to be more sensitive to discriminating the quantitative performance of DIA tools. Moreover, the DIA tools with advantages in quantitative accuracy were consistently revealed by this metric. The proposed metric can also help researchers in optimizing algorithms of the same DIA tool and sample preprocessing methods to enhance quantitative accuracy.
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Affiliation(s)
- Mengtian Shi
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Chiyuan Huang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Renhui Chen
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - David Da Yong Chen
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Binjun Yan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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13
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Dens C, Adams C, Laukens K, Bittremieux W. Machine Learning Strategies to Tackle Data Challenges in Mass Spectrometry-Based Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2143-2155. [PMID: 39074335 DOI: 10.1021/jasms.4c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
In computational proteomics, machine learning (ML) has emerged as a vital tool for enhancing data analysis. Despite significant advancements, the diversity of ML model architectures and the complexity of proteomics data present substantial challenges in the effective development and evaluation of these tools. Here, we highlight the necessity for high-quality, comprehensive data sets to train ML models and advocate for the standardization of data to support robust model development. We emphasize the instrumental role of key data sets like ProteomeTools and MassIVE-KB in advancing ML applications in proteomics and discuss the implications of data set size on model performance, highlighting that larger data sets typically yield more accurate models. To address data scarcity, we explore algorithmic strategies such as self-supervised pretraining and multitask learning. Ultimately, we hope that this discussion can serve as a call to action for the proteomics community to collaborate on data standardization and collection efforts, which are crucial for the sustainable advancement and refinement of ML methodologies in the field.
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Affiliation(s)
- Ceder Dens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
| | - Charlotte Adams
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
| | - Wout Bittremieux
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Middelheimlaan 1, 2020 Antwerpen, Belgium
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14
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Headley CA, Gautam S, Olmo-Fontanez A, Garcia-Vilanova A, Dwivedi V, Schami A, Weintraub S, Tsao PS, Torrelles JB, Turner J. Mitochondrial Transplantation Promotes Protective Effector and Memory CD4 + T Cell Response During Mycobacterium Tuberculosis Infection and Diminishes Exhaustion and Senescence in Elderly CD4 + T cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401077. [PMID: 39039808 PMCID: PMC11423092 DOI: 10.1002/advs.202401077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/16/2024] [Indexed: 07/24/2024]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), is a major global health concern, particularly affecting those with weakened immune systems, including the elderly. CD4+ T cell response is crucial for immunity against M.tb, but chronic infections and aging can lead to T cell exhaustion and senescence, worsening TB disease. Mitochondrial dysfunction, prevalent in aging and chronic diseases, disrupts cellular metabolism, increases oxidative stress, and impairs T-cell functions. This study investigates the effect of mitochondrial transplantation (mito-transfer) on CD4+ T cell differentiation and function in aged mouse models and human CD4+ T cells from elderly individuals. Mito-transfer in naïve CD4+ T cells is found to promote protective effector and memory T cell generation during M.tb infection in mice. Additionally, it improves elderly human T cell function by increasing mitochondrial mass and altering cytokine production, thereby reducing markers of exhaustion and senescence. These findings suggest mito-transfer as a novel approach to enhance aged CD4+ T cell functionality, potentially benefiting immune responses in the elderly and chronic TB patients. This has broader implications for diseases where mitochondrial dysfunction contributes to T-cell exhaustion and senescence.
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Affiliation(s)
- Colwyn A Headley
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, 43201, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shalini Gautam
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Angelica Olmo-Fontanez
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Andreu Garcia-Vilanova
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Varun Dwivedi
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Alyssa Schami
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Susan Weintraub
- Department of Biochemistry & Structural Biology, UT health San Antonio, San Antonio, TX, 78229, USA
| | - Philip S Tsao
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jordi B Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
- Internaltional Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Joanne Turner
- Host-Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
- Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
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15
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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16
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de Queiroz RM, Efe G, Guzman A, Hashimoto N, Kawashima Y, Tanaka T, Rustgi AK, Prives C. Mdm2 requires Sprouty4 to regulate focal adhesion formation and metastasis independent of p53. Nat Commun 2024; 15:7132. [PMID: 39164253 PMCID: PMC11336179 DOI: 10.1038/s41467-024-51488-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
Although the E3 ligase Mdm2 and its homologue and binding partner MdmX are the major regulators of the p53 tumor suppressor protein, it is now evident that Mdm2 and MdmX have multiple functions that do not involve p53. As one example, it is known that Mdm2 can regulate cell migration, although mechanistic insight into this function is still lacking. Here we show in cells lacking p53 expression that knockdown of Mdm2 or MdmX, as well as pharmacological inhibition of the Mdm2/MdmX complex, not only reduces cell migration and invasion, but also impairs cell spreading and focal adhesion formation. In addition, Mdm2 knockdown decreases metastasis in vivo. Interestingly, Mdm2 downregulates the expression of Sprouty4, which is required for the Mdm2 mediated effects on cell migration, focal adhesion formation and metastasis. Further, our findings indicate that Mdm2 dampening of Sprouty4 is a prerequisite for maintaining RhoA levels in the cancer cells that we have studied. Taken together we describe a molecular mechanism whereby the Mdm2/MdmX complex through Sprouty4 regulates cellular processes leading to increase metastatic capability independently of p53.
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Affiliation(s)
| | - Gizem Efe
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Asja Guzman
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Naoko Hashimoto
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Anil K Rustgi
- Herbert Irving Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
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17
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Langbøl M, Saruhanian A, Saruhanian S, Tiedemann D, Baskaran T, Vohra R, Rives AS, Moreira J, Prokosch V, Liu H, Lackmann JW, Müller S, Nielsen CH, Kolko M, Rovelt J. Proteomic and Cytokine Profiling in Plasma from Patients with Normal-Tension Glaucoma and Ocular Hypertension. Cell Mol Neurobiol 2024; 44:59. [PMID: 39150567 PMCID: PMC11329415 DOI: 10.1007/s10571-024-01492-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
Primary open-angle glaucoma (POAG) is subdivided depending on eye pressure. Patients with normal-tension glaucoma (NTG) have never had high intraocular pressure (IOP) measured while patients with ocular hypertension (OHT) have high eye pressure but no signs of glaucoma. Although IOP is considered to be a risk factor for all glaucoma patients, it is reasonable to assume that other risk factors such as inflammation play a role. We aimed to characterize the proteome and cytokine profile during hypoxia in plasma from patients with NTG (n = 10), OHT (n = 10), and controls (n = 10). Participants were exposed to hypoxia for two hours, followed by 30 min of normoxia. Samples were taken before ("baseline"), during ("hypoxia"), and after hypoxia ("recovery"). Proteomics based on liquid chromatography coupled with mass spectrometry (LC-MS) was performed. Cytokines were measured by Luminex assays. Bioinformatic analyses indicated the involvement of complement and coagulation cascades in NTG and OHT. Regulation of high-density lipoprotein 3 (HDL3) apolipoproteins suggested that changes in cholesterol metabolism are related to OHT. Hypoxia decreased the level of tumor necrosis factor-α (TNF-α) in OHT patients compared to controls. Circulating levels of interleukin-1β (IL-1β) and C-reactive protein (CRP) were decreased in NTG patients compared to controls during hypoxia. After recovery, plasma interleukin-6 (IL-6) was upregulated in patients with NTG and OHT. Current results indicate an enhanced systemic immune response in patients with NTG and OHT, which correlates with pathogenic events in glaucoma. Apolipoproteins may have anti-inflammatory effects, enabling OHT patients to withstand inflammation and development of glaucoma despite high IOP.
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Affiliation(s)
- Mia Langbøl
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark.
| | - Arevak Saruhanian
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Sarkis Saruhanian
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Veterinary & Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Daniel Tiedemann
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Thisayini Baskaran
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Rupali Vohra
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Amalie Santaolalla Rives
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - José Moreira
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
| | - Verena Prokosch
- Department of Ophthalmology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937, Cologne, Germany
| | - Hanhan Liu
- Department of Ophthalmology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937, Cologne, Germany
| | - Jan-Wilm Lackmann
- CECAD/CMMC Proteomics Facility, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Stefan Müller
- CECAD/CMMC Proteomics Facility, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Claus Henrik Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, 2200, Copenhagen, Denmark
- Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Miriam Kolko
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Jens Rovelt
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, Building 22, 2100, Copenhagen Ø, Denmark
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18
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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 vignettes 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 (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful 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. Data are available on Panorama Public and on ProteomeXchange under the identifier PXD051318.
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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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19
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Mojica E, Kültz D. A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms. J Proteome Res 2024; 23:2780-2794. [PMID: 37624673 PMCID: PMC11301685 DOI: 10.1021/acs.jproteome.3c00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Indexed: 08/27/2023]
Abstract
Histone post-translational modifications (PTMs) are epigenetic marks that play a critical role in the expression and maintenance of DNA, but they remain largely uninvestigated in nonmodel organisms due to technical challenges. To begin alleviating this issue, we developed a workflow for histone PTM analysis in Mozambique tilapia (Oreochromis mossambicus), being a widespread and environmentally hardy fish, using mass spectrometry methods. By incorporating multiple protein digestion methods into the preparation of each sample, we reliably quantified 214 biologically relevant histone PTMs. All of these histone PTMs, collectively referred to as the global histone PTM landscape, were characterized in the gills, kidney, and testes of this fish. By comparing the global histone PTM landscape between the three tissues, we found that 91.59% of histone PTMs were tissue-dependent. The workflow and tools for histone PTM analysis described in this study are now publicly available and enable comprehensive investigation into the influence of environmental stress on histone PTMs in nonmodel organisms. Given the functionality and flexibility of histone PTMs, we anticipate that the study of histone PTMs in ecologically relevant contexts will provide ground-breaking insights into comparative physiology and evolution.
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Affiliation(s)
- Elizabeth
A. Mojica
- Department of Animal Sciences, University of California - Davis, One Shields Avenue, Meyer Hall, Davis, California 95616, United States
| | - Dietmar Kültz
- Department of Animal Sciences, University of California - Davis, One Shields Avenue, Meyer Hall, Davis, California 95616, United States
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20
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Gu K, Kumabe H, Yamamoto T, Tashiro N, Masuda T, Ito S, Ohtsuki S. Improving Proteomic Identification Using Narrow Isolation Windows with Zeno SWATH Data-Independent Acquisition. J Proteome Res 2024; 23:3484-3495. [PMID: 38978496 DOI: 10.1021/acs.jproteome.4c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Data-independent acquisition (DIA) techniques such as sequential window acquisition of all theoretical mass spectra (SWATH) acquisition have emerged as the preferred strategies for proteomic analyses. Our study optimized the SWATH-DIA method using a narrow isolation window placement approach, improving its proteomic performance. We optimized the acquisition parameter combinations of narrow isolation windows with different widths (1.9 and 2.9 Da) on a ZenoTOF 7600 (Sciex); the acquired data were analyzed using DIA-NN (version 1.8.1). Narrow SWATH (nSWATH) identified 5916 and 7719 protein groups on the digested peptides, corresponding to 400 ng of protein from mouse liver and HEK293T cells, respectively, improving identification by 7.52 and 4.99%, respectively, compared to conventional SWATH. The median coefficient of variation of the quantified values was less than 6%. We further analyzed 200 ng of benchmark samples comprising peptides from known ratios ofEscherichia coli, yeast, and human peptides using nSWATH. Consequently, it achieved accuracy and precision comparable to those of conventional SWATH, identifying an average of 95,456 precursors and 9342 protein groups across three benchmark samples, representing 12.6 and 9.63% improved identification compared to conventional SWATH. The nSWATH method improved identification at various loading amounts of benchmark samples, identifying 40.7% more protein groups at 25 ng. These results demonstrate the improved performance of nSWATH, contributing to the acquisition of deeper proteomic data from complex biological samples.
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Affiliation(s)
- Kongxin Gu
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Haruka Kumabe
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takumi Yamamoto
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Naoto Tashiro
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shingo Ito
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, School of Pharmacy, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
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21
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Shannon AE, Boos CE, Searle BC, Hummon AB. Gas-Phase Fractionation Data-Independent Acquisition Analysis of 3D Cocultured Spheroid Tumor Model Reveals Altered Translational Processes and Signaling Using Proteomics. J Proteome Res 2024; 23:3188-3199. [PMID: 38412258 PMCID: PMC11296903 DOI: 10.1021/acs.jproteome.3c00786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Colorectal cancer (CRC) contains considerable heterogeneity; therefore, models of the disease must also reflect the multifarious components. Compared to traditional 2D models, 3D cellular models, such as tumor spheroids, have the utility to determine the drug efficacy of potential therapeutics. Monoculture spheroids are well-known to recapitulate gene expression, cell signaling, and pathophysiological gradients of avascularized tumors. However, they fail to mimic the stromal cell influence present in CRC, which is known to perturb drug efficacy and is associated with metastatic, late-stage colorectal cancer. This study seeks to develop a cocultured spheroid model using carcinoma and noncancerous fibroblast cells. We characterized the proteomic profile of cocultured spheroids in comparison to monocultured spheroids using data-independent acquisition with gas-phase fractionation. Specifically, we determined that proteomic differences related to translation and mTOR signaling are significantly increased in cocultured spheroids compared to monocultured spheroids. Proteins related to fibroblast function, such as exocytosis of coated vesicles and secretion of growth factors, were significantly differentially expressed in the cocultured spheroids. Finally, we compared the proteomic profiles of both the monocultured and cocultured spheroids against a publicly available data set derived from solid CRC tumors. We found that the proteome of the cocultured spheroids more closely resembles that of the patient samples, indicating their potential as tumor mimics.
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Affiliation(s)
- Ariana E Shannon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Claire E Boos
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Brian C Searle
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amanda B Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, Ohio 43210, United States
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22
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Shahror RA, Shosha E, Ji MH, Morris CA, Wild M, Zaman B, Mitchell CD, Tetelbom P, Leung YK, Phillips PH, Sallam AA, Fouda AY. Proteomic Analysis of Aqueous Humor in Central Retinal Artery Occlusion: Unveiling Novel Insights Into Disease Pathophysiology. Transl Vis Sci Technol 2024; 13:30. [PMID: 39163016 PMCID: PMC11343007 DOI: 10.1167/tvst.13.8.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/15/2024] [Indexed: 08/21/2024] Open
Abstract
Purpose Central retinal artery occlusion (CRAO) is an ocular emergency that results from acute blockage of the blood supply to the retina and leads to a sudden vision loss. Other forms of ischemic retinopathies include diabetic retinopathy (DR), which involves chronic retinal ischemia and remains the leading cause of blindness in working-age adults. This study is the first to conduct a proteomic analysis of aqueous humor (AH) from patients with CRAO with a comparative analysis using vitreous humor (VH) samples from patients with DR. Methods AH samples were collected from 10 patients with CRAO undergoing paracentesis and 10 controls undergoing cataract surgery. VH samples were collected from 10 patients with DR and 10 non-diabetic controls undergoing pars plana vitrectomy (PPV). Samples were analyzed using mass spectrometry. Results Compared with controls, AH levels of 36 differentially expressed proteins (DEPs) were identified in patients with CRAO. Qiagen Ingenuity Pathway Analysis (IPA) revealed 11 proteins linked to ophthalmic diseases. Notably, enolase 2, a glycolysis enzyme isoform primarily expressed in neurons, was upregulated, suggesting neuronal injury and enzyme release. Additionally, clusterin, a protective glycoprotein, was downregulated. ELISA was conducted to confirm proteomics data. VH samples from patients with DR exhibited changes in a distinct set of proteins, including ones previously reported in the literature. Conclusions The study provides novel insights into CRAO pathophysiology with multiple hits identified. Proteomic results differed between DR and CRAO studies, likely due to the different pathophysiology and disease duration. Translational Relevance This is the first proteomic analysis of CRAO AH, with the potential to identify future therapeutic targets.
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Affiliation(s)
- Rami A. Shahror
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Esraa Shosha
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Clinical Pharmacy Department, School of Pharmacy, Cairo University, Cairo, Egypt
| | - Marco H. Ji
- Department of Ophthalmology, Harvey & Bernice Jones Eye Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Division of Epidemiology & Clinical Applications, National Eye Institute, Bethesda, Maryland, USA
| | - Carol A. Morris
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Melissa Wild
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Bushra Zaman
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christian D. Mitchell
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Pedro Tetelbom
- Department of Ophthalmology, Harvey & Bernice Jones Eye Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yuet-Kin Leung
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Paul H. Phillips
- Department of Ophthalmology, Harvey & Bernice Jones Eye Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ahmed A. Sallam
- Department of Ophthalmology, Harvey & Bernice Jones Eye Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Abdelrahman Y. Fouda
- Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Clinical Pharmacy Department, School of Pharmacy, Cairo University, Cairo, Egypt
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23
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Binti S, Linder AG, Edeen PT, Fay DS. A conserved protein tyrosine phosphatase, PTPN-22, functions in diverse developmental processes in C. elegans. PLoS Genet 2024; 20:e1011219. [PMID: 39173071 PMCID: PMC11373843 DOI: 10.1371/journal.pgen.1011219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 09/04/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024] Open
Abstract
Protein tyrosine phosphatases non-receptor type (PTPNs) have been studied extensively in the context of the adaptive immune system; however, their roles beyond immunoregulation are less well explored. Here we identify novel functions for the conserved C. elegans phosphatase PTPN-22, establishing its role in nematode molting, cell adhesion, and cytoskeletal regulation. Through a non-biased genetic screen, we found that loss of PTPN-22 phosphatase activity suppressed molting defects caused by loss-of-function mutations in the conserved NIMA-related kinases NEKL-2 (human NEK8/NEK9) and NEKL-3 (human NEK6/NEK7), which act at the interface of membrane trafficking and actin regulation. To better understand the functions of PTPN-22, we carried out proximity labeling studies to identify candidate interactors of PTPN-22 during development. Through this approach we identified the CDC42 guanine-nucleotide exchange factor DNBP-1 (human DNMBP) as an in vivo partner of PTPN-22. Consistent with this interaction, loss of DNBP-1 also suppressed nekl-associated molting defects. Genetic analysis, co-localization studies, and proximity labeling revealed roles for PTPN-22 in several epidermal adhesion complexes, including C. elegans hemidesmosomes, suggesting that PTPN-22 plays a broad role in maintaining the structural integrity of tissues. Localization and proximity labeling also implicated PTPN-22 in functions connected to nucleocytoplasmic transport and mRNA regulation, particularly within the germline, as nearly one-third of proteins identified by PTPN-22 proximity labeling are known P granule components. Collectively, these studies highlight the utility of combined genetic and proteomic approaches for identifying novel gene functions.
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Affiliation(s)
- Shaonil Binti
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Adison G Linder
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Philip T Edeen
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - David S Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
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24
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Ghosh G, Shannon AE, Searle BC. Data acquisition approaches for single cell proteomics. Proteomics 2024:e2400022. [PMID: 39088833 DOI: 10.1002/pmic.202400022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 08/03/2024]
Abstract
Single-cell proteomics (SCP) aims to characterize the proteome of individual cells, providing insights into complex biological systems. It reveals subtle differences in distinct cellular populations that bulk proteome analysis may overlook, which is essential for understanding disease mechanisms and developing targeted therapies. Mass spectrometry (MS) methods in SCP allow the identification and quantification of thousands of proteins from individual cells. Two major challenges in SCP are the limited material in single-cell samples necessitating highly sensitive analytical techniques and the efficient processing of samples, as each biological sample requires thousands of single cell measurements. This review discusses MS advancements to mitigate these challenges using data-dependent acquisition (DDA) and data-independent acquisition (DIA). Additionally, we examine the use of short liquid chromatography gradients and sample multiplexing methods that increase the sample throughput and scalability of SCP experiments. We believe these methods will pave the way for improving our understanding of cellular heterogeneity and its implications for systems biology.
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Affiliation(s)
- Gautam Ghosh
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Ariana E Shannon
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
| | - Brian C Searle
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
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25
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Fröhlich K, Fahrner M, Brombacher E, Seredynska A, Maldacker M, Kreutz C, Schmidt A, Schilling O. Data-Independent Acquisition: A Milestone and Prospect in Clinical Mass Spectrometry-Based Proteomics. Mol Cell Proteomics 2024; 23:100800. [PMID: 38880244 PMCID: PMC11380018 DOI: 10.1016/j.mcpro.2024.100800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
Data-independent acquisition (DIA) has revolutionized the field of mass spectrometry (MS)-based proteomics over the past few years. DIA stands out for its ability to systematically sample all peptides in a given m/z range, allowing an unbiased acquisition of proteomics data. This greatly mitigates the issue of missing values and significantly enhances quantitative accuracy, precision, and reproducibility compared to many traditional methods. This review focuses on the critical role of DIA analysis software tools, primarily focusing on their capabilities and the challenges they address in proteomic research. Advances in MS technology, such as trapped ion mobility spectrometry, or high field asymmetric waveform ion mobility spectrometry require sophisticated analysis software capable of handling the increased data complexity and exploiting the full potential of DIA. We identify and critically evaluate leading software tools in the DIA landscape, discussing their unique features, and the reliability of their quantitative and qualitative outputs. We present the biological and clinical relevance of DIA-MS and discuss crucial publications that paved the way for in-depth proteomic characterization in patient-derived specimens. Furthermore, we provide a perspective on emerging trends in clinical applications and present upcoming challenges including standardization and certification of MS-based acquisition strategies in molecular diagnostics. While we emphasize the need for continuous development of software tools to keep pace with evolving technologies, we advise researchers against uncritically accepting the results from DIA software tools. Each tool may have its own biases, and some may not be as sensitive or reliable as others. Our overarching recommendation for both researchers and clinicians is to employ multiple DIA analysis tools, utilizing orthogonal analysis approaches to enhance the robustness and reliability of their findings.
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Affiliation(s)
- Klemens Fröhlich
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| | - Eva Brombacher
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Adrianna Seredynska
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maximilian Maldacker
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum Basel, University of Basel, Basel, Switzerland
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany.
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26
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Searle B, Shannon A, Teodorescu R, Song NJ, Heil L, Jacob C, Remes P, Li Z, Rubinstein M. Rapid assay development for low input targeted proteomics using a versatile linear ion trap. RESEARCH SQUARE 2024:rs.3.rs-4702746. [PMID: 39070662 PMCID: PMC11275998 DOI: 10.21203/rs.3.rs-4702746/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Advances in proteomics and mass spectrometry enable the study of limited cell populations, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive low-mass accuracy measurements, these instruments are effectively restricted to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. Here, we describe a workflow using a new hybrid quadrupole-LIT instrument that rapidly develops targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Using an automated software approach for scheduling parallel reaction monitoring assays (PRM), we show consistent quantification across three orders of magnitude in a matched-matrix background. We demonstrate measuring low-level proteins such as transcription factors and cytokines with quantitative linearity below two orders of magnitude in a 1 ng background proteome without requiring stable isotope-labeled standards. From a 1 ng sample, we found clear consistency between proteins in subsets of CD4+ and CD8+ T cells measured using high dimensional flow cytometry and LIT-based proteomics. Based on these results, we believe hybrid quadrupole-LIT instruments represent an economical solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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Affiliation(s)
| | | | | | | | | | | | | | - Zihai Li
- The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute
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27
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Sairenji TJ, Masuda S, Higuchi Y, Miyazaki M, Yajima H, Kwan Ee O, Fujiwara Y, Araki T, Shimokawa N, Koibuchi N. Plasma prolactin axis shift from placental to pituitary origin in late prepartum mice. Endocr J 2024; 71:661-674. [PMID: 38749736 DOI: 10.1507/endocrj.ej23-0724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/17/2024] Open
Abstract
The placenta secretes a prolactin (PRL)-like hormone PRL3B1 (placental lactogen II), a luteotropic hormone essential for maintaining pregnancy until labor in mice. A report from 1984 examined the secretion pattern of PRL3B1 in prepartum mice. In the current study, we found contradictory findings in the secretion pattern that invalidate the previous report. By measuring maternal plasma PRL3B1 and PRL every 4 hrs from gestational day 17 (G17), we newly discovered that maternal plasma PRL3B1 levels decrease rapidly in prepartum C57BL/6 mice. Interestingly, the onset of this decline coincided with the PRL surge at G18, demonstrating a plasma prolactin axis shift from placental to pituitary origin. We also found that maternal plasma progesterone regression precedes the onset of the PRL shift. The level of Prl3b1 mRNA was determined by RT-qPCR in the placenta and remained stable until parturition, implying that PRL3B1 peptide production or secretion was suppressed. We hypothesized that production of the PRL family, the 25 paralogous PRL proteins exclusively expressed in mice placenta, would decrease alongside PRL3B1 during this period. To investigate this hypothesis and to seek proteomic changes, we performed a shotgun proteome analysis of the placental tissue using data-independent acquisition mass spectrometry (DIA-MS). Up to 5,891 proteins were identified, including 17 PRL family members. Relative quantitative analysis between embryonic day 17 (E17) and E18 placentas showed no significant difference in the expression of PRL3B1 and most PRL family members except PRL7C1. These results suggest that PRL3B1 secretion from the placenta is suppressed at G18 (E18).
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Affiliation(s)
- Taku James Sairenji
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Shinnosuke Masuda
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
- Laboratory of Epigenetics and Metabolism, Institute of Molecular and Cellular Regulations, Gunma 371-8512, Japan
| | - Yuya Higuchi
- Department of Clinical Pharmacology and Therapeutics, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Mitsue Miyazaki
- Department of Clinical Pharmacology and Therapeutics, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
- Department of Bioscience and Laboratory Medicine, Hirosaki University Graduate School of Health Sciences, Aomori 036-8564, Japan
- Department of Nutrition, Takasaki University of Health and Welfare, Gunma 370-0033, Japan
| | - Hiroyuki Yajima
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Oh Kwan Ee
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Yuki Fujiwara
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Takuya Araki
- Department of Clinical Pharmacology and Therapeutics, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Noriaki Shimokawa
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
- Department of Nutrition, Takasaki University of Health and Welfare, Gunma 370-0033, Japan
| | - Noriyuki Koibuchi
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
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28
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Garcia-Vilanova A, Allué-Guardia A, Chacon NM, Akhter A, Singh DK, Kaushal D, Restrepo BI, Schlesinger LS, Turner J, Weintraub ST, Torrelles JB. Proteomic analysis of lung responses to SARS-CoV-2 infection in aged non-human primates: clinical and research relevance. GeroScience 2024:10.1007/s11357-024-01264-3. [PMID: 38969861 DOI: 10.1007/s11357-024-01264-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
With devastating health and socioeconomic impact worldwide, much work is left to understand the Coronavirus Disease 2019 (COVID-19), with emphasis in the severely affected elderly population. Here, we present a proteomics study of lung tissue obtained from aged vs. young rhesus macaques (Macaca mulatta) and olive baboons (Papio Anubis) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using age as a variable, we identified common proteomic profiles in the lungs of aged infected non-human primates (NHPs), including key regulators of immune function, as well as cell and tissue remodeling, and discuss the potential clinical relevance of such parameters. Further, we identified key differences in proteomic profiles between both NHP species, and compared those to what is known about SARS-CoV-2 in humans. Finally, we explored the translatability of these animal models in the context of aging and the human presentation of the COVID-19.
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Affiliation(s)
- Andreu Garcia-Vilanova
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Anna Allué-Guardia
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Nadine M Chacon
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Anwari Akhter
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Dhiraj Kumar Singh
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Deepak Kaushal
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Blanca I Restrepo
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
- University of Texas Health Science Center at Houston, School of Public Health, Brownsville Campus, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Larry S Schlesinger
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Joanne Turner
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
- Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jordi B Torrelles
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA.
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Shashikadze B, Flenkenthaler F, Kemter E, Franzmeier S, Stöckl JB, Haid M, Riols F, Rothe M, Pichl L, Renner S, Blutke A, Wolf E, Fröhlich T. Multi-omics analysis of diabetic pig lungs reveals molecular derangements underlying pulmonary complications of diabetes mellitus. Dis Model Mech 2024; 17:dmm050650. [PMID: 38900131 DOI: 10.1242/dmm.050650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/14/2024] [Indexed: 06/21/2024] Open
Abstract
Growing evidence shows that the lung is an organ prone to injury by diabetes mellitus. However, the molecular mechanisms of these pulmonary complications have not yet been characterized comprehensively. To systematically study the effects of insulin deficiency and hyperglycaemia on the lung, we combined proteomics and lipidomics with quantitative histomorphological analyses to compare lung tissue samples from a clinically relevant pig model for mutant INS gene-induced diabetes of youth (MIDY) with samples from wild-type littermate controls. Among others, the level of pulmonary surfactant-associated protein A (SFTPA1), a biomarker of lung injury, was moderately elevated. Furthermore, key proteins related to humoral immune response and extracellular matrix organization were significantly altered in abundance. Importantly, a lipoxygenase pathway was dysregulated as indicated by 2.5-fold reduction of polyunsaturated fatty acid lipoxygenase ALOX15 levels, associated with corresponding changes in the levels of lipids influenced by this enzyme. Our multi-omics study points to an involvement of reduced ALOX15 levels and an associated lack of eicosanoid switching as mechanisms contributing to a proinflammatory milieu in the lungs of subjects with diabetes mellitus.
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Affiliation(s)
- Bachuki Shashikadze
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
| | - Florian Flenkenthaler
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Elisabeth Kemter
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, 85764 Oberschleißheim, Germany
| | - Sophie Franzmeier
- Institute for Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, 80539, Germany
| | - Jan B Stöckl
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
| | - Mark Haid
- Metabolomics and Proteomics Core (MPC), Helmholtz Munich, 85764 Neuherberg, Germany
| | - Fabien Riols
- Metabolomics and Proteomics Core (MPC), Helmholtz Munich, 85764 Neuherberg, Germany
| | | | - Lisa Pichl
- Institute for Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, 80539, Germany
| | - Simone Renner
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, 85764 Oberschleißheim, Germany
| | - Andreas Blutke
- Institute for Veterinary Pathology, Center for Clinical Veterinary Medicine, LMU Munich, 80539, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, LMU Munich, 81377 Munich, Germany
- Center for Innovative Medical Models (CiMM), LMU Munich, 85764 Oberschleißheim, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany
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30
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Zhang Y, Hu C, Wu X, Song J. Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data. Bioinformatics 2024; 40:btae417. [PMID: 38960865 PMCID: PMC11223842 DOI: 10.1093/bioinformatics/btae417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 05/27/2024] [Accepted: 07/02/2024] [Indexed: 07/05/2024] Open
Abstract
MOTIVATION The data independent acquisition (DIA) mass spectrometry (MS) method is increasingly popular in the field of proteomics. But the loss of the correspondence between peptide ions and their spectra in DIA makes the identification challenging. One effective approach to reduce false positive identification is to calculate the deviation between the peptide's estimated retention time (RT) and measured RT. During this process, scaling the spectral library RT into the estimated RT, known as the RT calibration, is a prerequisite for calculating the deviation. Currently, within the DIA algorithm ecosystem, there is a lack of engine-independent and readily usable RT calibration toolkits. RESULTS In this work, we introduce Calib-RT, a RT calibration method tailored to the characteristics of RT data. This method can achieve the nonlinear calibration across various data scales and tolerate a certain level of noise interference. Calib-RT is expected to enrich the open source DIA algorithm toolchain and assist in the development of DIA identification algorithms. AVAILABILITY AND IMPLEMENTATION Calib-RT is released as an open source software under the MIT license and can be installed from PyPi as a python module. The source code is available on GitHub at https://github.com/chenghui03/Calib_RT.
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Affiliation(s)
- Yichi Zhang
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Chenghui Hu
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Xiaohui Wu
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
| | - Jian Song
- Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou 215000, China
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31
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Shin D, Kim Y, Park J, Kim Y. High-throughput Proteomics-Guided Biomarker Discovery of Hepatocellular Carcinoma. Biomed J 2024:100752. [PMID: 38901798 DOI: 10.1016/j.bj.2024.100752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Liver cancer stands as the fifth leading cause of cancer-related deaths globally. Hepatocellular carcinoma (HCC) comprises approximately 85%-90% of all primary liver malignancies. However, only 20-30% of HCC patients qualify for curative therapy, primarily due to the absence of reliable tools for early detection and prognosis of HCC. This underscores the critical need for molecular biomarkers for HCC management. Since proteins reflect disease status directly, proteomics has been utilized in biomarker developments for HCC. In particular, proteomics coupled with liquid chromatography-mass spectrometer (LC-MS) methods facilitate the process of discovering biomarker candidates for diagnosis, prognosis, and therapeutic strategies. In this work, we investigated LC-MS-based proteomics methods through recent reference reviews, with a particular focus on sample preparation and LC-MS methods appropriate for the discovery of HCC biomarkers and their clinical applications. We classified proteomics studies of HCC according to sample types, and we examined the coverage of protein biomarker candidates based on LC-MS methods in relation to study scales and goals. Comprehensively, we proposed protein biomarker candidates categorized by sample types and biomarker types for appropriate clinical use. In this review, we summarized recent LC-MS-based proteomics studies on HCC and proposed potential protein biomarkers. Our findings are expected to expand the understanding of HCC pathogenesis and enhance the efficiency of HCC diagnosis and prognosis, thereby contributing to improved patient outcomes.
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Affiliation(s)
- Dongyoon Shin
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam, Republic of Korea
| | - Yeongshin Kim
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam, Republic of Korea; Department of Medical Science, School of Medicine, CHA University, Seongnam, Republic of Korea
| | - Junho Park
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam, Republic of Korea; Department of Pharmacology, School of Medicine, CHA University, Seongnam, Republic of Korea.
| | - Youngsoo Kim
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam, Republic of Korea; Department of Medical Science, School of Medicine, CHA University, Seongnam, Republic of Korea.
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32
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Bakhtina AA, Wippel HH, Chavez JD, Bruce JE. Combining quantitative proteomics and interactomics for a deeper insight into molecular differences between human cell lines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598691. [PMID: 38915502 PMCID: PMC11195184 DOI: 10.1101/2024.06.12.598691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Cellular functional pathways have evolved through selection based on fitness benefits conferred through protein intra- and inter-molecular interactions that comprise all protein conformational features and protein-protein interactions, collectively referred to as the interactome. While the interactome is regulated by proteome levels, it is also regulated independently by, post translational modification, co-factor, and ligand levels, as well as local protein environmental factors, such as osmolyte concentration, pH, ionic strength, temperature and others. In modern biomedical research, cultivatable cell lines have become an indispensable tool, with selection of optimal cell lines that exhibit specific functional profiles being critical for success in many cases. While it is clear that cell lines derived from different cell types have differential proteome levels, increased understanding of large-scale functional differences requires additional information beyond abundance level measurements, including how protein conformations and interactions are altered in certain cell types to shape functional landscapes. Here, we employed quantitative in vivo protein cross-linking coupled to mass spectrometry to probe large-scale protein conformational and interaction changes among three commonly employed human cell lines, HEK293, MCF-7, and HeLa cells. Isobaric quantitative Protein Interaction Reporter (iqPIR) technologies were used to obtain quantitative values of cross-linked peptides across three cell lines. These data illustrated highly reproducible (R2 values larger than 0.8 for all biological replicates) quantitative interactome levels across multiple biological replicates. We also measured protein abundance levels in these cells using data independent acquisition quantitative proteomics methods. Combining quantitative interactome and proteomics information allowed visualization of cell type-specific interactome changes mediated by proteome level adaptations as well as independently regulated interactome changes to gain deeper insight into possible drivers of these changes. Among the biggest detected alterations in protein interactions and conformations are changes in cytoskeletal proteins, RNA-binding proteins, chromatin remodeling complexes, mitochondrial proteins, and others. Overall, these data demonstrate the utility and reproducibility of quantitative cross-linking to study systems-level interactome variations. Moreover, these results illustrate how combined quantitative interactomics and proteomics can provide unique insight on cellular functional landscapes.
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Affiliation(s)
- Anna A. Bakhtina
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Helisa H. Wippel
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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Bakhtina AA, Campbell MD, Sibley BD, Sanchez-Contreras M, Sweetwyne MT, Bruce JE. Intra-organ cell specific mitochondrial quantitative interactomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598354. [PMID: 38915719 PMCID: PMC11195139 DOI: 10.1101/2024.06.10.598354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Almost every organ consists of many cell types, each with its unique functions. Proteomes of these cell types are thus unique too. But it is reasonable to assume that interactome (inter and intra molecular interactions of proteins) are also distinct since protein interactions are what ultimately carry out the function. Podocytes and tubules are two cell types within kidney with vastly different functions: podocytes envelop the blood vessels in the glomerulus and act as filters while tubules are located downstream of the glomerulus and are responsible for reabsorption of important nutrients. It has been long known that for tubules mitochondria plays an important role as they require a lot of energy to carry out their functions. In podocytes, however, it has been assumed that mitochondria might not matter as much in both normal physiology and pathology1. Here we have applied quantitative cross-linking mass spectrometry to compare mitochondrial interactomes of tubules and podocytes using a transgenic mitochondrial tagging strategy to immunoprecipitate cell-specific mitochondria directly from whole kidney. We have uncovered that mitochondrial proteomes of these cell types are quite similar, although still showing unique features that correspond to known functions, such as high energy production through TCA cycle in tubules and requirements for detoxification in podocytes which are on the frontline of filtration where they encounter toxic compounds and therefore, as a non-renewing cell type they must have ways to protect themselves from cellular toxicity. But we gained much deeper insight with the interactomics data. We were able to find pathways differentially regulated in podocytes and tubules based on changing cross-link levels and not just protein levels. Among these pathways are betaine metabolism, lysine degradation, and many others. We have also demonstrated how quantitative interactomics could be used to detect different activity levels of an enzyme even when protein abundances of it are the same between cell types. We have validated this finding with an orthogonal activity assay. Overall, this work presents a new view of mitochondrial biology for two important, but functionally distinct, cell types within the mouse kidney showing both similarities and unique features. This data can continue to be explored to find new aspects of mitochondrial biology, especially in podocytes, where mitochondria has been understudied. In the future this methodology can also be applied to other organs to uncover differences in the function of cell types.
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Affiliation(s)
- A A Bakhtina
- University of Washington, Department of Genome Sciences
| | - M D Campbell
- University of Washington, Department of Anesthesiology
| | - B D Sibley
- University of Washington, Department of Laboratory Medicine and Pathology
| | | | - M T Sweetwyne
- University of Washington, Department of Laboratory Medicine and Pathology
| | - J E Bruce
- University of Washington, Department of Genome Sciences
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34
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Plubell DL, Remes PM, Wu CC, Jacob CC, Merrihew GE, Hsu C, Shulman N, MacLean BX, Heil L, Poston K, Montine T, MacCoss MJ. Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597431. [PMID: 38895256 PMCID: PMC11185584 DOI: 10.1101/2024.06.04.597431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The development of targeted assays that monitor biomedically relevant proteins is an important step in bridging discovery experiments to large scale clinical studies. Targeted assays are currently unable to scale to hundreds or thousands of targets. We demonstrate the generation of large-scale assays using a novel hybrid nominal mass instrument. The scale of these assays is achievable with the Stellar™ mass spectrometer through the accommodation of shifting retention times by real-time alignment, while being sensitive and fast enough to handle many concurrent targets. Assays were constructed using precursor information from gas-phase fractionated (GPF) data-independent acquisition (DIA). We demonstrate the ability to schedule methods from an orbitrap and linear ion trap acquired GPF DIA library and compare the quantification of a matrix-matched calibration curve from orbitrap DIA and linear ion trap parallel reaction monitoring (PRM). Two applications of these proposed workflows are shown with a cerebrospinal fluid (CSF) neurodegenerative disease protein PRM assay and with a Mag-Net enriched plasma extracellular vesicle (EV) protein survey PRM assay.
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Affiliation(s)
- Deanna L Plubell
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | - Christine C Wu
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | | | - Chris Hsu
- Department of Genome Sciences, University of Washington, Seattle WA
| | - Nick Shulman
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | | | - Kathleen Poston
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto CA, USA
| | - Tom Montine
- Department of Pathology, Stanford University, Palo Alto CA, USA
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35
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Endo Y, Teramoto M, Arakawa J, Ukita S, Toshima G, Suenaga Y, Sasaki K, Ayaori M, Nakayama H, Inoue Y, Ikewaki K. Obstructive sleep apnea syndrome attenuated high-density lipoprotein function. J Clin Lipidol 2024:S1933-2874(24)00199-5. [PMID: 39294021 DOI: 10.1016/j.jacl.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 09/20/2024]
Abstract
BACKGROUND Obstructive sleep apnea (OSA) is associated with an increased risk of cardiovascular disease. High-density lipoproteins (HDLs) exert anti-atherogenic effects, even on cholesterol efflux capacity (CEC). The HDL proteome is reportedly altered in patients with coronary artery disease. OBJECTIVE We hypothesized that OSA attenuates HDL function through an altered HDL proteome, which could be alleviated by continuous positive airway pressure (CPAP) therapy. METHODS Patients aged ≥20 years (n = 115) with suspected OSA were enrolled in this cross-sectional study, with 34 patients diagnosed with moderate and severe OSA included in the interventional study and treated with CPAP therapy for 12 weeks. To further investigate the HDL proteome in OSA, we conducted a discovery study by analyzing HDL proteomes in 10 patients. RESULTS In this study, CEC was significantly lower in the sleep apnea syndrome (SAS) group (apnea-hypopnea index [AHI] ≥5) than in the non-SAS group (AHI <5; 0.96 ± 0.14 vs. 1.06 ± 0.15, p = 0.01). Multiple regression analysis revealed that minimal pulse oxygen saturation (MinSpO2) was positively correlated with CEC. In the interventional study, a 12-week CPAP therapy did not affect CEC. We identified orosomucoid 1 (ORM1), an acute-phase inflammatory molecule, as a candidate protein for OSA-induced HDL dysfunction. Further validation study revealed that serum ORM1 levels were inversely associated with CEC, independent of HDL-cholesterol and high-sensitivity C-reactive protein. CONCLUSIONS HDL function was impaired in patients with OSA and a reduced CEC. However, CPAP therapy did not affect CEC. An altered HDL proteome, particularly with increased ORM1 levels, may be associated with impaired HDL function. TRIAL REGISTRATION This clinical study was registered with the University Hospital Medical Information Network Clinical Trials Registry (UMIN000025335 and UMIN000025341).
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Affiliation(s)
- Yasuhiro Endo
- Division of Anti-aging and Vascular Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan (Drs Endo, Teramoto, Arakawa, Suenaga, Sasaki, and Ikewaki); Division of Environmental Medicine, National Defense Medical College Research Institute, 3-2 Namiki, Tokorozawa, Saitama, Japan (Dr Endo).
| | - Manami Teramoto
- Division of Anti-aging and Vascular Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan (Drs Endo, Teramoto, Arakawa, Suenaga, Sasaki, and Ikewaki)
| | - Junko Arakawa
- Division of Anti-aging and Vascular Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan (Drs Endo, Teramoto, Arakawa, Suenaga, Sasaki, and Ikewaki)
| | - Shoko Ukita
- Biostatistics Unit, Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan (Drs Ukita and Toshima)
| | - Genta Toshima
- Biostatistics Unit, Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan (Drs Ukita and Toshima)
| | - Yumiko Suenaga
- Division of Anti-aging and Vascular Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan (Drs Endo, Teramoto, Arakawa, Suenaga, Sasaki, and Ikewaki)
| | - Kei Sasaki
- Division of Anti-aging and Vascular Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan (Drs Endo, Teramoto, Arakawa, Suenaga, Sasaki, and Ikewaki)
| | | | - Hideaki Nakayama
- Department of Somnology, Tokyo Medical University, Tokyo, Japan (Dr Nakayama)
| | - Yuichi Inoue
- Japan Somnology Center, Institute of Neuropsychiatry, Tokyo, Japan (Dr Inoue)
| | - Katsunori Ikewaki
- Division of Anti-aging and Vascular Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan (Drs Endo, Teramoto, Arakawa, Suenaga, Sasaki, and Ikewaki)
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36
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Wang J, Tan H, Fu Y, Mishra A, Sun H, Wang Z, Wu Z, Wang X, Serrano GE, Beach TG, Peng J, High AA. Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1253-1260. [PMID: 38754071 DOI: 10.1021/jasms.4c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Accurate and precise quantification is crucial in modern proteomics, particularly in the context of exploring low-amount samples. While the innovative 4D-data-independent acquisition (DIA) quantitative proteomics facilitated by timsTOF mass spectrometers gives enhanced sensitivity and selectivity for protein identification, the diaPASEF (parallel accumulation-serial fragmentation combined with data-independent acquisition) parameters have not been systematically optimized, and a comprehensive evaluation of the quantification is currently lacking. In this study, we conducted a thorough optimization of key parameters on a timsTOF SCP instrument, including sample loading amount (50 ng), ramp/accumulation time (140 ms), isolation window width (20 m/z), and gradient time (60 min). To further improve the identification of proteins in low-amount samples, we utilized different column settings and introduced 0.02% n-dodecyl-β-d-maltoside (DDM) in the sample reconstitution solution, resulting in a remarkable 19-fold increase in protein identification at the single-cell-equivalent level. Moreover, a comprehensive comparison of protein quantification using a tandem mass tag reporter (TMT-reporter), complement TMT ions (TMTc), and diaPASEF revealed a strong correlation between these methods. Both diaPASEF and TMTc have effectively addressed the issue of ratio compression, highlighting the diaPASEF method's effectiveness in achieving accurate quantification data compared to TMT reporter quantification. Additionally, an in-depth analysis of in-group variation positioned diaPASEF between the TMT-reporter and TMTc methods. Therefore, diaPASEF quantification on the timsTOF SCP instrument emerges as a precise and accurate methodology for quantitative proteomics, especially for samples with small amounts.
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Affiliation(s)
- Ju Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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Rios EI, Gonçalves D, Morano KA, Johnson JL. Quantitative proteomic analysis reveals unique Hsp90 cycle-dependent client interactions. Genetics 2024; 227:iyae057. [PMID: 38606935 PMCID: PMC11151932 DOI: 10.1093/genetics/iyae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
Hsp90 is an abundant and essential molecular chaperone that mediates the folding and activation of client proteins in a nucleotide-dependent cycle. Hsp90 inhibition directly or indirectly impacts the function of 10-15% of all proteins due to degradation of client proteins or indirect downstream effects. Due to its role in chaperoning oncogenic proteins, Hsp90 is an important drug target. However, compounds that occupy the ATP-binding pocket and broadly inhibit function have not achieved widespread use due to negative effects. More selective inhibitors are needed; however, it is unclear how to achieve selective inhibition. We conducted a quantitative proteomic analysis of soluble proteins in yeast strains expressing wild-type Hsp90 or mutants that disrupt different steps in the client folding pathway. Out of 2,482 proteins in our sample set (approximately 38% of yeast proteins), we observed statistically significant changes in abundance of 350 (14%) of those proteins (log2 fold change ≥ 1.5). Of these, 257/350 (∼73%) with the strongest differences in abundance were previously connected to Hsp90 function. Principal component analysis of the entire dataset revealed that the effects of the mutants could be separated into 3 primary clusters. As evidence that Hsp90 mutants affect different pools of clients, simultaneous co-expression of 2 mutants in different clusters restored wild-type growth. Our data suggest that the ability of Hsp90 to sample a wide range of conformations allows the chaperone to mediate folding of a broad array of clients and that disruption of conformational flexibility results in client defects dependent on those states.
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Affiliation(s)
- Erick I Rios
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Davi Gonçalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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Wen B, Freestone J, Riffle M, MacCoss MJ, Noble WS, Keich U. Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.01.596967. [PMID: 38895431 PMCID: PMC11185562 DOI: 10.1101/2024.06.01.596967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
A pressing statistical challenge in the field of mass spectrometry proteomics is how to assess whether a given software tool provides accurate error control. Each software tool for searching such data uses its own internally implemented methodology for reporting and controlling the error. Many of these software tools are closed source, with incompletely documented methodology, and the strategies for validating the error are inconsistent across tools. In this work, we identify three different methods for validating false discovery rate (FDR) control in use in the field, one of which is invalid, one of which can only provide a lower bound rather than an upper bound, and one of which is valid but under-powered. The result is that the field has a very poor understanding of how well we are doing with respect to FDR control, particularly for the analysis of data-independent acquisition (DIA) data. We therefore propose a new, more powerful method for evaluating FDR control in this setting, and we then employ that method, along with an existing lower bounding technique, to characterize a variety of popular search tools. We find that the search tools for analysis of data-dependent acquisition (DDA) data generally seem to control the FDR at the peptide level, whereas none of the DIA search tools consistently controls the FDR at the peptide level across all the datasets we investigated. Furthermore, this problem becomes much worse when the latter tools are evaluated at the protein level. These results may have significant implications for various downstream analyses, since proper FDR control has the potential to reduce noise in discovery lists and thereby boost statistical power.
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Affiliation(s)
- Bo Wen
- Department of Genome Sciences, University of Washington
| | - Jack Freestone
- School of Mathematics and Statistics, University of Sydney
| | | | | | - William S Noble
- Department of Genome Sciences, University of Washington
- Paul G. Allen School of Computer Science and Engineering, University of Washington
| | - Uri Keich
- School of Mathematics and Statistics, University of Sydney
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Akhter A, Moliva JI, Azad AK, Olmo-Fontánez A, Garcia-Vilanova A, Scordo JM, Gavrilin MA, Diaz PT, Endsley JJ, Weintraub ST, Schlesinger LS, Wewers MD, Torrelles JB. HIV infection impairs the host response to Mycobacterium tuberculosis infection by altering surfactant protein D function in the human lung alveolar mucosa. Mucosal Immunol 2024; 17:461-475. [PMID: 38184074 PMCID: PMC11253242 DOI: 10.1016/j.mucimm.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024]
Abstract
Tuberculosis is the leading cause of death for people living with HIV (PLWH). We hypothesized that altered functions of innate immune components in the human alveolar lining fluid of PLWH (HIV-ALF) drive susceptibility to Mycobacterium tuberculosis (M.tb) infection. Our results indicate a significant increase in oxidation of innate proteins and chemokine levels and significantly lower levels and function of complement components and Th1/Th2/Th17 cytokines in HIV-ALF versus control-ALF (non-HIV-infected people). We further found a deficiency of surfactant protein D (SP-D) and reduced binding of SP-D to M.tb that had been exposed to HIV-ALF. Primary human macrophages infected with M.tb exposed to HIV-ALF were significantly less capable of controlling the infection, which was reversed by SP-D replenishment in HIV-ALF. Thus, based on the limited number of participants in this study, our data suggest that PLWH without antiretroviral therapy (ART) have declining host innate defense function in their lung mucosa, thereby favoring M.tb and potentially other pulmonary infections.
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Affiliation(s)
- Anwari Akhter
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Juan I Moliva
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Abul K Azad
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Angélica Olmo-Fontánez
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA; Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, TX, USA
| | | | - Julia M Scordo
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Mikhail A Gavrilin
- Department of Internal Medicine, Pulmonary, Critical Care and Sleep Medicine Division, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Phillip T Diaz
- Department of Internal Medicine, Pulmonary, Critical Care and Sleep Medicine Division, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Janice J Endsley
- Departments of Microbiology & Immunology and Pathology, University of Texas Medical Branch Health, Galveston, TX, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Larry S Schlesinger
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Mark D Wewers
- Department of Internal Medicine, Pulmonary, Critical Care and Sleep Medicine Division, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Jordi B Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA; International Center for the Advancement of Research and Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA.
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40
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Shannon AE, Teodorescu RN, Soon N, Heil LR, Jacob CC, Remes PM, Rubinstein MP, Searle BC. A workflow for targeted proteomics assay development using a versatile linear ion trap. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596891. [PMID: 38853838 PMCID: PMC11160733 DOI: 10.1101/2024.05.31.596891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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41
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Hernández-Avilés C, Ramírez-Agámez L, Weintraub ST, Scoggin CF, Davis BW, Raudsepp T, Varner DD, Love CC. Proteomic analysis of sperm from fertile stallions and subfertile stallions due to impaired acrosomal exocytosis. Sci Rep 2024; 14:12446. [PMID: 38816557 PMCID: PMC11139894 DOI: 10.1038/s41598-024-63410-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
Thoroughbred stallions that carry a double-homozygous genotype A/A-A/A for SNPs rs397316122 and rs69101140 in exon 5 of the FKBP6 gene (chr13; EquCab3.0) are uniquely subfertile due to impaired acrosomal exocytosis (IAE). In this study, the sperm proteome in frozen/thawed semen from subfertile Thoroughbred stallions was studied and compared to that of frozen/thawed sperm from fertile Thoroughbred stallions. A total of 2,220 proteins was identified, of which 140 proteins were found to be differentially abundant in sperm from the subfertile stallions compared to that of fertile stallions (83 less and 57 more abundant). Proteins of differential abundance in sperm from the subfertile stallions were mainly overrepresented in the "metabolism" and the "metabolism of lipids" pathways. One of these proteins, arylsulfatase F (ARSF), was studied by immunofluorescence. A lower proportion of sperm displaying ARSF signal at the acrosome region was observed in sperm from subfertile Thoroughbred stallions. In addition, heterologous zona pellucida binding assays revealed that sperm from subfertile Thoroughbred stallions bound at a lower proportion to zonae pellucidae than sperm from fertile Thoroughbred stallions. In conclusion, a group of differential abundance proteins, including some of acrosome origin, were identified in sperm from subfertile stallions with acrosome dysfunction.
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Affiliation(s)
- Camilo Hernández-Avilés
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 500 Raymond Stotzer Parkway, College Station, TX, 77843, USA.
| | - Luisa Ramírez-Agámez
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 500 Raymond Stotzer Parkway, College Station, TX, 77843, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Charles F Scoggin
- LeBlanc Reproduction Center, Rood & Riddle Equine Hospital, Lexington, KY, USA
| | - Brian W Davis
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Dickson D Varner
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 500 Raymond Stotzer Parkway, College Station, TX, 77843, USA
| | - Charles C Love
- Equine Fertility Laboratory, Department of Large Animal Clinical Sciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, 500 Raymond Stotzer Parkway, College Station, TX, 77843, USA
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42
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Li K, Teo GC, Yang KL, Yu F, Nesvizhskii AI. diaTracer enables spectrum-centric analysis of diaPASEF proteomics data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595875. [PMID: 38854051 PMCID: PMC11160675 DOI: 10.1101/2024.05.25.595875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further improves the quantification accuracy and protein depth achievable using DIA. We introduce diaTracer, a new spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (m/z, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved "pseudo-MS/MS" spectra, facilitating direct ("spectral-library free") peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from cerebrospinal fluid (CSF) and plasma samples, data from phosphoproteomics and HLA immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass offset searches.
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Affiliation(s)
- Kai Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kevin L. Yang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I. Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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43
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Plubell DL, Huang E, Spencer SE, Poston K, Montine TJ, MacCoss MJ. Data Independent Acquisition to Inform the Development of Targeted Proteomics Assays Using a Triple Quadrupole Mass Spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596554. [PMID: 38853953 PMCID: PMC11160738 DOI: 10.1101/2024.05.29.596554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mass spectrometry based targeted proteomics methods provide sensitive and high-throughput analysis of selected proteins. To develop a targeted bottom-up proteomics assay, peptides must be evaluated as proxies for the measurement of a protein or proteoform in a biological matrix. Candidate peptide selection typically relies on predetermined biochemical properties, data from semi-stochastic sampling, or by empirical measurements. These strategies require extensive testing and method refinement due to the difficulties associated with prediction of peptide response in the biological matrix of interest. Gas-phase fractionated (GPF) narrow window data-independent acquisition (DIA) aids in the development of reproducible selected reaction monitoring (SRM) assays by providing matrix-specific information on peptide detectability and quantification by mass spectrometry. To demonstrate the suitability of DIA data for selecting peptide targets, we reimplement a portion of an existing assay to measure 98 Alzheimer's disease proteins in cerebrospinal fluid (CSF). Peptides were selected from GPF-DIA based on signal intensity and reproducibility. The resulting SRM assay exhibits similar quantitative precision to published data, despite the inclusion of different peptides between the assays. This workflow enables development of new assays without additional up-front data acquisition, demonstrated here through generation of a separate assay for an unrelated set of proteins in CSF from the same dataset.
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Affiliation(s)
- Deanna L Plubell
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Eric Huang
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Sandra E Spencer
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
| | - Kathleen Poston
- Stanford University, Department of Neurology & Neurological Sciences, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Stanford University, Department of Pathology, Stanford, CA, 94305, USA
| | - Michael J MacCoss
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195, USA
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44
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Yazaki J, Yamanashi T, Nemoto S, Kobayashi A, Han YW, Hasegawa T, Iwase A, Ishikawa M, Konno R, Imami K, Kawashima Y, Seita J. Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry. Biol Methods Protoc 2024; 9:bpae039. [PMID: 38884001 PMCID: PMC11180226 DOI: 10.1093/biomethods/bpae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)-protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.
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Affiliation(s)
- Junshi Yazaki
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Faculty of Agriculture, Laboratory for Genome Biology, Setsunan University, Osaka, 573-0101, Japan
| | - Takashi Yamanashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Shino Nemoto
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Atsuo Kobayashi
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yong-Woon Han
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Tomoko Hasegawa
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Akira Iwase
- Cell Function Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Ryo Konno
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Technology Development Team, Kazusa DNA Research Institute, Kisarazu, 292-0818, Japan
| | - Jun Seita
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
- Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, 103-0027, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, 305-8577, Japan
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45
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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46
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Gao Y, Li J, Hu K, Wang S, Yang S, Ai Q, Yan J. Phosphoproteomic analysis of APP/PS1 mice of Alzheimer's disease by DIA based mass spectrometry analysis with PRM verification. J Proteomics 2024; 299:105157. [PMID: 38462170 DOI: 10.1016/j.jprot.2024.105157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Traditional Chinese medicine has been utilized in China for approximately thousands of years in clinical settings to prevent Alzheimer's disease (AD) and enhance memory, despite the lack of a systematic exploration of its biological underpinnings. Exciting research has corroborated the beneficial effects of tetrahydroxy stilbene glycoside (TSG), an extract derived from Polygonum multiflorum, in delaying learning and memory impairment in a model that mimics AD. Therefore, the primary objective of this study is to investigate the major function of TSG upon protein regulation in AD. Herein, a novel approach, encompassing data independent acquisition (DIA), DIA phosphorylated proteomics, and parallel reaction monitoring (PRM), was utilized to integrate quantitative proteomic data collected from APP/PS1 mouse model exhibiting toxic intracellular aggregation of Aβ. Initially, we deliberated upon both single and multi-dimensional data pertaining to AD model mice. Furthermore, we authenticated disparities in protein phosphorylation quantity and expression, phosphorylation function, and ultimately phosphorylation kinase analysis. In order to validate the results, we utilized PRM ion monitoring technology to identify potential protein or peptide biomarkers. In the mixed samples, targeted detection of 50 target proteins revealed that 26 to 33 target proteins were stably detected by PRM. In summary, our findings provide new candidates for AD biomarker, which have been identified and validated through protein researches conducted on mouse brains. This offers a wealth of potential resources for extensive biomarker validation in neurodegenerative diseases. SIGNIFICANCE: DIA phosphorylated proteomics technique was used to detect and analyze phosphorylated proteins in brain tissues of mice with AD. Data were analyzed by various bioinformatics tools to explore the phosphorylation events and characterize them related to TSG. The results of DIA were further verified by PRM. Besides, we mapped the major metabolite classes emerging from the analyses to key biological pathways implicated in AD to understand the potential roles of the molecules and the interactions in triggering symptom onset and progression of AD. Meanwhile, we clarified that in the context of AD onset and TSG intervention, the changes in proteins, protein phosphorylation, phosphorylation kinases, and the internal connections.
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Affiliation(s)
- Yan Gao
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China; Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
| | - Juntong Li
- Nanjing University of Chinese Medicine, Nanjing, 210023, China; Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Kaichao Hu
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Changchun University of Chinese Medicine, Changchun 130117, China
| | - Shasha Wang
- Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Songwei Yang
- Hunan University of Chinese Medicine, Changsha 410208, China
| | - Qidi Ai
- Hunan University of Chinese Medicine, Changsha 410208, China
| | - Jiaqing Yan
- Department of Pharmacy, National Cancer Center/National Clinical Research Center for Cancer, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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47
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Ha A, Khoo A, Ignatchenko V, Khan S, Waas M, Vesprini D, Liu SK, Nyalwidhe JO, Semmes OJ, Boutros PC, Kislinger T. Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine. J Proteome Res 2024; 23:1768-1778. [PMID: 38580319 PMCID: PMC11077481 DOI: 10.1021/acs.jproteome.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Biofluids contain molecules in circulation and from nearby organs that can be indicative of disease states. Characterizing the proteome of biofluids with DIA-MS is an emerging area of interest for biomarker discovery; yet, there is limited consensus on DIA-MS data analysis approaches for analyzing large numbers of biofluids. To evaluate various DIA-MS workflows, we collected urine from a clinically heterogeneous cohort of prostate cancer patients and acquired data in DDA and DIA scan modes. We then searched the DIA data against urine spectral libraries generated using common library generation approaches or a library-free method. We show that DIA-MS doubles the sample throughput compared to standard DDA-MS with minimal losses to peptide detection. We further demonstrate that using a sample-specific spectral library generated from individual urines maximizes peptide detection compared to a library-free approach, a pan-human library, or libraries generated from pooled, fractionated urines. Adding urine subproteomes, such as the urinary extracellular vesicular proteome, to the urine spectral library further improves the detection of prostate proteins in unfractionated urine. Altogether, we present an optimized DIA-MS workflow and provide several high-quality, comprehensive prostate cancer urine spectral libraries that can streamline future biomarker discovery studies of prostate cancer using DIA-MS.
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Affiliation(s)
- Annie Ha
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Amanda Khoo
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Vladimir Ignatchenko
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Shahbaz Khan
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Matthew Waas
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
| | - Danny Vesprini
- Department
of Radiation Oncology, University of Toronto, Toronto, Ontario M5T 1P5, Canada
- Odette
Cancer Research Program, Sunnybrook Research
Institute, Toronto, Ontario M4N 3M5, Canada
| | - Stanley K. Liu
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Department
of Radiation Oncology, University of Toronto, Toronto, Ontario M5T 1P5, Canada
- Odette
Cancer Research Program, Sunnybrook Research
Institute, Toronto, Ontario M4N 3M5, Canada
| | - Julius O. Nyalwidhe
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23501, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, United States
| | - Oliver John Semmes
- Leroy
T. Canoles Jr. Cancer Research Center, Eastern
Virginia Medical School, Norfolk, Virginia 23501, United States
- Department
of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, United States
| | - Paul C. Boutros
- Department
of Human Genetics, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Department
of Urology, University of California, Los
Angeles, Los Angeles, California 90095, United States
- Institute
for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, United States
- Eli
and Edythe Broad Stem Cell Research Center, University of California, Los
Angeles, California 90095, United States
- Broad
Stem Cell Research Center, University of
California, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90024, United States
- Department
of Human Genetics, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Thomas Kislinger
- Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Princess
Margaret Cancer Centre, University Health
Network, Toronto, Ontario M5G 1L7, Canada
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48
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Das D, Wang X, Chiu YC, Bouamar H, Sharkey FE, Lopera JE, Lai Z, Weintraub ST, Han X, Zou Y, Chen HIH, Zeballos Torrez CR, Gu X, Cserhati M, Michalek JE, Halff GA, Chen Y, Zheng S, Cigarroa FG, Sun LZ. Integrative multi-omics characterization of hepatocellular carcinoma in Hispanic patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.27.24306447. [PMID: 38746245 PMCID: PMC11092709 DOI: 10.1101/2024.04.27.24306447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background The incidence and mortality rates of hepatocellular carcinoma (HCC) among Hispanics in the United States are much higher than those of non-Hispanic whites. We conducted comprehensive multi-omics analyses to understand molecular alterations in HCC among Hispanic patients. Methods Paired tumor and adjacent non-tumor samples were collected from 31 Hispanic HCC in South Texas (STX-Hispanic) for genomic, transcriptomic, proteomic, and metabolomic profiling. Additionally, serum lipids were profiled in 40 Hispanic and non-Hispanic patients with or without clinically diagnosed HCC. Results Exome sequencing revealed high mutation frequencies of AXIN2 and CTNNB1 in STX Hispanic HCCs, suggesting a predominant activation of the Wnt/β-catenin pathway. The TERT promoter mutation frequency was also remarkably high in the Hispanic cohort. Cell cycles and liver functions were identified as positively- and negatively-enriched, respectively, with gene set enrichment analysis. Gene sets representing specific liver metabolic pathways were associated with dysregulation of corresponding metabolites. Negative enrichment of liver adipogenesis and lipid metabolism corroborated with a significant reduction in most lipids in the serum samples of HCC patients. Two HCC subtypes from our Hispanic cohort were identified and validated with the TCGA liver cancer cohort. The subtype with better overall survival showed higher activity of immune and angiogenesis signatures, and lower activity of liver function-related gene signatures. It also had higher levels of immune checkpoint and immune exhaustion markers. Conclusions Our study revealed some specific molecular features of Hispanic HCC and potential biomarkers for therapeutic management of HCC and provides a unique resource for studying Hispanic HCC.
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49
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Sing JC, Charkow J, AlHigaylan M, Horecka I, Xu L, Röst HL. MassDash: A Web-Based Dashboard for Data-Independent Acquisition Mass Spectrometry Visualization. J Proteome Res 2024. [PMID: 38684072 DOI: 10.1021/acs.jproteome.4c00026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
With the increased usage and diversity of methods and instruments being applied to analyze Data-Independent Acquisition (DIA) data, visualization is becoming increasingly important to validate automated software results. Here we present MassDash, a cross-platform DIA mass spectrometry visualization and validation software for comparing features and results across popular tools. MassDash provides a web-based interface and Python package for interactive feature visualizations and summary report plots across multiple automated DIA feature detection tools, including OpenSwath, DIA-NN, and dreamDIA. Furthermore, MassDash processes peptides on the fly, enabling interactive visualization of peptides across dozens of runs simultaneously on a personal computer. MassDash supports various multidimensional visualizations across retention time, ion mobility, m/z, and intensity, providing additional insights into the data. The modular framework is easily extendable, enabling rapid algorithm development of novel peak-picker techniques, such as deep-learning-based approaches and refinement of existing tools. MassDash is open-source under a BSD 3-Clause license and freely available at https://github.com/Roestlab/massdash, and a demo version can be accessed at https://massdash.streamlit.app.
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Affiliation(s)
- Justin C Sing
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
| | - Joshua Charkow
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
| | - Mohammed AlHigaylan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
| | - Ira Horecka
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
| | - Leon Xu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
| | - Hannes L Röst
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario M5G 1A8, Canada
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Park SG, Keller A, Kaiser NK, Bruce JE. Interactome dynamics during heat stress signal transmission and reception. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591712. [PMID: 38746244 PMCID: PMC11092488 DOI: 10.1101/2024.04.29.591712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Among evolved molecular mechanisms, cellular stress response to altered environmental conditions to promote survival is among the most fundamental. The presence of stress-induced unfolded or misfolded proteins and molecular registration of these events constitute early steps in cellular stress response. However, what stress-induced changes in protein conformations and protein-protein interactions within cells initiate stress response and how these features are recognized by cellular systems are questions that have remained difficult to answer, requiring new approaches. Quantitative in vivo chemical cross-linking coupled with mass spectrometry (qXL-MS) is an emerging technology that provides new insight on protein conformations, protein-protein interactions and how the interactome changes during perturbation within cells, organelles, and even tissues. In this work, qXL-MS and quantitative proteome analyses were applied to identify significant time-dependent interactome changes that occur prior to large-scale proteome abundance remodeling within cells subjected to heat stress. Interactome changes were identified within minutes of applied heat stress, including stress-induced changes in chaperone systems as expected due to altered functional demand. However, global analysis of all interactome changes revealed the largest significant enrichment in the gene ontology molecular function term of RNA binding. This group included more than 100 proteins among multiple components of protein synthesis machinery, including mRNA binding, spliceosomes, and ribosomes. These interactome data provide new conformational insight on the complex relationship that exists between transcription, translation and cellular stress response mechanisms. Moreover, stress-dependent interactome changes suggest that in addition to conformational stabilization of RNA-binding proteins, adaptation of RNA as interacting ligands offers an additional fitness benefit resultant from generally lower RNA thermal stability. As such, RNA ligands also serve as fundamental temperature sensors that signal stress through decreased conformational regulation of their protein partners as was observed in these interactome dynamics.
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