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Article ; Online: Enriching extracellular vesicles for mass spectrometry.

Burton, Jordan B / Carruthers, Nicholas J / Stemmer, Paul M

2021 Volume 42, Issue 2, Page(s) 779–795

Abstract: Extracellular vesicles from plasma, other body fluids and cell culture media hold great promise in the search for biomarkers. Exosomes in particular, the vesicle type that is secreted after being produced in the endocytic pathway and having a diameter of ...

Abstract	Extracellular vesicles from plasma, other body fluids and cell culture media hold great promise in the search for biomarkers. Exosomes in particular, the vesicle type that is secreted after being produced in the endocytic pathway and having a diameter of 30-150 nm, are considered to be a conveyance for signaling molecules and, therefore, to hold valuable information regarding the health and activity status of the cells from which they are released. The vesicular nature of exosomes is central to all methods used to separate them from the highly abundant proteins in plasma and other fluids. The enrichment of the vesicles is essential for mass spectrometry-based analysis as they represent only a very small component of all plasma proteins. The progression of isolation techniques for exosomes from ultracentrifugation through chromatographic separation using hydrophobic packing materials shows that effective enrichment is possible and that high throughput approaches to exosome enrichment are achievable.
MeSH term(s)	Extracellular Vesicles/metabolism ; Ultracentrifugation ; Exosomes/chemistry ; Mass Spectrometry ; Blood Proteins/analysis
Chemical Substances	Blood Proteins
Language	English
Publishing date	2021-10-11
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1491946-1
ISSN	1098-2787 ; 0277-7037
ISSN (online)	1098-2787
ISSN	0277-7037
DOI	10.1002/mas.21738
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Article: Molecular and Cellular Crosstalk between Bone and Brain: Accessing Bidirectional Neural and Musculoskeletal Signaling during Aging and Disease.

Schurman, Charles A / Burton, Jordan B / Rose, Jacob / Ellerby, Lisa M / Alliston, Tamara / Schilling, Birgit

Journal of bone metabolism

2023 Volume 30, Issue 1, Page(s) 1–29

Abstract: Molecular omics technologies, including proteomics, have enabled the elucidation of key signaling pathways that mediate bidirectional communication between the brain and bone tissues. Here we provide a brief summary of the clinical and molecular evidence ...

Abstract	Molecular omics technologies, including proteomics, have enabled the elucidation of key signaling pathways that mediate bidirectional communication between the brain and bone tissues. Here we provide a brief summary of the clinical and molecular evidence of the need to study the bone-brain axis of cross-tissue cellular communication. Clear clinical and molecular evidence suggests biological interactions and similarities between bone and brain cells. Here we review the current mass spectrometric techniques for studying brain and bone diseases with an emphasis on neurodegenerative diseases and osteoarthritis/osteoporosis, respectively. Further study of the bone-brain axis on a molecular level and evaluation of the role of proteins, neuropeptides, osteokines, and hormones in molecular pathways linked to bone and brain diseases is critically needed. The use of mass spectrometry and other omics technologies to analyze these cross-tissue signaling events and interactions will help us better understand disease progression and comorbidities and potentially identify new pathways and targets for therapeutic interventions. Proteomic measurements are particularly favorable for investigating the role of signaling and secreted and circulating analytes and identifying molecular and metabolic pathways implicated in age-related diseases.
Language	English
Publishing date	2023-02-28
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2765291-9
ISSN	2287-7029 ; 2287-6375
ISSN (online)	2287-7029
ISSN	2287-6375
DOI	10.11005/jbm.2023.30.1.1
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Article: Pattern Analysis of Organellar Maps for Interpretation of Proteomic Data.

Burton, Jordan B / Carruthers, Nicholas J / Hou, Zhanjun / Matherly, Larry H / Stemmer, Paul M

Proteomes

2022 Volume 10, Issue 2

Abstract: Localization of organelle proteins by isotope tagging (LOPIT) maps are a coordinate-directed representation of proteome data that can aid in biological interpretation. Analysis of organellar association for proteins as displayed using LOPIT is evaluated ... ...

Abstract	Localization of organelle proteins by isotope tagging (LOPIT) maps are a coordinate-directed representation of proteome data that can aid in biological interpretation. Analysis of organellar association for proteins as displayed using LOPIT is evaluated and interpreted for two types of proteomic data sets. First, test and control group protein abundances and fold change data obtained in a proximity labeling experiment are plotted on a LOPIT map to evaluate the likelihood of true protein interactions. Selection of true positives based on co-localization of proteins in the organellar space is shown to be consistent with carboxylase enrichment which serves as a positive control for biotinylation in streptavidin affinity selected proteome data sets. The mapping in organellar space facilitates discrimination between the test and control groups and aids in identification of proteins of interest. The same representation of proteins in organellar space is used in the analysis of extracellular vesicle proteomes for which protein abundance and fold change data are evaluated. Vesicular protein organellar localization patterns provide information about the subcellular origin of the proteins in the samples which are isolates from the extracellular milieu. The organellar localization patterns are indicative of the provenance of the vesicular proteome origin and allow discrimination between proteomes prepared using different enrichment methods. The patterns in LOPIT displays are easy to understand and compare which aids in the biological interpretation of proteome data.
Language	English
Publishing date	2022-05-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720995-7
ISSN	2227-7382
ISSN	2227-7382
DOI	10.3390/proteomes10020018
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Article ; Online: Senescent characteristics of human corneal endothelial cells upon ultraviolet-A exposure.

Numa, Kohsaku / Patel, Sandip Kumar / Zhang, Zhixin A / Burton, Jordan B / Matsumoto, Akifumi / Hughes, Jun-Wei B / Sotozono, Chie / Schilling, Birgit / Desprez, Pierre-Yves / Campisi, Judith / Kitazawa, Koji

Aging

2024 Volume 16, Issue 8, Page(s) 6673–6693

Abstract: Purpose: The objective of this study was to investigate the senescent phenotypes of human corneal endothelial cells (hCEnCs) upon treatment with ultraviolet (UV)-A.: Methods: We assessed cell morphology, senescence-associated β-galactosidase (SA-β- ... ...

Abstract	Purpose: The objective of this study was to investigate the senescent phenotypes of human corneal endothelial cells (hCEnCs) upon treatment with ultraviolet (UV)-A. Methods: We assessed cell morphology, senescence-associated β-galactosidase (SA-β-gal) activity, cell proliferation and expression of senescence markers ( Results: Cells exposed to 5 J/cm2 of UV-A or to IR exhibited typical senescent phenotypes, including enlargement, increased SA-β-gal activity, decreased cell proliferation and elevated expression of Conclusions: In this study, where senescence was induced by UV-A, a more physiological stress for hCEnCs compared to IR, we determined that UV-A modulated the expression of many genes and proteins typically altered upon IR treatment, a more conventional method of senescence induction, even though UV-A also modulated specific pathways unrelated to IR.
MeSH term(s)	Humans ; Cellular Senescence/radiation effects ; Ultraviolet Rays/adverse effects ; Cell Proliferation/radiation effects ; Endothelial Cells/radiation effects ; Endothelial Cells/metabolism ; Endothelium, Corneal/radiation effects ; Endothelium, Corneal/metabolism ; Cells, Cultured ; Proteomics ; Cyclin-Dependent Kinase Inhibitor p21/metabolism ; Cyclin-Dependent Kinase Inhibitor p21/genetics ; beta-Galactosidase/metabolism ; beta-Galactosidase/genetics ; Cyclin-Dependent Kinase Inhibitor p16/metabolism ; Cyclin-Dependent Kinase Inhibitor p16/genetics
Chemical Substances	Cyclin-Dependent Kinase Inhibitor p21 ; beta-Galactosidase (EC 3.2.1.23) ; Cyclin-Dependent Kinase Inhibitor p16
Language	English
Publishing date	2024-04-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1945-4589
ISSN (online)	1945-4589
DOI	10.18632/aging.205761
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Article ; Online: Extracellular Matrix Orchestration of Tissue Remodeling in the Chronically Inflamed Mouse Colon.

Moutin, Elisa B / Bons, Joanna / Giavara, Giada / Lourenco, Filipe / Pan, Deng / Burton, Jordan B / Shah, Samah / Colombé, Mathilde / Gascard, Philippe / Tlsty, Thea / Schilling, Birgit / Winton, Douglas J

Cellular and molecular gastroenterology and hepatology

2024 Volume 17, Issue 4, Page(s) 639–656

Abstract: Background & aims: Chronic inflammatory illnesses are debilitating and recurrent conditions associated with significant comorbidities, including an increased risk of developing cancer. Extensive tissue remodeling is a hallmark of such illnesses, and is ... ...

Abstract	Background & aims: Chronic inflammatory illnesses are debilitating and recurrent conditions associated with significant comorbidities, including an increased risk of developing cancer. Extensive tissue remodeling is a hallmark of such illnesses, and is both a consequence and a mediator of disease progression. Despite previous characterization of epithelial and stromal remodeling during inflammatory bowel disease, a complete understanding of its impact on disease progression is lacking. Methods: A comprehensive proteomic pipeline using data-independent acquisition was applied to decellularized colon samples from the Muc2 knockout (Muc2 Results: The in-depth proteomic workflow used here allowed the addition of 34 proteins to the known colon matrisomal signature. Protein signatures of prepathologic and pathologic colitic states were extracted, differentiating the 2 states by expression of small leucine-rich proteoglycans. We outlined the role of this class and other matrisomal proteins in tissue remodeling during colitis, as well as the potential for coordinated regulation of cell types by matrisomal ligands. Conclusions: Our work highlights a central role for matrisomal proteins in tissue remodeling during colitis and defines orchestrating nodes that can be exploited in the selection of therapeutic targets.
MeSH term(s)	Mice ; Animals ; Proteomics ; Extracellular Matrix/metabolism ; Colitis/pathology ; Chronic Disease ; Disease Progression
Language	English
Publishing date	2024-01-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2819778-1
ISSN	2352-345X ; 2352-345X
ISSN (online)	2352-345X
ISSN	2352-345X
DOI	10.1016/j.jcmgh.2024.01.003
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Article ; Online: In-depth analysis of the Sirtuin 5-regulated mouse brain malonylome and succinylome using library-free data-independent acquisitions.

Bons, Joanna / Rose, Jacob / Zhang, Ran / Burton, Jordan B / Carrico, Christopher / Verdin, Eric / Schilling, Birgit

Proteomics

2022 Volume 23, Issue 3-4, Page(s) e2100371

Abstract: Post-translational modifications (PTMs) dynamically regulate proteins and biological pathways, typically through the combined effects of multiple PTMs. Lysine residues are targeted for various PTMs, including malonylation and succinylation. However, PTMs ...

Abstract	Post-translational modifications (PTMs) dynamically regulate proteins and biological pathways, typically through the combined effects of multiple PTMs. Lysine residues are targeted for various PTMs, including malonylation and succinylation. However, PTMs offer specific challenges to mass spectrometry-based proteomics during data acquisition and processing. Thus, novel and innovative workflows using data-independent acquisition (DIA) ensure confident PTM identification, precise site localization, and accurate and robust label-free quantification. In this study, we present a powerful approach that combines antibody-based enrichment with comprehensive DIA acquisitions and spectral library-free data processing using directDIA (Spectronaut). Identical DIA data can be used to generate spectral libraries and comprehensively identify and quantify PTMs, reducing the amount of enriched sample and acquisition time needed, while offering a fully automated workflow. We analyzed brains from wild-type and Sirtuin 5 (SIRT5)-knock-out mice, and discovered and quantified 466 malonylated and 2211 succinylated peptides. SIRT5 regulation remodeled the acylomes by targeting 164 malonylated and 578 succinylated sites. Affected pathways included carbohydrate and lipid metabolisms, synaptic vesicle cycle, and neurodegenerative diseases. We found 48 common SIRT5-regulated malonylation and succinylation sites, suggesting potential PTM crosstalk. This innovative and efficient workflow offers deeper insights into the mouse brain lysine malonylome and succinylome.
MeSH term(s)	Animals ; Mice ; Lysine/metabolism ; Mass Spectrometry ; Peptides/metabolism ; Protein Processing, Post-Translational ; Proteins/metabolism ; Sirtuins/metabolism ; Brain/metabolism
Chemical Substances	Lysine (K3Z4F929H6) ; Peptides ; Proteins ; Sirtuins (EC 3.5.1.-)
Language	English
Publishing date	2022-12-18
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202100371
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Article: Aging impairs the osteocytic regulation of collagen integrity and bone quality.

Schurman, Charles A / Kaya, Serra / Dole, Neha / Luna, Nadja M Maldonado / Castillo, Natalia / Potter, Ryan / Rose, Jacob P / Bons, Joanna / King, Christina D / Burton, Jordan B / Schilling, Birgit / Melov, Simon / Tang, Simon / Schaible, Eric / Alliston, Tamara

Bone research

2024 Volume 12, Issue 1, Page(s) 13

Abstract: Poor bone quality is a major factor in skeletal fragility in elderly individuals. The molecular mechanisms that establish and maintain bone quality, independent of bone mass, are unknown but are thought to be primarily determined by osteocytes. We ... ...

Abstract	Poor bone quality is a major factor in skeletal fragility in elderly individuals. The molecular mechanisms that establish and maintain bone quality, independent of bone mass, are unknown but are thought to be primarily determined by osteocytes. We hypothesize that the age-related decline in bone quality results from the suppression of osteocyte perilacunar/canalicular remodeling (PLR), which maintains bone material properties. We examined bones from young and aged mice with osteocyte-intrinsic repression of TGFβ signaling (TβRII
MeSH term(s)	Humans ; Aged ; Male ; Animals ; Mice ; Osteocytes ; Bone Remodeling/physiology ; Collagen/pharmacology ; Aging ; Transforming Growth Factor beta/pharmacology
Chemical Substances	Collagen (9007-34-5) ; Transforming Growth Factor beta
Language	English
Publishing date	2024-02-26
Publishing country	China
Document type	Journal Article
ZDB-ID	2803313-9
ISSN	2095-6231 ; 2095-4700
ISSN (online)	2095-6231
ISSN	2095-4700
DOI	10.1038/s41413-023-00303-7
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Article: Substantial Downregulation of Mitochondrial and Peroxisomal Proteins during Acute Kidney Injury revealed by Data-Independent Acquisition Proteomics.

Burton, Jordan B / Silva-Barbosa, Anne / Bons, Joanna / Rose, Jacob / Pfister, Katherine / Simona, Fabia / Gandhi, Tejas / Reiter, Lukas / Bernhardt, Oliver / Hunter, Christie L / Goetzman, Eric S / Sims-Lucas, Sunder / Schilling, Birgit

bioRxiv : the preprint server for biology

2023

Abstract: Acute kidney injury (AKI) manifests as a major health concern, particularly for the elderly. Understanding AKI-related proteome changes is critical for prevention and development of novel therapeutics to recover kidney function and to mitigate the ... ...

Abstract	Acute kidney injury (AKI) manifests as a major health concern, particularly for the elderly. Understanding AKI-related proteome changes is critical for prevention and development of novel therapeutics to recover kidney function and to mitigate the susceptibility for recurrent AKI or development of chronic kidney disease. In this study, mouse kidneys were subjected to ischemia-reperfusion injury, and the contralateral kidneys remained uninjured to enable comparison and assess injury-induced changes in the kidney proteome. A fast-acquisition rate ZenoTOF 7600 mass spectrometer was introduced for data-independent acquisition (DIA) for comprehensive protein identification and quantification. Short microflow gradients and the generation of a deep kidney-specific spectral library allowed for high-throughput, comprehensive protein quantification. Upon AKI, the kidney proteome was completely remodeled, and over half of the 3,945 quantified protein groups changed significantly. Downregulated proteins in the injured kidney were involved in energy production, including numerous peroxisomal matrix proteins that function in fatty acid oxidation, such as ACOX1, CAT, EHHADH, ACOT4, ACOT8, and Scp2. Injured mice exhibited severely declined health. The comprehensive and sensitive kidney-specific DIA assays highlighted here feature high-throughput analytical capabilities to achieve deep coverage of the kidney proteome and will serve as useful tools for developing novel therapeutics to remediate kidney function.
Language	English
Publishing date	2023-02-26
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.26.530107
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Article ; Online: Deep coverage and quantification of the bone proteome provides enhanced opportunities for new discoveries in skeletal biology and disease.

Rose, Jacob P / Schurman, Charles A / King, Christina D / Bons, Joanna / Patel, Sandip K / Burton, Jordan B / O'Broin, Amy / Alliston, Tamara / Schilling, Birgit

PloS one

2023 Volume 18, Issue 10, Page(s) e0292268

Abstract: Dysregulation of cell signaling in chondrocytes and in bone cells, such as osteocytes, osteoblasts, osteoclasts, and an elevated burden of senescent cells in cartilage and bone, are implicated in osteoarthritis (OA). Mass spectrometric analyses provides ... ...

Abstract	Dysregulation of cell signaling in chondrocytes and in bone cells, such as osteocytes, osteoblasts, osteoclasts, and an elevated burden of senescent cells in cartilage and bone, are implicated in osteoarthritis (OA). Mass spectrometric analyses provides a crucial molecular tool-kit to understand complex signaling relationships in age-related diseases, such as OA. Here we introduce a novel mass spectrometric workflow to promote proteomic studies of bone. This workflow uses highly specialized steps, including extensive overnight demineralization, pulverization, and incubation for 72 h in 6 M guanidine hydrochloride and EDTA, followed by proteolytic digestion. Analysis on a high-resolution Orbitrap Eclipse and Orbitrap Exploris 480 mass spectrometer using Data-Independent Acquisition (DIA) provides deep coverage of the bone proteome, and preserves post-translational modifications, such as hydroxyproline. A spectral library-free quantification strategy, directDIA, identified and quantified over 2,000 protein groups (with ≥ 2 unique peptides) from calcium-rich bone matrices. Key components identified were proteins of the extracellular matrix (ECM), bone-specific proteins (e.g., secreted protein acidic and cysteine rich, SPARC, and bone sialoprotein 2, IBSP), and signaling proteins (e.g., transforming growth factor beta-2, TGFB2), and lysyl oxidase homolog 2 (LOXL2), an important protein in collagen crosslinking. Post-translational modifications (PTMs) were identified without the need for specific enrichment. This includes collagen hydroxyproline modifications, chemical modifications for collagen self-assembly and network formation. Multiple senescence factors were identified, such as complement component 3 (C3) protein of the complement system and many matrix metalloproteinases, that might be monitored during age-related bone disease progression. Our innovative workflow yields in-depth protein coverage and quantification strategies to discover underlying biological mechanisms of bone aging and to provide tools to monitor therapeutic interventions. These novel tools to monitor the bone proteome open novel horizons to investigate bone-specific diseases, many of which are age-related.
MeSH term(s)	Humans ; Proteome/analysis ; Proteomics/methods ; Hydroxyproline ; Bone and Bones/metabolism ; Osteoarthritis/metabolism ; Collagen
Chemical Substances	Proteome ; Hydroxyproline (RMB44WO89X) ; Collagen (9007-34-5)
Language	English
Publishing date	2023-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0292268
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Article ; Online: Substantial downregulation of mitochondrial and peroxisomal proteins during acute kidney injury revealed by data-independent acquisition proteomics.

Proteomics

2023 Volume 24, Issue 5, Page(s) e2300162

Abstract	Acute kidney injury (AKI) manifests as a major health concern, particularly for the elderly. Understanding AKI-related proteome changes is critical for prevention and development of novel therapeutics to recover kidney function and to mitigate the susceptibility for recurrent AKI or development of chronic kidney disease. In this study, mouse kidneys were subjected to ischemia-reperfusion injury, and the contralateral kidneys remained uninjured to enable comparison and assess injury-induced changes in the kidney proteome. A ZenoTOF 7600 mass spectrometer was optimized for data-independent acquisition (DIA) to achieve comprehensive protein identification and quantification. Short microflow gradients and the generation of a deep kidney-specific spectral library allowed for high-throughput, comprehensive protein quantification. Upon AKI, the kidney proteome was completely remodeled, and over half of the 3945 quantified protein groups changed significantly. Downregulated proteins in the injured kidney were involved in energy production, including numerous peroxisomal matrix proteins that function in fatty acid oxidation, such as ACOX1, CAT, EHHADH, ACOT4, ACOT8, and Scp2. Injured kidneys exhibited severely damaged tissues and injury markers. The comprehensive and sensitive kidney-specific DIA-MS assays feature high-throughput analytical capabilities to achieve deep coverage of the kidney proteome, and will serve as useful tools for developing novel therapeutics to remediate kidney function.
MeSH term(s)	Humans ; Mice ; Animals ; Aged ; Proteomics ; Proteome ; Down-Regulation ; Kidney ; Acute Kidney Injury
Chemical Substances	Proteome
Language	English
Publishing date	2023-09-29
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202300162
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