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Subramanian V, Juhr D, Johnson LS, Yem JB, Giansanti P, Grumbach IM. Changes in the Proteome of the Circle of Willis during Aging Reveal Signatures of Vascular Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2024; 2024:4887877. [PMID: 38962180 PMCID: PMC11221951 DOI: 10.1155/2024/4887877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 04/22/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
Approximately 70% of all strokes occur in patients over 65 years old, and stroke increases the risk of developing dementia. The circle of Willis (CoW), the ring of arteries at the base of the brain, links the intracerebral arteries to one another to maintain adequate cerebral perfusion. The CoW proteome is affected in cerebrovascular and neurodegenerative diseases, but changes related to aging have not been described. Here, we report on a quantitative proteomics analysis comparing the CoW from five young (2-3-month-old) and five aged male (18-20-month-old) mice using gene ontology (GO) enrichment, ingenuity pathway analysis (IPA), and iPathwayGuide tools. This revealed 242 proteins that were significantly dysregulated with aging, among which 189 were upregulated and 53 downregulated. GO enrichment-based analysis identified blood coagulation as the top biological function that changed with age and integrin binding and extracellular matrix constituents as the top molecular functions. Consistent with these findings, iPathwayGuide-based impact analysis revealed associations between aging and the complement and coagulation, platelet activation, ECM-receptor interaction, and metabolic process pathways. Furthermore, IPA analysis revealed the enrichment of 97 canonical pathways that contribute to inflammatory responses, as well as 59 inflammation-associated upstream regulators including 39 transcription factors and 20 cytokines. Thus, aging-associated changes in the CoW proteome in male mice demonstrate increases in metabolic, thrombotic, and inflammatory processes.
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Affiliation(s)
- Vikram Subramanian
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
| | - Denise Juhr
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
| | - Lydia S. Johnson
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
| | - Justin B. Yem
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
| | - Piero Giansanti
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS@MRI)Technical University of Munich, Munich, Germany
| | - Isabella M. Grumbach
- Abboud Cardiovascular Research CenterDepartment of Internal MedicineCarver College of MedicineUniversity of Iowa, Iowa City, USA
- Free Radical and Radiation Biology ProgramDepartment of Radiation OncologyCarver College of MedicineUniversity of Iowa, Iowa City, USA
- Iowa City VA Healthcare System, Iowa City, IA, USA
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Mehlferber MM, Jeffery ED, Saquing J, Jordan BT, Sheynkman L, Murali M, Genet G, Acharya BR, Hirschi KK, Sheynkman GM. Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics. RNA Biol 2022; 19:1228-1243. [PMID: 36457147 PMCID: PMC9721438 DOI: 10.1080/15476286.2022.2141938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by alternative splicing of RNA to produce distinct protein isoforms. To characterize the RNA and protein isoform landscape within ECs, we applied a long read proteogenomics approach to analyse human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream mass-spectrometry (MS) analysis to infer protein isoform expression. We detected 53,863 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted "reference isoform" 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related gene CDH5, suggesting potential changes in its associated signalling pathways. Finally, we identified novel protein isoforms arising from a diversity of RNA splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high-resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.[Figure: see text].
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Affiliation(s)
- Madison M. Mehlferber
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Erin D. Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Jamie Saquing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ben T. Jordan
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Mayank Murali
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Gael Genet
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Bipul R. Acharya
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA,Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA,Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, the University of Manchester, UK
| | - Karen K. Hirschi
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA,Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Gloria M. Sheynkman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA,Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA,UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA,CONTACT Gloria M. Sheynkman The Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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Martinez-Pinna R, Ramos-Mozo P, Madrigal-Matute J, Blanco-Colio LM, Lopez JA, Calvo E, Camafeita E, Lindholt JS, Meilhac O, Delbosc S, Michel JB, de Ceniga MV, Egido J, Martin-Ventura JL. Identification of Peroxiredoxin-1 as a Novel Biomarker of Abdominal Aortic Aneurysm. Arterioscler Thromb Vasc Biol 2011; 31:935-43. [DOI: 10.1161/atvbaha.110.214429] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Roxana Martinez-Pinna
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Priscila Ramos-Mozo
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Julio Madrigal-Matute
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Luis M. Blanco-Colio
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Juan A. Lopez
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Enrique Calvo
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Emilio Camafeita
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Jes S. Lindholt
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Olivier Meilhac
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Sandrine Delbosc
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Jean-Baptiste Michel
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Melina Vega de Ceniga
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Jesus Egido
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
| | - Jose L. Martin-Ventura
- From the Vascular Research Laboratory, Instituto de Investigación Sanitaria-Fundación Jiménez Diaz-Autonoma University, Madrid, Spain (R.M.-P., P.R.-M., J.M.-M., L.M.B.-C., J.E., J.L.M.-V.); Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain (J.A.L., E. Calvo, E. Camafeita); Vascular Research Unit, Viborg Hospital, Viborg, Denmark (J.S.L.); Institut National de la Santé et de la Recherche Médicale U698, Paris, France (O.M., S.D., J.-B.M.); Université Denis
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