1
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Mulholland PJ, Berto S, Wilmarth PA, McMahan C, Ball LE, Woodward JJ. Adaptor protein complex 2 in the orbitofrontal cortex predicts alcohol use disorder. Mol Psychiatry 2023; 28:4766-4776. [PMID: 37679472 PMCID: PMC10918038 DOI: 10.1038/s41380-023-02236-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023]
Abstract
Alcohol use disorder (AUD) is a life-threatening disease characterized by compulsive drinking, cognitive deficits, and social impairment that continue despite negative consequences. The inability of individuals with AUD to regulate drinking may involve functional deficits in cortical areas that normally balance actions that have aspects of both reward and risk. Among these, the orbitofrontal cortex (OFC) is critically involved in goal-directed behavior and is thought to maintain a representation of reward value that guides decision making. In the present study, we analyzed post-mortem OFC brain samples collected from age- and sex-matched control subjects and those with AUD using proteomics, bioinformatics, machine learning, and reverse genetics approaches. Of the 4,500+ total unique proteins identified in the proteomics screen, there were 47 proteins that differed significantly by sex that were enriched in processes regulating extracellular matrix and axonal structure. Gene ontology enrichment analysis revealed that proteins differentially expressed in AUD cases were involved in synaptic and mitochondrial function, as well as transmembrane transporter activity. Alcohol-sensitive OFC proteins also mapped to abnormal social behaviors and social interactions. Machine learning analysis of the post-mortem OFC proteome revealed dysregulation of presynaptic (e.g., AP2A1) and mitochondrial proteins that predicted the occurrence and severity of AUD. Using a reverse genetics approach to validate a target protein, we found that prefrontal Ap2a1 expression significantly correlated with voluntary alcohol drinking in male and female genetically diverse mouse strains. Moreover, recombinant inbred strains that inherited the C57BL/6J allele at the Ap2a1 interval consumed higher amounts of alcohol than those that inherited the DBA/2J allele. Together, these findings highlight the impact of excessive alcohol consumption on the human OFC proteome and identify important cross-species cortical mechanisms and proteins that control drinking in individuals with AUD.
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Affiliation(s)
- Patrick J Mulholland
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, 29425, USA.
- Charleston Alcohol Research Center, Medical University of South Carolina, Charleston, SC, 29425, USA.
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Christopher McMahan
- School of Mathematical and Statistical Sciences, Clemson-MUSC Artificial Intelligence Hub, Clemson University, Clemson, SC, 29634-0975, USA
| | - Lauren E Ball
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - John J Woodward
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, 29425, USA
- Charleston Alcohol Research Center, Medical University of South Carolina, Charleston, SC, 29425, USA
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2
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Deleeuw V, Carlson E, Renard M, Zientek KD, Wilmarth PA, Reddy AP, Manalo EC, Tufa SF, Keene DR, Olbinado M, Stampanoni M, Kanki S, Yanagisawa H, Mosquera LM, Sips P, De Backer J, Sakai LY. Unraveling the role of TGFβ signaling in thoracic aortic aneurysm and dissection using Fbn1 mutant mouse models. Matrix Biol 2023; 123:17-33. [PMID: 37683955 DOI: 10.1016/j.matbio.2023.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 08/23/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Although abnormal TGFβ signaling is observed in several heritable forms of thoracic aortic aneurysms and dissections including Marfan syndrome, its precise role in aortic disease progression is still disputed. Using a mouse genetic approach and quantitative isobaric labeling proteomics, we sought to elucidate the role of TGFβ signaling in three Fbn1 mutant mouse models representing a range of aortic disease from microdissection (without aneurysm) to aneurysm (without rupture) to aneurysm and rupture. Results indicated that reduced TGFβ signaling and increased mast cell proteases were associated with microdissection. In contrast, increased abundance of extracellular matrix proteins, which could be reporters for positive TGFβ signaling, were associated with aneurysm. Marked reductions in collagens and fibrillins, and increased TGFβ signaling, were associated with aortic rupture. Our data indicate that TGFβ signaling performs context-dependent roles in the pathogenesis of thoracic aortic disease.
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Affiliation(s)
- Violette Deleeuw
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent B-9000, Belgium
| | - Eric Carlson
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Marjolijn Renard
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent B-9000, Belgium; Shriners Children's Hospital, 3101 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Keith D Zientek
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, OR 97239, United States
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, OR 97239, United States
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, OR 97239, United States
| | - Elise C Manalo
- Shriners Children's Hospital, 3101 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Sara F Tufa
- Shriners Children's Hospital, 3101 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Douglas R Keene
- Shriners Children's Hospital, 3101 SW Sam Jackson Park Road, Portland, OR 97239, United States
| | - Margie Olbinado
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Marco Stampanoni
- Paul Scherrer Institute, Forschungsstrasse 111, Villigen 5232, Switzerland
| | - Sachiko Kanki
- Department of Thoracic and Cardiovascular Surgery, Osaka Medical and Pharmaceutical University, 2-7 Daigaku-machi, Takatsuki, Osaka 569-0801 Japan
| | - Hiromi Yanagisawa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, The University of Tsukuba, Tsukuba, Ibaraki 305-8577 Japan
| | - Laura Muiño Mosquera
- Department of Pediatrics, Division of Pediatric Cardiology, Ghent University Hospital, Corneel Heymanslaan 10, Ghent B-9000, Belgium
| | - Patrick Sips
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent B-9000, Belgium
| | - Julie De Backer
- Department of Cardiology, Ghent University Hospital, Corneel Heymanslaan 10, Ghent B-9000, Belgium
| | - Lynn Y Sakai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, United States.
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3
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Shorey-Kendrick LE, Crosland BA, Spindel ER, McEvoy CT, Wilmarth PA, Reddy AP, Zientek KD, Roberts VHJ, D'Mello RJ, Ryan KS, Olyaei AF, Hagen OL, Drake MG, McCarty OJT, Scottoline BP, Lo JO. Author Correction: The amniotic fluid proteome changes across gestation in humans and rhesus macaques. Sci Rep 2023; 13:17640. [PMID: 37848475 PMCID: PMC10582017 DOI: 10.1038/s41598-023-44855-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - B Adam Crosland
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Cindy T McEvoy
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Ashok P Reddy
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Keith D Zientek
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Victoria H J Roberts
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Rahul J D'Mello
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Kimberly S Ryan
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Amy F Olyaei
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Olivia L Hagen
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Matthew G Drake
- Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Owen J T McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Brian P Scottoline
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Jamie O Lo
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA.
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
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4
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Shorey-Kendrick LE, Crosland BA, Spindel ER, McEvoy CT, Wilmarth PA, Reddy AP, Zientek KD, Roberts VHJ, D'Mello RJ, Ryan KS, Olyaei AF, Hagen OL, Drake MG, McCarty OJT, Scottoline BP, Lo JO. The amniotic fluid proteome changes across gestation in humans and rhesus macaques. Sci Rep 2023; 13:17039. [PMID: 37814009 PMCID: PMC10562452 DOI: 10.1038/s41598-023-44125-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 10/11/2023] Open
Abstract
Amniotic fluid is a complex biological medium that offers protection to the fetus and plays a key role in normal fetal nutrition, organogenesis, and potentially fetal programming. Amniotic fluid is also critically involved in longitudinally shaping the in utero milieu during pregnancy. Yet, the molecular mechanism(s) of action by which amniotic fluid regulates fetal development is ill-defined partly due to an incomplete understanding of the evolving composition of the amniotic fluid proteome. Prior research consisting of cross-sectional studies suggests that the amniotic fluid proteome changes as pregnancy advances, yet longitudinal alterations have not been confirmed because repeated sampling is prohibitive in humans. We therefore performed serial amniocenteses at early, mid, and late gestational time-points within the same pregnancies in a rhesus macaque model. Longitudinally-collected rhesus amniotic fluid samples were paired with gestational-age matched cross-sectional human samples. Utilizing LC-MS/MS isobaric labeling quantitative proteomics, we demonstrate considerable cross-species similarity between the amniotic fluid proteomes and large scale gestational-age associated changes in protein content throughout pregnancy. This is the first study to compare human and rhesus amniotic fluid proteomic profiles across gestation and establishes a reference amniotic fluid proteome. The non-human primate model holds promise as a translational platform for amniotic fluid studies.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - B Adam Crosland
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Cindy T McEvoy
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Ashok P Reddy
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Keith D Zientek
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Victoria H J Roberts
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Rahul J D'Mello
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Kimberly S Ryan
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Amy F Olyaei
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
| | - Olivia L Hagen
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Matthew G Drake
- Division of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Owen J T McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Brian P Scottoline
- Division of Neonatology. Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Jamie O Lo
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, 97239, USA.
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
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Palumbo MC, Gautam M, Sonneborn A, Kim K, Wilmarth PA, Reddy AP, Shi X, Marks DL, Sahay G, Abbas AI, Janowsky A. MicroRNA137-loaded lipid nanoparticles regulate synaptic proteins in the prefrontal cortex. Mol Ther 2023; 31:2975-2990. [PMID: 37644723 PMCID: PMC10556225 DOI: 10.1016/j.ymthe.2023.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/20/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023] Open
Abstract
Genome-wide association studies indicate that allele variants in MIR137, the host gene of microRNA137 (miR137), confer an increased risk of schizophrenia (SCZ). Aberrant expression of miR137 and its targets, many of which regulate synaptic functioning, are also associated with an increased risk of SCZ. Thus, miR137 represents an attractive target aimed at correcting the molecular basis for synaptic dysfunction in individuals with high genetic risk for SCZ. Advancements in nanotechnology utilize lipid nanoparticles (LNPs) to transport and deliver therapeutic RNA. However, there remains a gap in using LNPs to regulate gene and protein expression in the brain. To study the delivery of nucleic acids by LNPs to the brain, we found that LNPs released miR137 cargo and inhibited target transcripts of interest in neuroblastoma cells. Biodistribution of LNPs loaded with firefly luciferase mRNA remained localized to the mouse prefrontal cortex (PFC) injection site without circulating to off-target organs. LNPs encapsulating Cre mRNA preferentially co-expressed in neuronal over microglial or astrocytic cells. Using quantitative proteomics, we found miR137 modulated glutamatergic synaptic protein networks that are commonly dysregulated in SCZ. These studies support engineering the next generation of brain-specific LNPs to deliver RNA therapeutics and improve symptoms of central nervous system disorders.
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Affiliation(s)
- Michelle C Palumbo
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Milan Gautam
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA
| | - Alex Sonneborn
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kilsun Kim
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xiao Shi
- Department of Psychiatry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Daniel L Marks
- Department of Pediatrics, Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, Portland, OR 97239, USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR 97331, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Atheir I Abbas
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA; Department of Psychiatry, Oregon Health & Science University, Portland, OR 97239, USA; Research Service, Veterans Affairs Portland Health Care System, Portland, OR 97239, USA
| | - Aaron Janowsky
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA; Department of Psychiatry, Oregon Health & Science University, Portland, OR 97239, USA; Research Service, Veterans Affairs Portland Health Care System, Portland, OR 97239, USA.
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6
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Rivolta AA, Bujold AR, Wilmarth PA, Phinney BS, Navelski JP, Horohov DW, Sanz MG. Comparison of the broncoalveolar lavage fluid proteomics between foals and adult horses. PLoS One 2023; 18:e0290778. [PMID: 37669266 PMCID: PMC10479908 DOI: 10.1371/journal.pone.0290778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 08/15/2023] [Indexed: 09/07/2023] Open
Abstract
Neonates have different cellular composition in their bronchoalveolar lavage fluid (BALF) when compared to foals and adult horses; however, little is known about the non-cellular components of BALF. The objective of this study was to determine the proteomic composition of BALF in neonatal horses and to compare it to that of foals and adult horses. Bronchoalveolar lavage fluid samples of seven neonates (< 1 week age), four 5 to 7-week-old foals, and six adult horses were collected. Quantitative proteomics of the fluid was performed using tandem mass tag labeling followed by high resolution liquid chromatography tandem mass spectrometry and protein relative abundances were compared between groups using exact text. A total of 704 proteins were identified with gene ontology terms and were classified. Of these, 332 proteins were related to the immune system in neonates, foals, and adult horses. The most frequent molecular functions identified were binding and catalytic activity and the most common biological processes were cellular process, metabolic process, and biological regulation. There was a significant difference in the proteome of neonates when compared to foals and to adult horses. Neonates had less relative expression (FDR < 0.01) of many immune-related proteins, including immunoglobulins, proteins involved in the complement cascade, ferritin, BPI fold-containing family B member 1, and macrophage receptor MARCO. This is the first report of equine neonate BALF proteomics and reveals differential abundance of proteins when compared to BALF from adult horses. The lower relative abundance of immune-related proteins in neonates could contribute to their susceptibility to pulmonary infections.
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Affiliation(s)
- Alejandra A. Rivolta
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Adina R. Bujold
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Phillip A. Wilmarth
- Proteomic Shared Resource, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Brett S. Phinney
- Genome Center Proteomics Core Facility, UC Davis, Davis, California, United States of America
| | - Joseph P. Navelski
- School of Economic Sciences, Washington State University, Pullman, Washington, United States of America
| | - David W. Horohov
- Gluck Equine Research Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Macarena G. Sanz
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
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7
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Mulholland PJ, Berto S, Wilmarth PA, McMahan C, Ball LE, Woodward JJ. Adaptor protein complex 2 in the orbitofrontal cortex predicts alcohol use disorder. bioRxiv 2023:2023.05.28.542637. [PMID: 37398482 PMCID: PMC10312445 DOI: 10.1101/2023.05.28.542637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Alcohol use disorder (AUD) is a life-threatening disease characterized by compulsive drinking, cognitive deficits, and social impairment that continue despite negative consequences. The inability of individuals with AUD to regulate drinking may involve functional deficits in cortical areas that normally balance actions that have aspects of both reward and risk. Among these, the orbitofrontal cortex (OFC) is critically involved in goal-directed behavior and is thought to maintain a representation of reward value that guides decision making. In the present study, we analyzed post-mortem OFC brain samples collected from age- and sex-matched control subjects and those with AUD using proteomics, bioinformatics, machine learning, and reverse genetics approaches. Of the 4,500+ total unique proteins identified in the proteomics screen, there were 47 proteins that differed significantly by sex that were enriched in processes regulating extracellular matrix and axonal structure. Gene ontology enrichment analysis revealed that proteins differentially expressed in AUD cases were involved in synaptic and mitochondrial function, as well as transmembrane transporter activity. Alcohol-sensitive OFC proteins also mapped to abnormal social behaviors and social interactions. Machine learning analysis of the post-mortem OFC proteome revealed dysregulation of presynaptic (e.g., AP2A1) and mitochondrial proteins that predicted the occurrence and severity of AUD. Using a reverse genetics approach to validate a target protein, we found that prefrontal Ap2a1 expression significantly correlated with voluntary alcohol drinking in male and female genetically diverse mouse strains. Moreover, recombinant inbred strains that inherited the C57BL/6J allele at the Ap2a1 interval consumed higher amounts of alcohol than those that inherited the DBA/2J allele. Together, these findings highlight the impact of excessive alcohol consumption on the human OFC proteome and identify important cross-species cortical mechanisms and proteins that control drinking in individuals with AUD.
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8
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Hum Genet 2023; 142:927-947. [PMID: 37191732 PMCID: PMC10680127 DOI: 10.1007/s00439-023-02570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/04/2023] [Indexed: 05/17/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3300 proteins per sample (n = 5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ≥ 2.5 average spectral counts, ≥ 2.0 fold-enrichment, false discovery rate < 0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19713, USA.
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9
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Aryal S, Anand D, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. Proteomic profiling of retina and retinal pigment epithelium combined embryonic tissue to facilitate ocular disease gene discovery. Res Sq 2023:rs.3.rs-2652395. [PMID: 36993571 PMCID: PMC10055508 DOI: 10.21203/rs.3.rs-2652395/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To expedite gene discovery in eye development and its associated defects, we previously developed a bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery). However, iSyTE is presently limited to lens tissue and is predominantly based on transcriptomics datasets. Therefore, to extend iSyTE to other eye tissues on the proteome level, we performed high-throughput tandem mass spectrometry (MS/MS) on mouse embryonic day (E)14.5 retina and retinal pigment epithelium combined tissue and identified an average of 3,300 proteins per sample (n=5). High-throughput expression profiling-based gene discovery approaches-involving either transcriptomics or proteomics-pose a key challenge of prioritizing candidates from thousands of RNA/proteins expressed. To address this, we used MS/MS proteome data from mouse whole embryonic body (WB) as a reference dataset and performed comparative analysis-termed "in silico WB-subtraction"-with the retina proteome dataset. In silico WB-subtraction identified 90 high-priority proteins with retina-enriched expression at stringency criteria of ³2.5 average spectral counts, ³2.0 fold-enrichment, False Discovery Rate <0.01. These top candidates represent a pool of retina-enriched proteins, several of which are associated with retinal biology and/or defects (e.g., Aldh1a1, Ank2, Ank3, Dcn, Dync2h1, Egfr, Ephb2, Fbln5, Fbn2, Hras, Igf2bp1, Msi1, Rbp1, Rlbp1, Tenm3, Yap1, etc.), indicating the effectiveness of this approach. Importantly, in silico WB-subtraction also identified several new high-priority candidates with potential regulatory function in retina development. Finally, proteins exhibiting expression or enriched-expression in the retina are made accessible in a user-friendly manner at iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), to allow effective visualization of this information and facilitate eye gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Hongzhan Huang
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
| | - Ashok P. Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Larry L. David
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19713 USA
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10
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Aljawad MF, Faisal AHMA, Alqanbar MF, Wilmarth PA, Hassan BQ. Tandem mass tag-based quantitative proteomic analysis of cervical cancer. Proteomics Clin Appl 2023; 17:e2100105. [PMID: 36029187 DOI: 10.1002/prca.202100105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/20/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND Cervical cancer is a common cancer in women caused by high-risk human papillomavirus (Hr-HPV). Many potential biomarkers have been proposed for precancerous lesions and cancer diagnosis and some of these markers studied for prognosis. This study determined potential biomarkers for cervical cancer diagnosis in regard to HPV genotype by using isobaric labeling quantitative proteomics. METHODS in the current study, there were 75 formalin fixed paraffin embedded (FFPE) uterine cervical samples that used to determine the 14 HPV genotypes and the viral load of each genotype was determined. The tandem mass tag (TMT) proteomic work was performed on four FFPE samples of cervical cancer and four FFPE of control samples. The validation of biomarkers from cervical proteome were evaluated using Immunohistochemistry (IHC) testing. RESULTS The most frequent HPV genotype among all other genotypes was HPV 16. There were 2753 proteins quantified by TMT and 336 of these proteins had significant differential abundances. KPNA2, MCM2, COL1A1, and DCN were selected based on functional enrichment analysis and validated by Immunohistochemistry (IHC) testing. The staining of IHC confirmed the upregulation of KPNA2 and MCM2 expression in cervical neoplasia and the downregulation of DCN and COL1A1 in some cervical cancer group subjects. CONCLUSION The KPNA2 marker was compared to other previously reported biomarkers and is a putative biomarker to be validated in further studies, specifically the relationship with HPV load.
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Affiliation(s)
- Mohammed F Aljawad
- Genetic Engineering and Biotechnology Institute, University of Baghdad, Baghdad, Iraq
| | | | - Mohammed F Alqanbar
- Department of Pathology, College of Medicine, University of Kerbala, Baghdad, Iraq
| | - Phillip A Wilmarth
- Proteomic Shared Resource, Oregon Health & Science University, Portland, Oregon, USA
| | - Basima Q Hassan
- Genetic Engineering and Biotechnology Institute, University of Baghdad, Baghdad, Iraq
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11
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Jalilian I, Muppala S, Ali M, Anderson JD, Phinney B, Salemi M, Wilmarth PA, Murphy CJ, Thomasy SM, Raghunathan V. Cell derived matrices from bovine corneal endothelial cells as a model to study cellular dysfunction. Exp Eye Res 2023; 226:109303. [PMID: 36343671 DOI: 10.1016/j.exer.2022.109303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/12/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
Abstract
PURPOSE Fuchs endothelial corneal dystrophy (FECD) is a progressive corneal disease that impacts the structure and stiffness of the Descemet's membrane (DM), the substratum for corneal endothelial cells (CECs). These structural alterations of the DM could contribute to the loss of the CECs resulting in corneal edema and blindness. Oxidative stress and transforming growth factor-β (TGF-β) pathways have been implicated in endothelial cell loss and endothelial to mesenchymal transition of CECs in FECD. Ascorbic acid (AA) is found at high concentrations in FECD and its impact on CEC survival has been investigated. However, how TGF-β and AA effect the composition and rigidity of the CEC's matrix remains unknown. METHODS In this study, we investigated the effect of AA, TGF-β1 and TGF-β3 on the deposition, ultrastructure, stiffness, and composition of the extracellular matrix (ECM) secreted by primary bovine corneal endothelial cells (BCECs). RESULTS Immunofluorescence and electron microscopy post-decellularization demonstrated a robust deposition and distinct structure of ECM in response to treatments. AFM measurements showed that the modulus of the matrix in BCECs treated with TGF-β1 and TGF-β3 was significantly lower than the controls. There was no difference in the stiffness of the matrix between the AA-treated cell and controls. Gene Ontology analysis of the proteomics results revealed that AA modulates the oxidative stress pathway in the matrix while TGF-β induces the expression of matrix proteins collagen IV, laminin, and lysyl oxidase homolog 1. CONCLUSIONS Molecular pathways identified in this study demonstrate the differential role of soluble factors in the pathogenesis of FECD.
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Affiliation(s)
- Iman Jalilian
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Santoshi Muppala
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA; Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Maryam Ali
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Johnathon D Anderson
- Department of Otolaryngology, School of Medicine, University of California, Davis, Sacramento, CA, 95817, USA
| | - Brett Phinney
- Proteomics Core, University of California, Davis Genome Center, Davis, CA, 95616, USA
| | - Michelle Salemi
- Proteomics Core, University of California, Davis Genome Center, Davis, CA, 95616, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resources, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Christopher J Murphy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA; Department of Ophthalmology & Vision Science, School of Medicine, UC Davis Medical Center, Sacramento, CA, 95817, USA
| | - Sara M Thomasy
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA; Department of Ophthalmology & Vision Science, School of Medicine, UC Davis Medical Center, Sacramento, CA, 95817, USA.
| | - VijayKrishna Raghunathan
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, TX, 77204, USA; Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, TX, 77204, USA.
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12
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Rehman HM, Chen S, Zhang S, Khalid M, Uzair M, Wilmarth PA, Ahmad S, Lam HM. Membrane Proteomic Profiling of Soybean Leaf and Root Tissues Uncovers Salt-Stress-Responsive Membrane Proteins. Int J Mol Sci 2022; 23:13270. [PMID: 36362058 PMCID: PMC9655375 DOI: 10.3390/ijms232113270] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Cultivated soybean (Glycine max (L.)), the world's most important legume crop, has high-to-moderate salt sensitivity. Being the frontier for sensing and controlling solute transport, membrane proteins could be involved in cell signaling, osmoregulation, and stress-sensing mechanisms, but their roles in abiotic stresses are still largely unknown. By analyzing salt-induced membrane proteomic changes in the roots and leaves of salt-sensitive soybean cultivar (C08) seedlings germinated under NaCl, we detected 972 membrane proteins, with those present in both leaves and roots annotated as receptor kinases, calcium-sensing proteins, abscisic acid receptors, cation and anion channel proteins, proton pumps, amide and peptide transporters, and vesicle transport-related proteins etc. Endocytosis, linoleic acid metabolism, and fatty acid biosynthesis pathway-related proteins were enriched in roots whereas phagosome, spliceosome and soluble NSF attachment protein receptor (SNARE) interaction-related proteins were enriched in leaves. Using label-free quantitation, 129 differentially expressed membrane proteins were found in both tissues upon NaCl treatment. Additionally, the 140 NaCl-induced proteins identified in roots and 57 in leaves are vesicle-, mitochondrial-, and chloroplast-associated membrane proteins and those with functions related to ion transport, protein transport, ATP hydrolysis, protein folding, and receptor kinases, etc. Our proteomic results were verified against corresponding gene expression patterns from published C08 RNA-seq data, demonstrating the importance of solute transport and sensing in salt stress responses.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Shengjie Chen
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shoudong Zhang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Memoona Khalid
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Uzair
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Shakeel Ahmad
- Seed Center, Ministry of Environment, Water & Agriculture, Riyadh 14712, Saudi Arabia
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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13
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Sagawa CHD, Assis RDAB, Zaini PA, Saxe H, Wilmarth PA, Salemi M, Phinney BS, Dandekar AM. De Novo Arginine Synthesis Is Required for Full Virulence of Xanthomonas arboricola pv. juglandis During Walnut Bacterial Blight Disease. Phytopathology 2022; 112:1500-1512. [PMID: 34941365 DOI: 10.1094/phyto-07-21-0302-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Walnut blight (WB) disease caused by Xanthomonas arboricola pv. juglandis (Xaj) threatens orchards worldwide. Nitrogen metabolism in this bacterial pathogen is dependent on arginine, a nitrogen-enriched amino acid that can either be synthesized or provided by the plant host. The arginine biosynthetic pathway uses argininosuccinate synthase (argG), associated with increased bacterial virulence. We examined the effects of bacterial arginine and nitrogen metabolism on the plant response during WB by proteomic analysis of the mutant strain Xaj argG-. Phenotypically, the mutant strain produced 42% fewer symptoms and survived in the plant tissue with 2.5-fold reduced growth compared with wild type, while showing itself to be auxotrophic for arginine in vitro. Proteomic analysis of infected tissue enabled the profiling of 676 Xaj proteins and 3,296 walnut proteins using isobaric labeling in a data-dependent acquisition approach. Comparative analysis of differentially expressed proteins revealed distinct plant responses. Xaj wild type (WT) triggered processes of catabolism and oxidative stress in the host under observed disease symptoms, while most of the host biosynthetic processes triggered by Xaj WT were inhibited during Xaj argG- infection. Overall, the Xaj proteins revealed a drastic shift in carbon and energy management induced by disruption of nitrogen metabolism while the top differentially expressed proteins included a Fis transcriptional regulator and a peptidyl-prolyl isomerase. Our results show the critical role of de novo arginine biosynthesis to sustain virulence and minimal growth during WB. This study is timely and critical as copper-based control methods are losing their effectiveness, and new sustainable methods are urgently needed in orchard environments.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Cíntia H D Sagawa
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Renata de A B Assis
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG 35400-000, Brazil
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Houston Saxe
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, U.S.A
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, CA 95616, U.S.A
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, CA 95616, U.S.A
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
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14
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Yunga ST, Gower AJ, Melrose AR, Fitzgerald MK, Rajendran A, Lusardi TA, Armstrong RJ, Minnier J, Jordan KR, McCarty OJT, David LL, Wilmarth PA, Reddy AP, Aslan JE. Effects of ex vivo blood anticoagulation and preanalytical processing time on the proteome content of platelets. J Thromb Haemost 2022; 20:1437-1450. [PMID: 35253976 PMCID: PMC9887642 DOI: 10.1111/jth.15694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Ex vivo assays of platelet function critically inform mechanistic and clinical hematology studies, where effects of divergent blood processing methods on platelet composition are apparent, but unspecified. OBJECTIVE Here, we evaluate how different blood anticoagulation options and processing times affect platelet function and protein content ex vivo. METHODS Parallel blood samples were collected from healthy human donors into sodium citrate, acid citrate dextrose, EDTA or heparin, and processed over an extended time course for functional and biochemical experiments, including platelet proteome quantification with multiplexed tandem mass tag (TMT) labeling and triple quadrupole mass spectrometry (MS). RESULTS Each anticoagulant had time-dependent effects on platelet function in whole blood. For instance, heparin enhanced platelet agonist reactivity, platelet-monocyte aggregate formation and platelet extracellular vesicle release, while EDTA increased platelet α-granule secretion. Following platelet isolation, TMT-MS quantified 3357 proteins amongst all prepared platelet samples. Altogether, >400 proteins were differentially abundant in platelets isolated from blood processed at 24 h versus 1 h post-phlebotomy, including proteins pertinent to membrane trafficking and exocytosis. Anticoagulant-specific effects on platelet proteomes included increased complement system and decreased α-granule proteins in platelets from EDTA-anticoagulated blood. Platelets prepared from heparinized blood had higher levels of histone and neutrophil-associated proteins in a manner related to neutrophil extracellular trap (NET) formation and platelet:NET interactions in whole blood ex vivo. CONCLUSION Our results demonstrate that different anticoagulants routinely used for blood collection have varying effects on platelets ex vivo, where methodology-associated alterations in platelet proteome may influence mechanistic, translational and biomarker studies.
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Affiliation(s)
- Samuel Tassi Yunga
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Austin J. Gower
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Alexander R. Melrose
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Meghan K. Fitzgerald
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Ashmitha Rajendran
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Theresa A. Lusardi
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Randall J. Armstrong
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Jessica Minnier
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Kelley R. Jordan
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Owen J. T. McCarty
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Larry L. David
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Chemical Physiology & Biochemistry, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Ashok P. Reddy
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Joseph E. Aslan
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Chemical Physiology & Biochemistry, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
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15
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Park D, Reddy AP, Wilmarth PA, Jensen JT, Han L. Mucus secretions from a conditionally reprogrammed primary endocervical cell culture. F S Sci 2022; 3:159-165. [PMID: 35560013 PMCID: PMC9947459 DOI: 10.1016/j.xfss.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To determine if the secretions collected from a conditionally reprogrammed primary endocervical cell culture are suitable surrogates for mucus studies. DESIGN Experimental. SETTING University research center. ANIMAL(S) Female rhesus macaque (n = 2). INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Quantitative proteomic analysis using tandem mass tag mass spectrometry liquid chromatography/tandem mass spectrometry. RESULT(S) We identified 3,047 proteins, common proteins present in both primary endocervical cell cultures and the mucus of rhesus macaques. We found a 71% overlap in the top 500 most prevalent proteins in the samples. Cell culture secretions contained many essential mucus proteins, including MUC5B, the primary mucin of the endocervix. CONCLUSION(S) Similarities in secreted proteins suggest that conditionally reprogrammed primary endocervical cells could be used to study mucus secretion in vitro.
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Affiliation(s)
- Daye Park
- Augusta University/University of Georgia Medical Partnership, Athens, Georgia.
| | - Ashok P. Reddy
- Proteomic Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Phillip A. Wilmarth
- Proteomic Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey T. Jensen
- Oregon Health & Science University, Department of Obstetrics and Gynecology, Portland, OR, USA,Oregon National Primate Research Center, Division of Reproductive and Developmental Sciences, Portland, OR, USA
| | - Leo Han
- Oregon Health & Science University, Department of Obstetrics and Gynecology, Portland, OR, USA,Oregon National Primate Research Center, Division of Reproductive and Developmental Sciences, Portland, OR, USA
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16
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De Maria A, Zientek KD, David LL, Wilmarth PA, Bhorade AM, Harocopos GJ, Huang AJW, Hong AR, Siegfried CJ, Tsai LM, Sheybani A, Bassnett S. Compositional Analysis of Extracellular Aggregates in the Eyes of Patients With Exfoliation Syndrome and Exfoliation Glaucoma. Invest Ophthalmol Vis Sci 2021; 62:27. [PMID: 34964803 PMCID: PMC8740535 DOI: 10.1167/iovs.62.15.27] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Exfoliation syndrome (XFS) is a condition characterized by the production of insoluble fibrillar aggregates (exfoliation material; XFM) in the eye and elsewhere. Many patients with XFS progress to exfoliation glaucoma (XFG), a significant cause of global blindness. We used quantitative mass spectrometry to analyze the composition of XFM in lens capsule specimens and in aqueous humor (AH) samples from patients with XFS, patients with XFG and unaffected individuals. Methods Pieces of lens capsule and samples of AH were obtained with consent from patients undergoing cataract surgery. Tryptic digests of capsule or AH were analyzed by high-performance liquid chromatography–mass spectrometry and relative differences between samples were quantified using the tandem mass tag technique. The distribution of XFM on the capsular surface was visualized by SEM and super-resolution light microscopy. Results A small set of proteins was consistently upregulated in capsule samples from patients with XFS and patients with XFG, including microfibril components fibrillin-1, latent transforming growth factor-β–binding protein-2 and latent transforming growth factor-β–binding protein-3. Lysyl oxidase-like 1, a cross-linking enzyme associated with XFS in genetic studies, was an abundant XFM constituent. Ligands of the transforming growth factor-β superfamily were prominent, including LEFTY2, a protein best known for its role in establishing the embryonic body axis. Elevated levels of LEFTY2 were also detected in AH from patients with XFG, a finding confirmed subsequently by ELISA. Conclusions This analysis verified the presence of suspected XFM proteins and identified novel components. Quantitative comparisons between patient samples revealed a consistent XFM proteome characterized by strong expression of fibrillin-1, lysyl oxidase-like-1, and LEFTY2. Elevated levels of LEFTY2 in the AH of patients with XFG may serve as a biomarker for the disease.
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Affiliation(s)
- Alicia De Maria
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Keith D Zientek
- Proteomics Shared Resource, Oregon Health and Science University, Portland, Oregon, United States
| | - Larry L David
- Department of Chemical Physiology & Biochemistry, Oregon Health and Science University, Portland, Oregon, United States
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, Oregon, United States
| | - Anjali M Bhorade
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - George J Harocopos
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Andrew J W Huang
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Augustine R Hong
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Carla J Siegfried
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Linda M Tsai
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Arsham Sheybani
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Steven Bassnett
- Department of Ophthalmology & Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
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17
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Khazaei H, Khazaei D, Verma R, Ng J, Wilmarth PA, David LL, Rosenbaum JT. The potential of tear proteomics for diagnosis and management of orbital inflammatory disorders including Graves' ophthalmopathy. Exp Eye Res 2021; 213:108813. [PMID: 34742692 DOI: 10.1016/j.exer.2021.108813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/10/2021] [Accepted: 10/26/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Orbital compartments harbor a variety of tissues that can be independently targeted in a plethora of disorders resulting in sight-threatening risks. Orbital inflammatory disorders (OID) including Graves' ophthalmopathy, sarcoidosis, IgG4 disease, granulomatosis with polyangiitis, and nonspecific orbital inflammation constitute an important cause of pain, diplopia and vision loss. Physical examination, laboratory tests, imaging, and even biopsy are not always adequate to classify orbital inflammation which is frequently deemed "nonspecific". Tear sampling and testing provide a potential "window" to the orbital disease process through a non-invasive technique that allows longitudinal sampling as the disease evolves. Using PubMed/Medline, we identified potentially relevant articles on tear proteomics published in the English language between 1988 and 2021. Of 303 citations obtained, 225 contained empirical data on tear proteins, including 33 publications on inflammatory conditions, 15 in glaucoma, 15 in thyroid eye disease, 1 in sarcoidosis (75) and 2 in uveitis (77,78). Review articles were used to identify an additional 56 relevant articles through citation search. In this review, we provide a short introduction to the potential use of tears as a diagnostic fluid and tool to investigate the mechanism of ocular diseases. A general review of previous tear proteomics studies is also provided, with a focus on Graves' ophthalmopathy (GO), and a discussion of unmet needs in the diagnosis and treatment of orbital inflammatory disease (OID). The review concludes by pointing out current limitations of mass spectrometric analysis of tear proteins and summarizes future needs in the field.
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Cooper S, Wilmarth PA, Cunliffe JM, Klimek J, Pang J, Tassi Yunga S, Minnier J, Reddy A, David L, Aslan JE. Platelet proteome dynamics in hibernating 13-lined ground squirrels. Physiol Genomics 2021; 53:473-485. [PMID: 34677084 PMCID: PMC8616595 DOI: 10.1152/physiolgenomics.00078.2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/21/2021] [Accepted: 10/14/2021] [Indexed: 12/13/2022] Open
Abstract
Hibernating mammals undergo a dramatic drop in temperature and blood flow during torpor, yet avoid stasis blood clotting through mechanisms that remain unspecified. The effects of hibernation on hemostasis are especially complex, as cold temperatures generally activate platelets, resulting in platelet clearance and cold storage lesions in the context of blood transfusion. With a hibernating body temperature of 4°C-8°C, 13-lined ground squirrels (Ictidomys tridecemlineatus) provide a model to study hemostasis as well as platelet cold storage lesion resistance during hibernation. Here, we quantified and systematically compared proteomes of platelets collected from ground squirrels at summer (active), fall (entrance), and winter (topor) to elucidate how molecular-level changes in platelets may support hemostatic adaptations in torpor. Platelets were isolated from a total of 11 squirrels in June, October, and January. Platelet lysates from each animal were digested with trypsin prior to 11-plex tandem mass tag (TMT) labeling, followed by LC-MS/MS analysis for relative protein quantification. We measured >700 proteins with significant variations in abundance in platelets over the course of entrance, torpor, and activity-including systems of proteins regulating translation, secretion, metabolism, complement, and coagulation cascades. We also noted species-specific differences in levels of hemostatic, secretory, and inflammatory regulators in ground squirrel platelets relative to human platelets. Altogether, we provide the first ever proteomic characterization of platelets from hibernating animals, where systematic changes in metabolic, hemostatic, and other proteins may account for physiological adaptations in torpor and also inform translational effort to improve cold storage of human platelets for transfusion.
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Affiliation(s)
- Scott Cooper
- Biology Department, University of Wisconsin-La Crosse, La Crosse, Wisconsin
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon
| | - Jennifer M Cunliffe
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon
| | - John Klimek
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon
| | - Jiaqing Pang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
| | - Samuel Tassi Yunga
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, Oregon
| | - Jessica Minnier
- Division of Cardiology, Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon
| | - Ashok Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon
| | - Larry David
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon
| | - Joseph E Aslan
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, Oregon
- Division of Cardiology, Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon
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19
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Assis RDAB, Sagawa CHD, Zaini PA, Saxe HJ, Wilmarth PA, Phinney BS, Salemi M, Moreira LM, Dandekar AM. A Secreted Chorismate Mutase from Xanthomonas arboricola pv. juglandis Attenuates Virulence and Walnut Blight Symptoms. Int J Mol Sci 2021; 22:10374. [PMID: 34638715 PMCID: PMC8508651 DOI: 10.3390/ijms221910374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 01/11/2023] Open
Abstract
Walnut blight is a significant above-ground disease of walnuts caused by Xanthomonas arboricola pv. juglandis (Xaj). The secreted form of chorismate mutase (CM), a key enzyme of the shikimate pathway regulating plant immunity, is highly conserved between plant-associated beta and gamma proteobacteria including phytopathogens belonging to the Xanthomonadaceae family. To define its role in walnut blight disease, a dysfunctional mutant of chorismate mutase was created in a copper resistant strain Xaj417 (XajCM). Infections of immature walnut Juglans regia (Jr) fruit with XajCM were hypervirulent compared with infections with the wildtype Xaj417 strain. The in vitro growth rate, size and cellular morphology were similar between the wild-type and XajCM mutant strains, however the quantification of bacterial cells by dPCR within walnut hull tissues showed a 27% increase in XajCM seven days post-infection. To define the mechanism of hypervirulence, proteome analysis was conducted to compare walnut hull tissues inoculated with the wild type to those inoculated with the XajCM mutant strain. Proteome analysis revealed 3296 Jr proteins (five decreased and ten increased with FDR ≤ 0.05) and 676 Xaj417 proteins (235 increased in XajCM with FDR ≤ 0.05). Interestingly, the most abundant protein in Xaj was a polygalacturonase, while in Jr it was a polygalacturonase inhibitor. These results suggest that this secreted chorismate mutase may be an important virulence suppressor gene that regulates Xaj417 virulence response, allowing for improved bacterial survival in the plant tissues.
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Affiliation(s)
- Renata de A. B. Assis
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (R.d.A.B.A.); (C.H.D.S.); (P.A.Z.); (H.J.S.)
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, MG, Brazil
| | - Cíntia H. D. Sagawa
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (R.d.A.B.A.); (C.H.D.S.); (P.A.Z.); (H.J.S.)
| | - Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (R.d.A.B.A.); (C.H.D.S.); (P.A.Z.); (H.J.S.)
| | - Houston J. Saxe
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (R.d.A.B.A.); (C.H.D.S.); (P.A.Z.); (H.J.S.)
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, CA 95616, USA; (B.S.P.); (M.S.)
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, CA 95616, USA; (B.S.P.); (M.S.)
| | - Leandro M. Moreira
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, MG, Brazil
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (R.d.A.B.A.); (C.H.D.S.); (P.A.Z.); (H.J.S.)
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20
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Han L, Park D, Reddy A, Wilmarth PA, Jensen JT. Comparing endocervical mucus proteome of humans and rhesus macaques. Proteomics Clin Appl 2021; 15:e2100023. [PMID: 33991406 PMCID: PMC8653767 DOI: 10.1002/prca.202100023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/14/2021] [Indexed: 01/19/2023]
Abstract
PURPOSE Endocervical mucus changes play a key role in regulating fertility throughout the menstrual cycle and in response to hormonal contraceptives. Non-human primates (NHP) provide the most translational animal model for reproductive tract studies, as they have hormonally-regulated menstrual cycles and mucus changes, similar to women. EXPERIMENTAL DESIGN We used TMT labelling and LC-LC/MS to compare the proteins found in the mucus of the rhesus macaque to the mucus of the human endocervix. Data are available via ProteomeXchange with identifier PXD021710. RESULTS We found 3048 total proteins present in both rhesus mucus and human mucus, and of these, 57% showed a similar expression pattern. An even higher similarity occurred in the top 500 most prevalent proteins, with overlap in 341 (68%) proteins. Mucin MUC5B was the most highly expressed mucin protein (top 10 expressed proteins in both) but other key proteins related to mucus structure were present in both samples. CONCLUSIONS AND CLINICAL RELEVANCE We find that the mucus proteome of the endocervical mucus is highly conserved in NHP and women. This supports use of the NHP model system for studies of the endocervix and trials of novel fertility treatments targeting the cervix.
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Affiliation(s)
- Leo Han
- Oregon Health & Science University, Department of Obstetrics and Gynecology, Portland, OR
- Oregon National Primate Research Center, Division of Reproductive and Developmental Sciences, Portland, OR
| | - Daye Park
- Augusta University / University of Georgia Medical Partnership, Athens, GA
| | - Ashok Reddy
- Proteomic Shared Resource, Oregon Health & Science University, Portland, OR USA
| | - Phillip A. Wilmarth
- Proteomic Shared Resource, Oregon Health & Science University, Portland, OR USA
| | - Jeffrey T. Jensen
- Oregon Health & Science University, Department of Obstetrics and Gynecology, Portland, OR
- Oregon National Primate Research Center, Division of Reproductive and Developmental Sciences, Portland, OR
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21
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Babur Ö, Melrose AR, Cunliffe JM, Klimek J, Pang J, Sepp ALI, Zilberman-Rudenko J, Tassi Yunga S, Zheng T, Parra-Izquierdo I, Minnier J, McCarty OJT, Demir E, Reddy AP, Wilmarth PA, David LL, Aslan JE. Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs. Blood 2020; 136:2346-2358. [PMID: 32640021 PMCID: PMC7702475 DOI: 10.1182/blood.2020005496] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Platelets engage cues of pending vascular injury through coordinated adhesion, secretion, and aggregation responses. These rapid, progressive changes in platelet form and function are orchestrated downstream of specific receptors on the platelet surface and through intracellular signaling mechanisms that remain systematically undefined. This study brings together cell physiological and phosphoproteomics methods to profile signaling mechanisms downstream of the immunotyrosine activation motif (ITAM) platelet collagen receptor GPVI. Peptide tandem mass tag (TMT) labeling, sample multiplexing, synchronous precursor selection (SPS), and triple stage tandem mass spectrometry (MS3) detected >3000 significant (false discovery rate < 0.05) phosphorylation events on >1300 proteins over conditions initiating and progressing GPVI-mediated platelet activation. With literature-guided causal inference tools, >300 site-specific signaling relations were mapped from phosphoproteomics data among key and emerging GPVI effectors (ie, FcRγ, Syk, PLCγ2, PKCδ, DAPP1). Through signaling validation studies and functional screening, other less-characterized targets were also considered within the context of GPVI/ITAM pathways, including Ras/MAPK axis proteins (ie, KSR1, SOS1, STAT1, Hsp27). Highly regulated GPVI/ITAM targets out of context of curated knowledge were also illuminated, including a system of >40 Rab GTPases and associated regulatory proteins, where GPVI-mediated Rab7 S72 phosphorylation and endolysosomal maturation were blocked by TAK1 inhibition. In addition to serving as a model for generating and testing hypotheses from omics datasets, this study puts forth a means to identify hemostatic effectors, biomarkers, and therapeutic targets relevant to thrombosis, vascular inflammation, and other platelet-associated disease states.
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Affiliation(s)
- Özgün Babur
- Department of Molecular and Medical Genetics
- Computational Biology Program
| | | | | | | | | | | | | | | | | | | | | | | | - Emek Demir
- Department of Molecular and Medical Genetics
- Computational Biology Program
| | | | | | - Larry L David
- Proteomics Shared Resource
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR
| | - Joseph E Aslan
- Knight Cardiovascular Institute
- Department of Biomedical Engineering
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR
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22
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Plubell DL, Fenton AM, Rosario S, Bergstrom P, Wilmarth PA, Clark W, Zakai NA, Quinn JF, Minnier J, Alkayed NJ, Fazio S, Pamir N. High-Density Lipoprotein Carries Markers That Track With Recovery From Stroke. Circ Res 2020; 127:1274-1287. [PMID: 32844720 PMCID: PMC7581542 DOI: 10.1161/circresaha.120.316526] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RATIONALE Prospective cohort studies question the value of HDL-C (high-density lipoprotein cholesterol) for stroke risk prediction. OBJECTIVE Investigate the relationship between long-term functional recovery and HDL proteome and function. METHODS AND RESULTS Changes in HDL protein composition and function (cholesterol efflux capacity) in patients after acute ischemic stroke at 2 time points (24 hours, 35 patients; 96 hours, 20 patients) and in 35 control subjects were measured. The recovery from stroke was assessed by 3 months, the National Institutes of Health Stroke Scale and modified Rankin scale scores. When compared with control subject after adjustments for sex and HDL-C levels, 12 proteins some of which participate in acute phase response and platelet activation (APMAP [adipocyte plasma membrane-associated protein], GPLD1 [phosphate inositol-glycan specific phospholipase D], APOE [apolipoprotein E], IHH [Indian hedgehog protein], ITIH4 [inter-alpha-trypsin inhibitor chain H4], SAA2 [serum amyloid A2], APOA4 [apolipoprotein A-IV], CLU [clusterin], ANTRX2 [anthrax toxin receptor 2], PON1 [serum paraoxonase/arylesterase], SERPINA1 [alpha-1-antitrypsin], and APOF [apolipoprotein F]) were significantly (adjusted P<0.05) altered in stroke HDL at 96 hours. The first 8 of these proteins were also significantly altered at 24 hours. Consistent with inflammatory remodeling, cholesterol efflux capacity was reduced by 32% (P<0.001) at both time points. Baseline stroke severity adjusted regression model showed that changes within 96-hour poststroke in APOF, APOL1, APMAP, APOC4 (apolipoprotein C4), APOM (apolipoprotein M), PCYOX1 (prenylcysteine oxidase 1), PON1, and APOE correlate with stroke recovery scores (R2=0.38-0.73, adjusted P<0.05). APOF (R2=0.73) and APOL1 (R2=0.60) continued to significantly correlate with recovery scores after accounting for tPA (tissue-type plasminogen activator) treatment. CONCLUSIONS Changes in HDL proteins during early acute phase of stroke associate with recovery. Monitoring HDL proteins may provide clinical biomarkers that inform on stroke recuperation.
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Affiliation(s)
- Deanna L. Plubell
- Knight Cardiovascular Institute, Department of Medicine, Oregon Health & Science University
| | - Alex M. Fenton
- Knight Cardiovascular Institute, Department of Medicine, Oregon Health & Science University
| | - Sara Rosario
- Knight Cardiovascular Institute, Department of Medicine, Oregon Health & Science University
| | - Paige Bergstrom
- Knight Cardiovascular Institute, Department of Medicine, Oregon Health & Science University
| | | | - Wayne Clark
- Department of Neurology, Oregon Health & Science University
| | - Neil A. Zakai
- Department of Medicine, Larner College of Medicine, University of Vermont
| | | | - Jessica Minnier
- Knight Cardiovascular Institute, Department of Medicine, Oregon Health & Science University
- School of Public Health, Oregon Health & Science University
| | - Nabil J. Alkayed
- Knight Cardiovascular Institute, Department of Medicine, Oregon Health & Science University
| | - Sergio Fazio
- Knight Cardiovascular Institute, Department of Medicine, Oregon Health & Science University
| | - Nathalie Pamir
- Knight Cardiovascular Institute, Department of Medicine, Oregon Health & Science University
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23
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H. D. Sagawa C, de A. B. Assis R, Zaini PA, Wilmarth PA, Phinney BS, Moreira LM, Dandekar AM. Proteome Analysis of Walnut Bacterial Blight Disease. Int J Mol Sci 2020; 21:E7453. [PMID: 33050347 PMCID: PMC7593943 DOI: 10.3390/ijms21207453] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/21/2022] Open
Abstract
The interaction between the plant host, walnut (Juglans regia; Jr), and a deadly pathogen (Xanthomonas arboricola pv. juglandis 417; Xaj) can lead to walnut bacterial blight (WB), which depletes walnut productivity by degrading the nut quality. Here, we dissect this pathosystem using tandem mass tag quantitative proteomics. Walnut hull tissues inoculated with Xaj were compared to mock-inoculated tissues, and 3972 proteins were identified, of which 3296 are from Jr and 676 from Xaj. Proteins with differential abundance include oxidoreductases, proteases, and enzymes involved in energy metabolism and amino acid interconversion pathways. Defense responses and plant hormone biosynthesis were also increased. Xaj proteins detected in infected tissues demonstrate its ability to adapt to the host microenvironment, limiting iron availability, coping with copper toxicity, and maintaining energy and intermediary metabolism. Secreted proteases and extracellular secretion apparatus such as type IV pilus for twitching motility and type III secretion effectors indicate putative factors recognized by the host. Taken together, these results suggest intense degradation processes, oxidative stress, and general arrest of the biosynthetic metabolism in infected nuts. Our results provide insights into molecular mechanisms and highlight potential molecular tools for early detection and disease control strategies.
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Affiliation(s)
- Cíntia H. D. Sagawa
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
| | - Renata de A. B. Assis
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil;
| | - Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA;
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, CA 95616, USA;
| | - Leandro M. Moreira
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil;
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (C.H.D.S.); (R.d.A.B.A.); (P.A.Z.)
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24
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Horsophonphong S, Sercia A, França CM, Tahayeri A, Reddy AP, Wilmarth PA, Surarit R, Smith AJ, Ferracane JL, Bertassoni LE. Equivalence of human and bovine dentin matrix molecules for dental pulp regeneration: proteomic analysis and biological function. Arch Oral Biol 2020; 119:104888. [PMID: 32932150 DOI: 10.1016/j.archoralbio.2020.104888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/13/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To compare proteomics and biological function of human dentin matrix molecules (hDMMs) and bovine dentin matrix molecules (bDMMs). DESIGN Dentin powder from human or bovine teeth (n = 4) was demineralized in 10% (v/v) ethylenediaminetetraacetic acid for 7 days. The extracts were dialyzed, lyophilized and proteins were characterized using liquid chromatography-tandem mass spectrometry and shotgun proteomic analysis. To study biological function, mouse-derived undifferentiated dental pulp cells (OD21) were treated with 0.01, 0.1 or 1 μg/mL of hDMMs or bDMMs and proliferation was measured after 24 hours and 48 hours using 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Cell migration was assessed after 24 hours using a Boyden chamber. Alizarin Red S staining was used to evaluate mineral formation. RESULTS There were 307 proteins identified, of which 93 proteins were common to both species. Gene Ontology functional analysis demonstrated similar pattern of biological process in both species which consisted mainly of tissue development and biomineralization. hDMMs and bDMMs both enhanced cell proliferation. After 24 hours, all concentrations of bDMMs promoted cell proliferation (p ≤ 0.05), while hDMMs did not affect proliferation. After 48 hours, groups with 1μg/mL of bDMMs and 0.01μg/mL of hDMMs had increased cell proliferation compared to control (p ≤ 0.0001). All concentrations of hDMMs and bDMMs enhanced cell migration and mineralization (p ≤ 0.0001). CONCLUSION bDMMs has similar biological functions as hDMMs. Moreover, bDMMs stimulated cell proliferation, migration and differentiation similar to hDMMs.
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Affiliation(s)
- Sivaporn Horsophonphong
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR, USA; Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand; Department of Pediatric Dentistry, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Ashley Sercia
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR, USA
| | - Cristiane M França
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR, USA
| | - Anthony Tahayeri
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and & Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and & Science University, Portland, OR, 97239, USA
| | - Rudee Surarit
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Anthony J Smith
- School of Dentistry, University of Birmingham, Birmingham, UK
| | - Jack L Ferracane
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR, USA
| | - Luiz E Bertassoni
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, OR, USA; Center for Regenerative Medicine, School of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, USA; Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, Portland, OR, USA.
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25
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Helena Duarte Sagawa C, Zaini PA, de A. B. Assis R, Saxe H, Salemi M, Jacobson A, Wilmarth PA, Phinney BS, M. Dandekar A. Deep Learning Neural Network Prediction Method Improves Proteome Profiling of Vascular Sap of Grapevines during Pierce's Disease Development. Biology (Basel) 2020; 9:biology9090261. [PMID: 32882865 PMCID: PMC7565608 DOI: 10.3390/biology9090261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 12/31/2022]
Abstract
Plant secretome studies highlight the importance of vascular plant defense proteins against pathogens. Studies on Pierce’s disease of grapevines caused by the xylem-limited bacterium Xylella fastidiosa (Xf) have detected proteins and pathways associated with its pathobiology. Despite the biological importance of the secreted proteins in the extracellular space to plant survival and development, proteome studies are scarce due to methodological challenges. Prosit, a deep learning neural network prediction method is a powerful tool for improving proteome profiling by data-independent acquisition (DIA). We explored the potential of Prosit’s in silico spectral library predictions to improve DIA proteomic analysis of vascular leaf sap from grapevines with Pierce’s disease. The combination of DIA and Prosit-predicted libraries increased the total number of identified grapevine proteins from 145 to 360 and Xf proteins from 18 to 90 compared to gas-phase fractionation (GPF) libraries. The new proteins increased the range of molecular weights, assisted in the identification of more exclusive peptides per protein, and increased identification of low-abundance proteins. These improvements allowed identification of new functional pathways associated with cellular responses to oxidative stress, to be investigated further.
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Affiliation(s)
- Cíntia Helena Duarte Sagawa
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, CA 95616, USA; (C.H.D.S.); (P.A.Z.); (R.d.A.B.A.); (H.S.); (A.J.)
| | - Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, CA 95616, USA; (C.H.D.S.); (P.A.Z.); (R.d.A.B.A.); (H.S.); (A.J.)
| | - Renata de A. B. Assis
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, CA 95616, USA; (C.H.D.S.); (P.A.Z.); (R.d.A.B.A.); (H.S.); (A.J.)
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, 122-Bauxita, Ouro Preto-MG 35400-000, Brazil
| | - Houston Saxe
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, CA 95616, USA; (C.H.D.S.); (P.A.Z.); (R.d.A.B.A.); (H.S.); (A.J.)
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, 1 Shields Ave, CA 95616, USA; (M.S.); (B.S.P.)
| | - Aaron Jacobson
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, CA 95616, USA; (C.H.D.S.); (P.A.Z.); (R.d.A.B.A.); (H.S.); (A.J.)
| | - Phillip A. Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Medical Research Building, 3252 SW Research Drive, Portland, OR 97239, USA;
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, 1 Shields Ave, CA 95616, USA; (M.S.); (B.S.P.)
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, CA 95616, USA; (C.H.D.S.); (P.A.Z.); (R.d.A.B.A.); (H.S.); (A.J.)
- Correspondence:
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26
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Aryal S, Anand D, Hernandez FG, Weatherbee BAT, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery: application to lens development and cataract. Hum Genet 2019; 139:151-184. [PMID: 31797049 DOI: 10.1007/s00439-019-02095-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/24/2019] [Indexed: 12/20/2022]
Abstract
While the bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery) effectively identifies human cataract-associated genes, it is currently based on just transcriptome data, and thus, it is necessary to include protein-level information to gain greater confidence in gene prioritization. Here, we expand iSyTE through development of a novel proteome-based resource on the lens and demonstrate its utility in cataract gene discovery. We applied high-throughput tandem mass spectrometry (MS/MS) to generate a global protein expression profile of mouse lens at embryonic day (E)14.5, which identified 2371 lens-expressed proteins. A major challenge of high-throughput expression profiling is identification of high-priority candidates among the thousands of expressed proteins. To address this problem, we generated new MS/MS proteome data on mouse whole embryonic body (WB). WB proteome was then used as a reference dataset for performing "in silico WB-subtraction" comparative analysis with the lens proteome, which effectively identified 422 proteins with lens-enriched expression at ≥ 2.5 average spectral counts, ≥ 2.0 fold enrichment (FDR < 0.01) cut-off. These top 20% candidates represent a rich pool of high-priority proteins in the lens including known human cataract-linked genes and many new potential regulators of lens development and homeostasis. This rich information is made publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), which enables user-friendly visualization of promising candidates, thus making iSyTE a comprehensive tool for cataract gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Francisco G Hernandez
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Bailey A T Weatherbee
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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27
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Abdelhamed S, Butler JT, Doron B, Halse A, Nemecek E, Wilmarth PA, Marks DL, Chang BH, Horton T, Kurre P. Extracellular vesicles impose quiescence on residual hematopoietic stem cells in the leukemic niche. EMBO Rep 2019; 20:e47546. [PMID: 31267709 PMCID: PMC6607014 DOI: 10.15252/embr.201847546] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/03/2019] [Accepted: 05/13/2019] [Indexed: 01/19/2023] Open
Abstract
Progressive remodeling of the bone marrow microenvironment is recognized as an integral aspect of leukemogenesis. Expanding acute myeloid leukemia (AML) clones not only alter stroma composition, but also actively constrain hematopoiesis, representing a significant source of patient morbidity and mortality. Recent studies revealed the surprising resistance of long-term hematopoietic stem cells (LT-HSC) to elimination from the leukemic niche. Here, we examine the fate and function of residual LT-HSC in the BM of murine xenografts with emphasis on the role of AML-derived extracellular vesicles (EV). AML-EV rapidly enter HSC, and their trafficking elicits protein synthesis suppression and LT-HSC quiescence. Mechanistically, AML-EV transfer a panel of miRNA, including miR-1246, that target the mTOR subunit Raptor, causing ribosomal protein S6 hypo-phosphorylation, which in turn impairs protein synthesis in LT-HSC. While HSC functionally recover from quiescence upon transplantation to an AML-naive environment, they maintain relative gains in repopulation capacity. These phenotypic changes are accompanied by DNA double-strand breaks and evidence of a sustained DNA-damage response. In sum, AML-EV contribute to niche-dependent, reversible quiescence and elicit persisting DNA damage in LT-HSC.
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MESH Headings
- Animals
- Cell Line, Tumor
- Cells, Cultured
- DNA Breaks, Double-Stranded
- Extracellular Vesicles/metabolism
- Female
- Hematopoietic Stem Cells/metabolism
- Hematopoietic Stem Cells/pathology
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Mice
- Mice, Inbred C57BL
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Regulatory-Associated Protein of mTOR/genetics
- Regulatory-Associated Protein of mTOR/metabolism
- Ribosomal Protein S6/genetics
- Stem Cell Niche
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Affiliation(s)
- Sherif Abdelhamed
- Department of PediatricsPapé Family Pediatric Research InstituteOregon Health & Science UniversityPortlandORUSA
- Knight Cancer InstituteOregon Health & Science UniversityPortlandORUSA
| | - John T Butler
- Department of PediatricsPapé Family Pediatric Research InstituteOregon Health & Science UniversityPortlandORUSA
- Department of Biomedical EngineeringOregon Health & Science UniversityPortlandORUSA
| | - Ben Doron
- Department of PediatricsPapé Family Pediatric Research InstituteOregon Health & Science UniversityPortlandORUSA
| | - Amber Halse
- Department of PediatricsPapé Family Pediatric Research InstituteOregon Health & Science UniversityPortlandORUSA
| | - Eneida Nemecek
- Department of PediatricsPapé Family Pediatric Research InstituteOregon Health & Science UniversityPortlandORUSA
- Knight Cancer InstituteOregon Health & Science UniversityPortlandORUSA
| | - Phillip A Wilmarth
- Department of Biochemistry and Molecular BiologyOregon Health & Science UniversityPortlandORUSA
- Proteomics Shared ResourcesOregon Health & Science UniversityPortlandORUSA
| | - Daniel L Marks
- Department of PediatricsPapé Family Pediatric Research InstituteOregon Health & Science UniversityPortlandORUSA
- Knight Cancer InstituteOregon Health & Science UniversityPortlandORUSA
- Brenden‐Colson Center for Pancreatic CareOregon Health & Science UniversityPortlandORUSA
| | - Bill H Chang
- Department of PediatricsPapé Family Pediatric Research InstituteOregon Health & Science UniversityPortlandORUSA
- Knight Cancer InstituteOregon Health & Science UniversityPortlandORUSA
| | - Terzah Horton
- Texas Children's Cancer and Hematology CentersBaylor College of MedicineHoustonTXUSA
| | - Peter Kurre
- Children's Hospital of PhiladelphiaComprehensive Bone Marrow Failure CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
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28
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Wakeham CM, Wilmarth PA, Cunliffe JM, Klimek JE, Ren G, David LL, Morgans CW. Identification of PKCα-dependent phosphoproteins in mouse retina. J Proteomics 2019; 206:103423. [PMID: 31255707 DOI: 10.1016/j.jprot.2019.103423] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 12/11/2022]
Abstract
Adjusting to a wide range of light intensities is an essential feature of retinal rod bipolar cell (RBC) function. While persuasive evidence suggests this modulation involves phosphorylation by protein kinase C-alpha (PKCα), the targets of PKCα phosphorylation in the retina have not been identified. PKCα activity and phosphorylation in RBCs was examined by immunofluorescence confocal microscopy using a conformation-specific PKCα antibody and antibodies to phosphorylated PKC motifs. PKCα activity was dependent on light and expression of TRPM1, and RBC dendrites were the primary sites of light-dependent phosphorylation. PKCα-dependent retinal phosphoproteins were identified using a phosphoproteomics approach to compare total protein and phosphopeptide abundance between phorbol ester-treated wild type and PKCα knockout (PKCα-KO) mouse retinas. Phosphopeptide mass spectrometry identified over 1100 phosphopeptides in mouse retina, with 12 displaying significantly greater phosphorylation in WT compared to PKCα-KO samples. The differentially phosphorylated proteins fall into the following functional groups: cytoskeleton/trafficking (4 proteins), ECM/adhesion (2 proteins), signaling (2 proteins), transcriptional regulation (3 proteins), and homeostasis/metabolism (1 protein). Two strongly differentially expressed phosphoproteins, BORG4 and TPBG, were localized to the synaptic layers of the retina, and may play a role in PKCα-dependent modulation of RBC physiology. Data are available via ProteomeXchange with identifier PXD012906. SIGNIFICANCE: Retinal rod bipolar cells (RBCs), the second-order neurons of the mammalian rod visual pathway, are able to modulate their sensitivity to remain functional across a wide range of light intensities, from starlight to daylight. Evidence suggests that this modulation requires the serine/threonine kinase, PKCα, though the specific mechanism by which PKCα modulates RBC physiology is unknown. This study examined PKCα phosophorylation patterns in mouse rod bipolar cells and then used a phosphoproteomics approach to identify PKCα-dependent phosphoproteins in the mouse retina. A small number of retinal proteins showed significant PKCα-dependent phosphorylation, including BORG4 and TPBG, suggesting a potential contribution to PKCα-dependent modulation of RBC physiology.
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Affiliation(s)
- Colin M Wakeham
- Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA
| | - Jennifer M Cunliffe
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA
| | - John E Klimek
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA
| | - Gaoying Ren
- Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR 97239, USA; Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Catherine W Morgans
- Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA.
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29
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Zhao Y, Wilmarth PA, Cheng C, Limi S, Fowler VM, Zheng D, David LL, Cvekl A. Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers. Exp Eye Res 2019; 179:32-46. [PMID: 30359574 PMCID: PMC6360118 DOI: 10.1016/j.exer.2018.10.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/31/2018] [Accepted: 10/20/2018] [Indexed: 12/21/2022]
Abstract
Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular compositions of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein compositions between the lens epithelium and fibers, we employed tandem mass spectrometry (2D-LC/MS) analysis of microdissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular processes and subcellular localizations, were adapted for the lens. Expression levels of both epithelial and fiber proteomes were compared with whole lens proteome and mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins (e.g. Carhsp1), translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal [e.g. non-muscle myosin IIA heavy chain (Myh9) and βB2-spectrin (Sptbn2)] and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown functions in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets represent the first mouse lens epithelium and fiber cell proteomes, establish comparative analyses of protein and RNA-Seq data, and characterize the major proteome remodeling required to form the mature lens fiber cells.
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Affiliation(s)
- Yilin Zhao
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Phillip A Wilmarth
- Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Catherine Cheng
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Saima Limi
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Velia M Fowler
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deyou Zheng
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Neurology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Larry L David
- Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Ales Cvekl
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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30
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Smith JR, David LL, Appukuttan B, Wilmarth PA. Angiogenic and Immunologic Proteins Identified by Deep Proteomic Profiling of Human Retinal and Choroidal Vascular Endothelial Cells: Potential Targets for New Biologic Drugs. Am J Ophthalmol 2018; 193:197-229. [PMID: 29559410 PMCID: PMC6109601 DOI: 10.1016/j.ajo.2018.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 03/06/2018] [Indexed: 12/19/2022]
Abstract
PURPOSE Diseases that involve retinal or choroidal vascular endothelial cells are leading causes of vision loss: age-related macular degeneration, retinal ischemic vasculopathies, and noninfectious posterior uveitis. Proteins differentially expressed by these endothelial cell populations are potential drug targets. We used deep proteomic profiling to define the molecular phenotype of human retinal and choroidal endothelial cells at the protein level. METHODS Retinal and choroidal vascular endothelial cells were separately isolated from 5 human eye pairs by selection on CD31. Total protein was extracted and digested, and peptide fractions were analyzed by reverse-phase liquid chromatography tandem mass spectrometry. Peptide sequences were assigned to fragment ion spectra, and proteins were inferred from openly accessible protein databases. Protein abundance was determined by spectral counting. Publicly available software packages were used to identify proteins that were differentially expressed between human retinal and choroidal endothelial cells, and to classify proteins that were highly abundant in each endothelial cell population. RESULTS Human retinal and/or choroidal vascular endothelial cells expressed 5042 nonredundant proteins. Setting the differential expression false discovery rate at 0.05, 498 proteins of 3454 quantifiable proteins (14.4%) with minimum mean spectral counts of 2.5 were differentially abundant in the 2 cell populations. Retinal and choroidal endothelial cells were enriched in angiogenic proteins, and retinal endothelial cells were also enriched in immunologic proteins. CONCLUSIONS This work describes the different protein expression profiles of human retinal and choroidal vascular endothelial cells, and provides multiple candidates for further study as novel treatments or drug targets for posterior eye diseases. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.
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Affiliation(s)
- Justine R Smith
- Flinders University, Adelaide, Australia; Oregon Health & Science University, Portland, Oregon, USA.
| | - Larry L David
- Flinders University, Adelaide, Australia; Oregon Health & Science University, Portland, Oregon, USA
| | - Binoy Appukuttan
- Flinders University, Adelaide, Australia; Oregon Health & Science University, Portland, Oregon, USA
| | - Phillip A Wilmarth
- Flinders University, Adelaide, Australia; Oregon Health & Science University, Portland, Oregon, USA
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31
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Plubell DL, Fenton AM, Wilmarth PA, Bergstrom P, Zhao Y, Minnier J, Heinecke JW, Yang X, Pamir N. GM-CSF driven myeloid cells in adipose tissue link weight gain and insulin resistance via formation of 2-aminoadipate. Sci Rep 2018; 8:11485. [PMID: 30065264 PMCID: PMC6068153 DOI: 10.1038/s41598-018-29250-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023] Open
Abstract
In a GM-CSF driven myeloid cell deficient mouse model (Csf2−/−) that has preserved insulin sensitivity despite increased adiposity, we used unbiased three-dimensional integration of proteome profiles, metabolic profiles, and gene regulatory networks to understand adipose tissue proteome-wide changes and their metabolic implications. Multi-dimensional liquid chromatography mass spectrometry and extended multiplex mass labeling was used to analyze proteomes of epididymal adipose tissues isolated from Csf2+/+ and Csf2−/− mice that were fed low fat, high fat, or high fat plus cholesterol diets for 8 weeks. The metabolic health (as measured by body weight, adiposity, plasma fasting glucose, insulin, triglycerides, phospholipids, total cholesterol levels, and glucose and insulin tolerance tests) deteriorated with diet for both genotypes, while mice lacking Csf2 were protected from insulin resistance. Regardless of diet, 30 mostly mitochondrial, branch chain amino acids (BCAA), and lysine metabolism proteins were altered between Csf2−/− and Csf2+/+ mice (FDR < 0.05). Lack of GM-CSF driven myeloid cells lead to reduced adipose tissue 2-oxoglutarate dehydrogenase complex (DHTKD1) levels and subsequent increase in plasma 2-aminoadipate (2-AA) levels, both of which are reported to correlate with insulin resistance. Tissue DHTKD1 levels were >4-fold upregulated and plasma 2-AA levels were >2 fold reduced in Csf2−/− mice (p < 0.05). GM-CSF driven myeloid cells link peripheral insulin sensitivity to adiposity via lysine metabolism involving DHTKD1/2-AA axis in a diet independent manner.
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Affiliation(s)
- Deanna L Plubell
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alexandra M Fenton
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Paige Bergstrom
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Jessica Minnier
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jay W Heinecke
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Nathalie Pamir
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA.
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32
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Vranka JA, Staverosky JA, Reddy AP, Wilmarth PA, David LL, Acott TS, Russell P, Raghunathan VK. Biomechanical Rigidity and Quantitative Proteomics Analysis of Segmental Regions of the Trabecular Meshwork at Physiologic and Elevated Pressures. Invest Ophthalmol Vis Sci 2018; 59:246-259. [PMID: 29340639 PMCID: PMC5770183 DOI: 10.1167/iovs.17-22759] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Purpose The extracellular matrix (ECM) of the trabecular meshwork (TM) modulates resistance to aqueous humor outflow, thereby regulating IOP. Glaucoma, a leading cause of irreversible blindness worldwide, is associated with changes in the ECM of the TM. The elastic modulus of glaucomatous TM is larger than age-matched normal TM; however, the biomechanical properties of segmental low (LF) and high flow (HF) TM regions and their response to elevated pressure, are unknown. Methods We perfused human anterior segments at two pressures using an ex vivo organ culture system. After extraction, we measured the elastic modulus of HF and LF TM regions by atomic force microscopy and quantitated protein differences by proteomics analyses. Results The elastic modulus of LF regions was 2.3-fold larger than HF regions at physiological (1×) pressure, and 7.4-fold or 3.5-fold larger than HF regions at elevated (2×) pressure after 24 or 72 hours, respectively. Using quantitative proteomics, comparisons were made between HF and LF regions at 1× or 2× pressure. Significant ECM protein differences were observed between LF and HF regions perfused at 2×, and between HF regions at 1× compared to 2× pressures. Decorin, TGF-β–induced protein, keratocan, lumican, dermatopontin, and thrombospondin 4 were common differential candidates in both comparisons. Conclusions These data show changes in biomechanical properties of segmental regions within the TM in response to elevated pressure, and levels of specific ECM proteins. Further studies are needed to determine whether these ECM proteins are specifically involved in outflow resistance and IOP homeostasis.
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Affiliation(s)
- Janice A Vranka
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Julia A Staverosky
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States
| | - Ashok P Reddy
- Proteomics Shared Resources, Oregon Health & Science University, Portland, Oregon, United States
| | - Phillip A Wilmarth
- Proteomics Shared Resources, Oregon Health & Science University, Portland, Oregon, United States.,Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States
| | - Larry L David
- Proteomics Shared Resources, Oregon Health & Science University, Portland, Oregon, United States.,Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States
| | - Ted S Acott
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States.,Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States
| | - Paul Russell
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, United States
| | - Vijay Krishna Raghunathan
- Department of Basic Sciences, The Ocular Surface Institute, College of Optometry, University of Houston, Houston, Texas, United States.,Department of Biomedical Engineering, Cullen College of Engineering, University of Houston, Houston, Texas, United States
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33
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Plubell D, Predazzi I, McKelvey J, Clarke J, Letaw J, Raboin MJ, Wilmarth PA, Curran J, Fazio S, Pamir N, Vinson A. Abstract 180: Missense Mutations in ABCA1 and CETP Associate with Changes in the HDL Proteome in Primate Half-Sibs Discordant for HDL Cholesterol Levels. Arterioscler Thromb Vasc Biol 2018. [DOI: 10.1161/atvb.38.suppl_1.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
HDL protein composition and corresponding function may impact cardiovascular disease risk. Identifying genetic variation that influences the HDL proteome may reveal modifiable HDL functions that impact this risk. We studied genetic determinants of the HDL proteome in a cohort of rhesus macaques enriched for extreme HDL cholesterol levels (HDL-c). We selected macaques from 2 distinct paternal half-sibships, each comprising 8 half-sib pairs matched for age-class and sex, but with large differences in HDL-c (N=22 genomes). HDL was isolated by ultracentrifugation and the protein cargo analyzed by mass spectrometry. Identified peptide sequences were compared to a Swiss-Prot canonical human protein database using BLAST to determine ortholog matches. Among the proteins identified, 64 are among the 229 reported in similar human studies, and 45 of these 64 are among the 95 highest-confidence HDL proteins tracked by the HDL Proteome Watch. We performed deep exome sequencing, and assessed predicted function for all genetic variants in macaques, among 23 genes associated with HDL disorders or variation in HDL-c in humans. We focused on the higher-impact variants most likely to have conserved effects between macaques and humans by proximity (i.e., <10 bp) to known human mutations. This produced a set of 3 missense variants in
ABCA1
associated with Tangier disease and HDL deficiency, and 4 missense variants in
CETP
associated with CETP deficiency, reduced CETP activity, and hyper- and hypoalphalipoproteinemias. Using a measured genotype approach, we tested for association of all 7 variants with adjusted spectral counts, while accounting for age and sex, and applied a false discovery rate (FDR) of 20% to all nominally significant results. After controlling for FDR, 3 missense variants in
ABCA1
were significantly associated with spectral counts for
VCAM1
,
ITGA2
, and
ITGB1
(nominal P-values 0.0005-0.0026), and 4 missense variants in
CETP
were significantly associated with spectral counts for
APOA2
,
APOC3
,
C4BPA
, and
PLTP
(nominal P-values 0.0002-0.0038). While our results require replication, these proteins suggest that changes in HDL-c in macaques are associated with changes in HDL that modulate vascular inflammation, immune response, and particle remodeling.
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Affiliation(s)
| | | | | | | | - John Letaw
- Oregon Health Science Univ, Portland, OR
| | | | | | - Joanne Curran
- South Texas Diabetes and Obesity Institute, Univ. of Texas Rio Grande Valley, Brownsville, TX
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Hulett TW, Jensen SM, Wilmarth PA, Reddy AP, Ballesteros-Merino C, Afentoulis ME, Dubay C, David LL, Fox BA. Coordinated responses to individual tumor antigens by IgG antibody and CD8+ T cells following cancer vaccination. J Immunother Cancer 2018; 6:27. [PMID: 29618380 PMCID: PMC5885379 DOI: 10.1186/s40425-018-0331-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 02/27/2018] [Indexed: 12/11/2022] Open
Abstract
Background One of today’s greatest hurdles for cancer immunotherapy is the absence of information regarding which tumor antigens are already recognized by patients receiving immunotherapies, and whether those therapies then boost or generate an immune response against tumor proteins. For CD8+ T cells in particular, patient-specific immune recognition and responses at the level of individual tumor antigens are rarely characterized. Because of this, some immunologists have turned to serum antibodies as an alternative measure of antigen-specific anti-tumor immunity. In this work, we sought to simultaneously interrogate serum IgG and CD8+ T cell recognition of individual tumor antigens to determine whether antigen-specific serum IgG antibodies provide a window into the behavior of antigen-specific CD8+ T cell responses. Using antibody-based assays to evaluate immune response repertoires and focus T cell antigen exploration could afford substantial advantages for discovering and monitoring the anti-cancer immune responses of patients enrolled on clinical trials. Methods We vaccinated female BALB/c mice with a novel combination of an autophagosome-enriched vaccine derived from 4T1 mammary carcinoma along with poly-I:C adjuvant, then screened serum for IgG binding to arrays of 15mer peptides containing known mutation sites in 4T1. Simultaneously, we primed CD8+ T cell cultures from these same animals with 8-11mer peptides derived from these antigens. These primed T cells were then stimulated to measure recognition of the peptides or live 4T1 cells by IFNγ release. Results Vaccinated animals demonstrate increases in antigen-specific CD8+ T cell recognition of 4T1 tumor cells and peptides. For proteins confirmed in 4T1 cells and vaccine by mass spectrometry, there is a correlation between this increased CD8+ T cell IFNγ release and serum IgG binding to individual peptide antigens. Conclusions These results suggest it is possible to observe some features of a patient’s antigen-specific T cell repertoire via an antibody surrogate, which has implications for tumor antigen discovery and clinical monitoring of antigen-specific anti-tumor immunity. Electronic supplementary material The online version of this article (10.1186/s40425-018-0331-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tyler W Hulett
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, 2N56 North Pavilion, 4805 NE Glisan St., Portland, OR, 97213, USA.,Department of Molecular Microbiology & Immunology, Oregon Health & Science University Portland, Oregon, 97239, USA
| | - Shawn M Jensen
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, 2N56 North Pavilion, 4805 NE Glisan St., Portland, OR, 97213, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University Portland, Oregon, 97239, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health & Science University Portland, Oregon, 97239, USA
| | - Carmen Ballesteros-Merino
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, 2N56 North Pavilion, 4805 NE Glisan St., Portland, OR, 97213, USA
| | - Michael E Afentoulis
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, 2N56 North Pavilion, 4805 NE Glisan St., Portland, OR, 97213, USA
| | - Christopher Dubay
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, 2N56 North Pavilion, 4805 NE Glisan St., Portland, OR, 97213, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health & Science University Portland, Oregon, 97239, USA.,Department of Biochemistry and Molecular Biology, Oregon Health & Science University Portland, Oregon, 97239, USA
| | - Bernard A Fox
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Cancer Institute, 2N56 North Pavilion, 4805 NE Glisan St., Portland, OR, 97213, USA. .,Department of Molecular Microbiology & Immunology, Oregon Health & Science University Portland, Oregon, 97239, USA.
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Rozanov DV, Rozanov ND, Chiotti KE, Reddy A, Wilmarth PA, David LL, Cha SW, Woo S, Pevzner P, Bafna V, Burrows GG, Rantala JK, Levin T, Anur P, Johnson-Camacho K, Tabatabaei S, Munson DJ, Bruno TC, Slansky JE, Kappler JW, Hirano N, Boegel S, Fox BA, Egelston C, Simons DL, Jimenez G, Lee PP, Gray JW, Spellman PT. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. J Proteomics 2018; 176:13-23. [PMID: 29331515 DOI: 10.1016/j.jprot.2018.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/01/2017] [Accepted: 01/04/2018] [Indexed: 12/30/2022]
Abstract
To build a catalog of peptides presented by breast cancer cells, we undertook systematic MHC class I immunoprecipitation followed by elution of MHC class I-loaded peptides in breast cancer cells. We determined the sequence of 3196 MHC class I ligands representing 1921 proteins from a panel of 20 breast cancer cell lines. After removing duplicate peptides, i.e., the same peptide eluted from more than one cell line, the total number of unique peptides was 2740. Of the unique peptides eluted, more than 1750 had been previously identified, and of these, sixteen have been shown to be immunogenic. Importantly, half of these immunogenic peptides were shared between different breast cancer cell lines. MHC class I binding probability was used to plot the distribution of the eluted peptides in accordance with the binding score for each breast cancer cell line. We also determined that the tested breast cancer cells presented 89 mutation-containing peptides and peptides derived from aberrantly translated genes, 7 of which were shared between four or two different cell lines. Overall, the high throughput identification of MHC class I-loaded peptides is an effective strategy for systematic characterization of cancer peptides, and could be employed for design of multi-peptide anticancer vaccines. SIGNIFICANCE By employing proteomic analyses of eluted peptides from breast cancer cells, the current study has built an initial HLA-I-typed antigen collection for breast cancer research. It was also determined that immunogenic epitopes can be identified using established cell lines and that shared immunogenic peptides can be found in different cancer types such as breast cancer and leukemia. Importantly, out of 3196 eluted peptides that included duplicate peptides in different cells 89 peptides either contained mutation in their sequence or were derived from aberrant translation suggesting that mutation-containing epitopes are on the order of 2-3% in breast cancer cells. Finally, our results suggest that interfering with MHC class I function is one of the mechanisms of how tumor cells escape immune system attack.
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Affiliation(s)
- Dmitri V Rozanov
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States.
| | | | - Kami E Chiotti
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
| | - Ashok Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, United States
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, United States
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, United States
| | - Seung W Cha
- Electrical and Computer Engineering, University of California, San Diego, CA, United States
| | - Sunghee Woo
- School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Pavel Pevzner
- The NIH Center for Computational Mass Spectrometry, University of California, San Diego, San Diego, CA, United States
| | - Vineet Bafna
- Computer Science & Engineering, University of California, San Diego, CA, United States
| | - Gregory G Burrows
- Neurology and Biochemistry & Molecular Biology, Oregon Health and Science University, Portland, OR, United States
| | | | - Trevor Levin
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States
| | - Pavana Anur
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
| | - Katie Johnson-Camacho
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
| | - Shaadi Tabatabaei
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
| | - Daniel J Munson
- Department of Immunology & Microbiology, University of Colorado, Denver, CO, United States
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jill E Slansky
- Department of Immunology & Microbiology, University of Colorado, Denver, CO, United States
| | - John W Kappler
- National Jewish Medical and Research Center, Denver, CO, United States
| | - Naoto Hirano
- Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Sebastian Boegel
- University Medical Center, Johannes Gutenberg-University, Mainz, Germany
| | - Bernard A Fox
- Laboratory of Molecular and Tumor Immunology, Chiles Research Institute Providence PDX Medical Center, Portland, OR, United States
| | - Colt Egelston
- City of Hope National Medical Center, Duarte, CA, United States
| | - Diana L Simons
- City of Hope National Medical Center, Duarte, CA, United States
| | - Grecia Jimenez
- City of Hope National Medical Center, Duarte, CA, United States
| | - Peter P Lee
- City of Hope National Medical Center, Duarte, CA, United States
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States; Center for Health & Healing, Oregon Health and Science University, Portland, OR, United States
| | - Paul T Spellman
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
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Whitson JA, Wilmarth PA, Klimek J, Monnier VM, David L, Fan X. Proteomic analysis of the glutathione-deficient LEGSKO mouse lens reveals activation of EMT signaling, loss of lens specific markers, and changes in stress response proteins. Free Radic Biol Med 2017; 113:84-96. [PMID: 28951044 PMCID: PMC5699945 DOI: 10.1016/j.freeradbiomed.2017.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/21/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022]
Abstract
PURPOSE To determine global protein expression changes in the lens of the GSH-deficient LEGSKO mouse model of age-related cataract for comparison with recently published gene expression data obtained by RNA-Seq transcriptome analysis. METHODS Lenses were separated into epithelial and cortical fiber sections, digested with trypsin, and labeled with isobaric tags (10-plex TMTTM). Peptides were analyzed by LC-MS/MS (Orbitrap Fusion) and mapped to the mouse proteome for relative protein quantification. RESULTS 1871 proteins in lens epithelia and 870 proteins in lens fiber cells were quantified. 40 proteins in LEGSKO epithelia, 14 proteins in LEGSKO fiber cells, 22 proteins in buthionine sulfoximine (BSO)-treated LEGSKO epithelia, and 55 proteins in BSO-treated LEGSKO fiber cells had significantly (p<0.05, FDR<0.1) altered protein expression compared to WT controls. HSF4 and MAF transcription factors were the most common upstream regulators of the response to GSH-deficiency. Many detoxification proteins, including aldehyde dehydrogenases, peroxiredoxins, and quinone oxidoreductase, were upregulated but several glutathione S-transferases were downregulated. Several cellular stress response proteins showed regulation changes, including an upregulation of HERPUD1, downregulation of heme oxygenase, and mixed changes in heat shock proteins. NRF2-regulated proteins showed broad upregulation in BSO-treated LEGSKO fiber cells, but not in other groups. Strong trends were seen in downregulation of lens specific proteins, including β- and γ-crystallins, lengsin, and phakinin, and in epithelial-mesenchymal transition (EMT)-related changes. Western blot analysis of LEGSKO lens epithelia confirmed expression changes in several proteins. CONCLUSIONS This dataset confirms at the proteomic level many findings from the recently determined GSH-deficient lens transcriptome and provides new insight into the roles of GSH in the lens, how the lens adapts to oxidative stress, and how GSH affects EMT in the lens.
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Affiliation(s)
- Jeremy A Whitson
- Case Western Reserve University, Department of Pathology, 2301 Cornell Rd, Cleveland, OH 44106, USA
| | - Phillip A Wilmarth
- Oregon Health Sciences University, Department of Biochemistry & Molecular Biology, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA
| | - John Klimek
- Proteomics Shared Resource, Oregon Health & Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA
| | - Vincent M Monnier
- Case Western Reserve University, Department of Pathology, 2301 Cornell Rd, Cleveland, OH 44106, USA; Case Western Reserve University, Department of Biochemistry, 2109 Adelbert Road, Cleveland, OH 44106, USA
| | - Larry David
- Oregon Health Sciences University, Department of Biochemistry & Molecular Biology, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA
| | - Xingjun Fan
- Case Western Reserve University, Department of Pathology, 2301 Cornell Rd, Cleveland, OH 44106, USA.
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Abstract
Purpose The zonule of Zinn (ciliary zonule) is a system of fibers that centers the crystalline lens on the optical axis of the eye. Mutations in zonule components underlie syndromic conditions associated with a broad range of ocular pathologies, including microspherophakia and ectopia lentis. Here, we used HPLC-mass spectrometry to determine the molecular composition of the zonule. Methods Tryptic digests of human and bovine zonular samples were analyzed by HPLC-mass spectrometry. The distribution of selected components was confirmed by immunofluorescence confocal microscopy. In bovine samples, the composition of the equatorial zonule was compared to that of the hyaloid zonule and vitreous humor. Results The 52 proteins common to the zonules of both species accounted for >95% of the zonular protein. Glycoproteins constituted the main structural components, with two proteins, FBN1 and LTBP2, constituting 70%-80% of the protein. Other abundant components were MFAP2, EMILIN-1, and ADAMTSL-6. Lysyl oxidase-like 1, a crosslinking enzyme implicated in collagen and elastin biogenesis, was detected at significant levels. The equatorial and hyaloid zonular samples were compositionally similar to each other, although the hyaloid sample was relatively enriched in the proteoglycan opticin and the fibrillar collagens COL2A1, COL11A1, COL5A2, and COL5A3. Conclusions The zonular proteome was surprisingly complex. In addition to structural components, it contained signaling proteins, protease inhibitors, and crosslinking enzymes. The equatorial and hyaloid zonules were similar in composition, but the latter may form part of a composite structure, the hyaloid membrane, that stabilizes the vitreous face.
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Affiliation(s)
- Alicia De Maria
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Phillip A Wilmarth
- Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, United States
| | - Larry L David
- Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, United States
| | - Steven Bassnett
- Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States
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Plubell DL, Wilmarth PA, Zhao Y, Fenton AM, Minnier J, Reddy AP, Klimek J, Yang X, David LL, Pamir N. Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue. Mol Cell Proteomics 2017; 16:873-890. [PMID: 28325852 DOI: 10.1074/mcp.m116.065524] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/28/2017] [Indexed: 01/17/2023] Open
Abstract
The lack of high-throughput methods to analyze the adipose tissue protein composition limits our understanding of the protein networks responsible for age and diet related metabolic response. We have developed an approach using multiple-dimension liquid chromatography tandem mass spectrometry and extended multiplexing (24 biological samples) with tandem mass tags (TMT) labeling to analyze proteomes of epididymal adipose tissues isolated from mice fed either low or high fat diet for a short or a long-term, and from mice that aged on low versus high fat diets. The peripheral metabolic health (as measured by body weight, adiposity, plasma fasting glucose, insulin, triglycerides, total cholesterol levels, and glucose and insulin tolerance tests) deteriorated with diet and advancing age, with long-term high fat diet exposure being the worst. In response to short-term high fat diet, 43 proteins representing lipid metabolism (e.g. AACS, ACOX1, ACLY) and red-ox pathways (e.g. CPD2, CYP2E, SOD3) were significantly altered (FDR < 10%). Long-term high fat diet significantly altered 55 proteins associated with immune response (e.g. IGTB2, IFIT3, LGALS1) and rennin angiotensin system (e.g. ENPEP, CMA1, CPA3, ANPEP). Age-related changes on low fat diet significantly altered only 18 proteins representing mainly urea cycle (e.g. OTC, ARG1, CPS1), and amino acid biosynthesis (e.g. GMT, AKR1C6). Surprisingly, high fat diet driven age-related changes culminated with alterations in 155 proteins involving primarily the urea cycle (e.g. ARG1, CPS1), immune response/complement activation (e.g. C3, C4b, C8, C9, CFB, CFH, FGA), extracellular remodeling (e.g. EFEMP1, FBN1, FBN2, LTBP4, FERMT2, ECM1, EMILIN2, ITIH3) and apoptosis (e.g. YAP1, HIP1, NDRG1, PRKCD, MUL1) pathways. Using our adipose tissue tailored approach we have identified both age-related and high fat diet specific proteomic signatures highlighting a pronounced involvement of arginine metabolism in response to advancing age, and branched chain amino acid metabolism in early response to high fat feeding. Data are available via ProteomeXchange with identifier PXD005953.
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Affiliation(s)
- Deanna L Plubell
- From the ‡Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon
| | - Phillip A Wilmarth
- §Proteomics Shared Resources, Oregon Health & Sciences University, Portland, Oregon
| | - Yuqi Zhao
- ¶Department of Integrative Biology and Physiology, University of California, Los Angeles, California
| | - Alexandra M Fenton
- From the ‡Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon
| | - Jessica Minnier
- From the ‡Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon
| | - Ashok P Reddy
- §Proteomics Shared Resources, Oregon Health & Sciences University, Portland, Oregon
| | - John Klimek
- §Proteomics Shared Resources, Oregon Health & Sciences University, Portland, Oregon
| | - Xia Yang
- ¶Department of Integrative Biology and Physiology, University of California, Los Angeles, California
| | - Larry L David
- §Proteomics Shared Resources, Oregon Health & Sciences University, Portland, Oregon
| | - Nathalie Pamir
- From the ‡Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon;
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Abstract
Characterization of proteins that mediate mechanotransduction by hair cells, the sensory cells of the inner ear, is hampered by the scarcity of these cells and their sensory organelle, the hair bundle. Mass spectrometry, with its high sensitivity and identification precision, is the ideal method for determining which proteins are present in bundles and what proteins they interact with. We describe here the isolation of mouse hair bundles, as well as preparation of bundle protein samples for mass spectrometry. We also describe protocols for data-dependent (shotgun) and parallel reaction monitoring (targeted) mass spectrometry that allow us to identify and quantify proteins of the hair bundle. These sensitive methods are particularly useful for comparing proteomes of wild-type mice and mice with deafness mutations affecting hair-bundle proteins.
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Affiliation(s)
- J F Krey
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR, United States; Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - P A Wilmarth
- Oregon Health & Science University, Portland, OR, United States
| | - L L David
- Oregon Health & Science University, Portland, OR, United States
| | - P G Barr-Gillespie
- Oregon Hearing Research Center, Oregon Health & Science University, Portland, OR, United States; Vollum Institute, Oregon Health & Science University, Portland, OR, United States; Oregon Health & Science University, Portland, OR, United States.
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Chen Y, Sagar V, Len HS, Peterson K, Fan J, Mishra S, McMurtry J, Wilmarth PA, David LL, Wistow G. γ-Crystallins of the chicken lens: remnants of an ancient vertebrate gene family in birds. FEBS J 2016; 283:1516-30. [PMID: 26913478 DOI: 10.1111/febs.13689] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/02/2016] [Accepted: 02/18/2016] [Indexed: 11/30/2022]
Abstract
γ-Crystallins, abundant proteins of vertebrate lenses, were thought to be absent from birds. However, bird genomes contain well-conserved genes for γS- and γN-crystallins. Although expressed sequence tag analysis of chicken eye found no transcripts for these genes, RT-PCR detected spliced transcripts for both genes in chicken lens, with lower levels in cornea and retina/retinal pigment epithelium. The level of mRNA for γS in chicken lens was relatively very low even though the chicken crygs gene promoter had lens-preferred activity similar to that of mouse. Chicken γS was detected by a peptide antibody in lens, but not in other ocular tissues. Low levels of γS and γN proteins were detected in chicken lens by shotgun mass spectroscopy. Water-soluble and water-insoluble lens fractions were analyzed and 1934 proteins (< 1% false discovery rate) were detected, increasing the known chicken lens proteome 30-fold. Although chicken γS is well conserved in protein sequence, it has one notable difference in leucine 16, replacing a surface glutamine conserved in other γ-crystallins, possibly affecting solubility. However, L16 and engineered Q16 versions were both highly soluble and had indistinguishable circular dichroism, tryptophan fluorescence and heat stability (melting temperature Tm ~ 65 °C) profiles. L16 has been present in birds for over 100 million years and may have been adopted for a specific protein interaction in the bird lens. However, evolution has clearly reduced or eliminated expression of ancestral γ-crystallins in bird lenses. The conservation of genes for γS- and γN-crystallins suggests they may have been preserved for reasons unrelated to the bulk properties of the lens.
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Affiliation(s)
- Yingwei Chen
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vatsala Sagar
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hoay-Shuen Len
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katherine Peterson
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianguo Fan
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sanghamitra Mishra
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - John McMurtry
- USDA, ARS, Southern Plains Area, East College Station, TX, USA
| | - Phillip A Wilmarth
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Larry L David
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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Burrows GG, Van't Hof W, Reddy AP, Wilmarth PA, David LL, Raber A, Bogaerts A, Timmerman L, Pinxteren J, Roobrouck VD, Deans RJ, Maziarz RT. Solution-Phase Crosstalk and Regulatory Interactions Between Multipotent Adult Progenitor Cells and Peripheral Blood Mononuclear Cells. Stem Cells Transl Med 2015; 4:1436-49. [PMID: 26494783 PMCID: PMC4675500 DOI: 10.5966/sctm.2014-0225] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 08/03/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Multipotent adult progenitor cells (MAPCs) are adult adherent stromal stem cells currently being assessed in clinical trials for acute graft versus host disease with demonstrated immunomodulatory capabilities and the potential to ameliorate detrimental autoimmune and inflammation-related processes. Anti-CD3/anti-CD28 (3/28) activation of T cells within the peripheral blood mononuclear cell (PBMC) compartment was performed in the presence or absence of MAPCs. Liquid chromatography-coupled tandem mass spectrometry was used to characterize the differential secretion of proteins, and transcriptional profiling was used to monitor mRNA expression changes in both cell populations. Overall, 239 secreted and/or ectodomain-shed proteins were detected in the secretomes of PBMCs and MAPCs. In addition, 3/28 activation of PBMCs induced differential expression of 2,925 genes, and 22% of these transcripts were differentially expressed on exposure to MAPCs in Transwell. MAPCs exposed to 3/28-activated PBMCs showed differential expression of 1,247 MAPC genes. Crosstalk was demonstrated by reciprocal transcriptional regulation. Secretome proteins and transcriptional signatures were used to predict molecular activities by which MAPCs could dampen local and systemic inflammatory responses. These data support the hypothesis that MAPCs block PBMC proliferation via cell cycle arrest coupled to metabolic stress in the form of tryptophan depletion, resulting in GCN2 kinase activation, downstream signaling, and inhibition of cyclin D1 translation. These data also provide a plausible explanation for the immune privilege reported with administration of donor MAPCs. Although most components of the major histocompatibility complex class II antigen presentation pathway were markedly transcriptionally upregulated, cell surface expression of human leukocyte antigen-DR is minimal on MAPCs exposed to 3/28-activated PBMCs. SIGNIFICANCE This study documents experiments quantifying solution-phase crosstalk between multipotent adult progenitor cells (MAPCs) and peripheral blood mononuclear cells. The secretome and transcriptional changes quantified suggest mechanisms by which MAPCs are hypothesized to provide both local and systemic immunoregulation of inflammation. The potential impact of these studies includes development of a robust experimental framework to be used for preclinical evaluation of the specific mechanisms by which beneficial effects are obtained after treatment of patients with MAPCs.
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Affiliation(s)
- Gregory G Burrows
- Center for Hematologic Malignancies, Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA Department of Neurology, Oregon Health and Science University, Portland, Oregon, USA Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Wouter Van't Hof
- Regenerative Medicine Program, Athersys Inc., Cleveland, Ohio, USA National Center for Regenerative Medicine, Cleveland, Ohio, USA
| | - Ashok P Reddy
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Phillip A Wilmarth
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Larry L David
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon, USA
| | - Amy Raber
- Regenerative Medicine Program, Athersys Inc., Cleveland, Ohio, USA
| | | | | | | | | | - Robert J Deans
- Regenerative Medicine Program, Athersys Inc., Cleveland, Ohio, USA National Center for Regenerative Medicine, Cleveland, Ohio, USA ReGenesys, Inc., Leuven, Belgium
| | - Richard T Maziarz
- Center for Hematologic Malignancies, Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, USA
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Vanderwerf SM, Buck DC, Wilmarth PA, Sears LM, David LL, Morton DB, Neve KA. Role for Rab10 in Methamphetamine-Induced Behavior. PLoS One 2015; 10:e0136167. [PMID: 26291453 PMCID: PMC4546301 DOI: 10.1371/journal.pone.0136167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/31/2015] [Indexed: 11/18/2022] Open
Abstract
Lipid rafts are specialized, cholesterol-rich membrane compartments that help to organize transmembrane signaling by restricting or promoting interactions with subsets of the cellular proteome. The hypothesis driving this study was that identifying proteins whose relative abundance in rafts is altered by the abused psychostimulant methamphetamine would contribute to fully describing the pathways involved in acute and chronic effects of the drug. Using a detergent-free method for preparing rafts from rat brain striatal membranes, we identified density gradient fractions enriched in the raft protein flotillin but deficient in calnexin and the transferrin receptor, markers of non-raft membranes. Dopamine D1- and D2-like receptor binding activity was highly enriched in the raft fractions, but pretreating rats with methamphetamine (2 mg/kg) once or repeatedly for 11 days did not alter the distribution of the receptors. LC-MS analysis of the protein composition of raft fractions from rats treated once with methamphetamine or saline identified methamphetamine-induced changes in the relative abundance of 23 raft proteins, including the monomeric GTP-binding protein Rab10, whose abundance in rafts was decreased 2.1-fold by acute methamphetamine treatment. Decreased raft localization was associated with a selective decrease in the abundance of Rab10 in a membrane fraction that includes synaptic vesicles and endosomes. Inhibiting Rab10 activity by pan-neuronal expression of a dominant-negative Rab10 mutant in Drosophila melanogaster decreased methamphetamine-induced activity and mortality and decreased caffeine-stimulated activity but not mortality, whereas inhibiting Rab10 activity selectively in cholinergic neurons had no effect. These results suggest that activation and redistribution of Rab10 is critical for some of the behavioral effects of psychostimulants.
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Affiliation(s)
- Scott M. Vanderwerf
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon, United States of America
- Department of Integrative Biosciences, Oregon Health & Science University, Portland, Oregon, United States of America
| | - David C. Buck
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Phillip A. Wilmarth
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Leila M. Sears
- Department of Integrative Biosciences, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Larry L. David
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - David B. Morton
- Department of Integrative Biosciences, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Kim A. Neve
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon, United States of America
- Research Service, VA Portland Health Care System, Portland, Oregon, United States of America
- * E-mail:
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43
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Huan J, Hornick NI, Goloviznina NA, Kamimae-Lanning AN, David LL, Wilmarth PA, Mori T, Chevillet JR, Narla A, Roberts CT, Loriaux MM, Chang BH, Kurre P. Coordinate regulation of residual bone marrow function by paracrine trafficking of AML exosomes. Leukemia 2015; 29:2285-95. [PMID: 26108689 DOI: 10.1038/leu.2015.163] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/19/2015] [Accepted: 06/11/2015] [Indexed: 12/20/2022]
Abstract
We recently demonstrated that acute myeloid leukemia (AML) cell lines and patient-derived blasts release exosomes that carry RNA and protein; following an in vitro transfer, AML exosomes produce proangiogenic changes in bystander cells. We reasoned that paracrine exosome trafficking may have a broader role in shaping the leukemic niche. In a series of in vitro studies and murine xenografts, we demonstrate that AML exosomes downregulate critical retention factors (Scf, Cxcl12) in stromal cells, leading to hematopoietic stem and progenitor cell (HSPC) mobilization from the bone marrow. Exosome trafficking also regulates HSPC directly, and we demonstrate declining clonogenicity, loss of CXCR4 and c-Kit expression, and the consistent repression of several hematopoietic transcription factors, including c-Myb, Cebp-β and Hoxa-9. Additional experiments using a model of extramedullary AML or direct intrafemoral injection of purified exosomes reveal that the erosion of HSPC function can occur independent of direct cell-cell contact with leukemia cells. Finally, using a novel multiplex proteomics technique, we identified candidate pathways involved in the direct exosome-mediated modulation of HSPC function. In aggregate, this work suggests that AML exosomes participate in the suppression of residual hematopoietic function that precedes widespread leukemic invasion of the bone marrow directly and indirectly via stromal components.
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Affiliation(s)
- J Huan
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA
| | - N I Hornick
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA
| | - N A Goloviznina
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA
| | - A N Kamimae-Lanning
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA
| | - L L David
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, USA
| | - P A Wilmarth
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, USA
| | - T Mori
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - J R Chevillet
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - A Narla
- Division of Hematology/Oncology, Stanford University, Palo Alto, CA, USA
| | - C T Roberts
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Department of Medicine, Oregon Health & Science University, Portland, OR, USA.,Oregon National Primate Research Center, Beaverton, OR, USA
| | - M M Loriaux
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - B H Chang
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - P Kurre
- Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA.,Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR, USA.,Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
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44
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Lampi KJ, Wilmarth PA, Murray MR, David LL. Lens β-crystallins: the role of deamidation and related modifications in aging and cataract. Prog Biophys Mol Biol 2014; 115:21-31. [PMID: 24613629 DOI: 10.1016/j.pbiomolbio.2014.02.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 11/26/2022]
Abstract
Crystallins are the major proteins in the lens of the eye and function to maintain transparency of the lens. Of the human crystallins, α, β, and γ, the β-crystallins remain the most elusive in their structural significance due to their greater number of subunits and possible oligomer formations. The β-crystallins are also heavily modified during aging. This review focuses on the functional significance of deamidation and the related modifications of racemization and isomerization, the major modifications in β-crystallins of the aged human lens. Elucidating the role of these modifications in cataract formation has been slow, because they are analytically among the most difficult post-translational modifications to study. Recent results suggest that many amides deamidate to similar extent in normal aged and cataractous lenses, while others may undergo greater deamidation in cataract. Mimicking deamidation at critical structural regions induces structural changes that disrupt the stability of the β-crystallins and lead to their aggregation in vitro. Deamidations at the surface disrupt interactions with other crystallins. Additionally, the α-crystallin chaperone is unable to completely prevent deamidated β-crystallins from insolubilization. Therefore, deamidation of β-crystallins may enhance their precipitation and light scattering in vivo contributing to cataract formation. Future experiments are needed to quantify differences in deamidation rates at all Asn and Gln residues within crystallins from aged and cataractous lenses, as well as racemization and isomerization which potentially perturb protein structure greater than deamidation alone. Quantitative data is greatly needed to investigate the importance of these major age-related modifications in cataract formation.
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Affiliation(s)
- Kirsten J Lampi
- Oregon Health & Science University, Integrative Biosciences, 611 SW Campus Drive, Portland, OR 97239, USA.
| | - Phillip A Wilmarth
- Oregon Health & Science University, Biochemistry and Molecular Biology, 3181 Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Matthew R Murray
- Oregon Health & Science University, Integrative Biosciences, 611 SW Campus Drive, Portland, OR 97239, USA
| | - Larry L David
- Oregon Health & Science University, Biochemistry and Molecular Biology, 3181 Sam Jackson Park Road, Portland, OR 97239-3098, USA
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45
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Shang F, Wilmarth PA, Chang ML, Liu K, David LL, Caceres MA, Wawrousek E, Taylor A. Newborn mouse lens proteome and its alteration by lysine 6 mutant ubiquitin. J Proteome Res 2014; 13:1177-89. [PMID: 24450463 PMCID: PMC3993935 DOI: 10.1021/pr400801v] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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Ubiquitin is a tag that often initiates
degradation of proteins by
the proteasome in the ubiquitin proteasome system. Targeted expression
of K6W mutant ubiquitin (K6W-Ub) in the lens results in defects in
lens development and cataract formation, suggesting critical functions
for ubiquitin in lens. To study the developmental processes that require
intact ubiquitin, we executed the most extensive characterization
of the lens proteome to date. We quantified lens protein expression
changes in multiple replicate pools of P1 wild-type and K6W-Ub-expressing
mouse lenses. Lens proteins were digested with trypsin, peptides were
separated using strong cation exchange and reversed-phase liquid chromatography,
and tandem mass (MS/MS) spectra were collected with a linear ion trap.
Transgenic mice that expressed low levels of K6W-Ub (low expressers)
had normal, clear lenses at birth, whereas the lenses that expressed
high levels of K6W-Ub (higher expressers) had abnormal lenses and
cataracts at birth. A total of 2052 proteins were identified, of which
996 were reliably quantified and compared between wild-type and K6W-Ub
transgenic mice. Consistent with a delayed developmental program,
fiber-cell-specific proteins, such as γ-crystallins (γA,
γB, γC, and γE), were down-regulated in K6W-Ub higher
expressers. Up-regulated proteins were involved in energy metabolism,
signal transduction, and proteolysis. The K6W-Ub low expressers exhibited
delayed onset and milder cataract consistent with smaller changes
in protein expression. Because lens protein expression changes occurred
prior to lens morphological abnormalities and cataract formation in
K6W-Ub low expressers, it appears that expression of K6W-Ub sets in
motion a process of altered protein expression that results in developmental
defects and cataract.
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Affiliation(s)
- Fu Shang
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University , 711 Washington Steet, Boston, Massachusetts 02111, United States
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46
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Krey JF, Wilmarth PA, Shin JB, Klimek J, Sherman NE, Jeffery ED, Choi D, David LL, Barr-Gillespie PG. Accurate label-free protein quantitation with high- and low-resolution mass spectrometers. J Proteome Res 2013; 13:1034-1044. [PMID: 24295401 DOI: 10.1021/pr401017h] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Label-free quantitation of proteins analyzed by tandem mass spectrometry uses either integrated peak intensity from the parent-ion mass analysis (MS1) or features from fragment-ion analysis (MS2), such as spectral counts or summed fragment-ion intensity. We directly compared MS1 and MS2 quantitation by analyzing human protein standards diluted into Escherichia coli extracts on an Orbitrap mass spectrometer. We found that summed MS2 intensities were nearly as accurate as integrated MS1 intensities, and both outperformed MS2 spectral counting in accuracy and linearity. We compared these results to those obtained from two low-resolution ion-trap mass spectrometers; summed MS2 intensities from LTQ and LTQ Velos instruments were similar in accuracy to those from the Orbitrap. Data from all three instruments are available via ProteomeXchange with identifier PXD000602. Abundance measurements using MS1 or MS2 intensities had limitations, however. While measured protein concentration was on average well-correlated with the known concentration, there was considerable protein-to-protein variation. Moreover, not all human proteins diluted to a mole fraction of 10(-3) or lower were detected, with a strong falloff below 10(-4) mole fraction. These results show that MS1 and MS2 intensities are simple measures of protein abundance that are on average accurate but should be limited to quantitation of proteins of intermediate to higher fractional abundance.
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Affiliation(s)
- Jocelyn F Krey
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR
| | - Phillip A Wilmarth
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
| | - Jung-Bum Shin
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR
| | - John Klimek
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR
| | - Nicholas E Sherman
- W.M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, VA
| | - Erin D Jeffery
- W.M. Keck Biomedical Mass Spectrometry Lab, University of Virginia, Charlottesville, VA
| | - Dongseok Choi
- Department of Public Health & Preventative Medicine, Oregon Health & Science University, Portland, OR
| | - Larry L David
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR.,Proteomics Shared Resource, Oregon Health & Science University, Portland, OR
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR
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47
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Avenarius MR, Saylor KW, Lundeberg MR, Wilmarth PA, Shin JB, Spinelli KJ, Pagana JM, Andrade L, Kachar B, Choi D, David LL, Barr-Gillespie PG. Correlation of actin crosslinker and capper expression levels with stereocilia growth phases. Mol Cell Proteomics 2013; 13:606-20. [PMID: 24319057 DOI: 10.1074/mcp.m113.033704] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
During development of the chick cochlea, actin crosslinkers and barbed-end cappers presumably influence growth and remodeling of the actin paracrystal of hair cell stereocilia. We used mass spectrometry to identify and quantify major actin-associated proteins of the cochlear sensory epithelium from E14 to E21, when stereocilia widen and lengthen. Tight actin crosslinkers (i.e. fascins, plastins, and espin) are expressed dynamically during cochlear epithelium development between E7 and E21, with FSCN2 replacing FSCN1 and plastins remaining low in abundance. Capping protein, a barbed-end actin capper, is located at stereocilia tips; it is abundant during growth phase II, when stereocilia have ceased elongating and are increasing in diameter. Capping protein levels then decline during growth phase III, when stereocilia reinitiate barbed-end elongation. Although actin crosslinkers are readily detected by electron microscopy in developing chick cochlea stereocilia, quantitative mass spectrometry of stereocilia isolated from E21 chick cochlea indicated that tight crosslinkers are present there in stoichiometric ratios relative to actin that are much lower than their ratios for vestibular stereocilia. These results demonstrate the value of quantitation of global protein expression in chick cochlea during stereocilia development.
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Affiliation(s)
- Matthew R Avenarius
- Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, Portland, Oregon 97239
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48
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Lo JO, Reddy AP, Wilmarth PA, Roberts VHJ, Kinhnarath A, Snyder J, Rincon MP, Gravett MG, Nagalla SR, Pereira LM. Proteomic analysis of cervical vaginal fluid proteins among women in recurrent preterm labor. J Matern Fetal Neonatal Med 2013; 27:1183-8. [PMID: 24102235 DOI: 10.3109/14767058.2013.852172] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Proteomic analysis of four cervical-vaginal fluid (CVF) proteins to identify biomarkers of recurrent preterm birth (rPTB) in at-risk women prior to onset of preterm labor. METHODS Nested case control study from 2007 to 2011 of women with prior spontaneous preterm birth(s) (PTB) who underwent serial CVF sampling. Mass spectrometry analysis was used and ELISA analysis was performed to validate candidates. RESULTS 108 patients were enrolled and 10 cases and 20 gestational age matched controls were analyzed after exclusions. Of 748 CVF proteins identified, 72 had statistically significant (p < 0.05) expression differences and 38 were highly differentially expressed (p < 0.01). Four candidate proteins were abundant and involved in immune/inflammatory response, but ELISA analysis did not confirm altered expression patterns. CONCLUSION The lack of confirmation of potential biomarkers identified by mass spectrometry and ELISA demonstrates the challenges of validating PTB biomarkers and suggests that a panel of biomarkers would improve the predictive value of CVF testing.
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Burrows GG, Van't Hof W, Newell LF, Reddy A, Wilmarth PA, David LL, Raber A, Bogaerts A, Pinxteren J, Deans RJ, Maziarz RT. Dissection of the human multipotent adult progenitor cell secretome by proteomic analysis. Stem Cells Transl Med 2013; 2:745-57. [PMID: 23981727 DOI: 10.5966/sctm.2013-0031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Multipotent adult progenitor cells (MAPCs) are adult adherent stromal stem cells currently being assessed in acute graft versus host disease clinical trials with demonstrated immunomodulatory capabilities and the potential to ameliorate detrimental autoimmune and inflammation-related processes. Our previous studies documented that MAPCs secrete factors that play a role in regulating T-cell activity. Here we expand our studies using a proteomics approach to characterize and quantify MAPC secretome components secreted over 72 hours in vitro under steady-state conditions and in the presence of the inflammatory triggers interferon-γ and lipopolysaccharide, or a tolerogenic CD74 ligand, RTL1000. MAPCs differentially responded to each of the tested stimuli, secreting molecules that regulate the biological activity of the extracellular matrix (ECM), including proteins that make up the ECM itself, proteins that regulate its construction/deconstruction, and proteins that serve to attach and detach growth factors from ECM components for redistribution upon appropriate stimulation. MAPCs secreted a wide array of proteases, some detectable in their zymogen forms. MAPCs also secreted protease inhibitors that would regulate protease activity. MAPCs secreted chemokines and cytokines that could provide molecular guidance cues to various cell types, including neutrophils, macrophages, and T cells. In addition, MAPCs secreted factors involved in maintenance of a homeostatic environment, regulating such diverse programs as innate immunity, angiogenesis/angiostasis, targeted delivery of growth factors, and the matrix-metalloprotease cascade.
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50
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Giblin FJ, David LL, Wilmarth PA, Leverenz VR, Simpanya MF. Shotgun proteomic analysis of S-thiolation sites of guinea pig lens nuclear crystallins following oxidative stress in vivo. Mol Vis 2013; 19:267-80. [PMID: 23401655 PMCID: PMC3566901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/01/2013] [Indexed: 10/30/2022] Open
Abstract
PURPOSE To compare levels of S-glutathiolation and S-cysteinylation occurring at more than 60 cysteine residues of 12 different guinea pig lens water-soluble nuclear crystallins following treatment of the animals with hyperbaric oxygen (HBO). METHODS Guinea pigs (initially 18 months old) were treated 30X (3X per week for 10 weeks) with HBO (2.5 atm 100% O(2) for 2.5 h) as a model to study the formation of nuclear cataract. This treatment produces a moderate increase in lens nuclear light scatter (compared to denser scatter occurring after 80 HBO treatments), with five- to sixfold increases in levels of protein-bound glutathione (PSSG) and protein-bound cysteine (PSSC). Trypsin digests of lens nuclear water-soluble proteins were analyzed with two-dimensional liquid chromatography and mass spectrometry to identify specific cysteine residues binding either glutathione or cysteine. Lens nuclei of age-matched untreated animals were used as controls. RESULTS All major crystallins, except αB, were modified to some extent by either S-glutathiolation or S-cysteinylation. Overall, 72% of the cysteine residues of guinea pig lens nuclear crystallins were shown to be capable of binding glutathione, cysteine, or both molecules. The crystallin with the highest level of modification was βA1/A3 (six of eight -SH groups), and that with the lowest (two of five -SH groups) was βA2. O(2)-induced increases in PSSG levels were 2.8, 2.4, and 4.1 times control for γA-, γB-, and γC-crystallins, respectively. Comparable increases in PSSC levels for the three γ-crystallins were 2.3, 2.7, and 2.4 times control, respectively. βB2-crystallin showed the highest amount of O(2)-induced PSSG formation of any of the crystallins, as well as a substantial level of control PSSG, and nearly all of this was due to a single residue, C67, a site also present in human βB2-crystallin. Overall, 32 of the 44 modified cysteine residues were homologous with the human. CONCLUSIONS This large-scale study successfully identified lens crystallin cysteine residues that bound glutathione and/or cysteine under normal or oxidative stress conditions. The high percentage of protein -SH groups that are modified by S-thiolation in the guinea pig lens nucleus demonstrates the substantial protein sulfhydryl redox buffer capability present in the center of the lens. The results suggest that PSSG and PSSC formation may act to delay O(2)-induced insolubilization of γA-, γB-, and γC-crystallins, and β-crystallins, but with a greater effect on the γ-crystallins at an early stage of oxidative stress. The study has shown that technological approaches are now available to investigate in considerable detail the role of specific lens -SH groups in nuclear cataractogenesis.
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Affiliation(s)
| | - Larry L. David
- Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
| | - Phillip A. Wilmarth
- Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR
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