1
|
Halverson-Kolkind KA, Caputo N, Lampi KJ, Srivastava O, David LL. Measurement of absolute abundance of crystallins in human and αA N101D transgenic mouse lenses using 15N-labeled crystallin standards. Exp Eye Res 2024; 248:110115. [PMID: 39368693 DOI: 10.1016/j.exer.2024.110115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Revised: 09/17/2024] [Accepted: 10/02/2024] [Indexed: 10/07/2024]
Abstract
Stable isotope labeled standards of all major human lens crystallins were created to measure the abundance of lens endogenous crystallins from birth to adulthood. All major human crystallins (αA, αB, βA2, βA3/A1, βA4, βB1, βB2, βB3, γA, γB, γC, γD, γS) were cloned with N-terminal 6 x His tagged SUMO for ease of purification and the ability to generate natural N-termini by SUMO protease cleavage when producing crystallins for structure/function studies. They were then expressed in 15N-enriched media, quantified by mass spectrometry, and mixed in proportions found in young human lens to act as an artificial lens standard. The absolute quantification method was tested using soluble protein from 5-day, 23-day, 18-month, and 18-year-old human lenses spiked with the 15N artificial lens standard. Proteins were trypsinized, relative ratios of light and heavy labeled peptides determined using high-resolution precursor and data independent MS2 scans, and data analysis performed using Skyline software. Crystallin abundances were measured in both human donor lenses and in transgenic mouse αA N101D cataract lenses. Technical replicates of human crystallin abundance measurements were performed with average coefficients of variation of approximately 2% across all 13 crystallins. αA crystallin comprised 27% of the soluble protein of 5-day-old lens and decreased to 16% by 18-years of age. Over this time period αB increased from 6% to 9% and the αA/αB ratio decreased from 4.5/1 to 2/1. γS-crystallin also increased nearly 2-fold from 7% to 12%, becoming the 3rd most abundant protein in adult lens, while βB1 increased from 14% to 20%, becoming the most abundant crystallin of adult lens. Minor crystallins βA2, βB3, and γA comprised only about 1% each of the newborn lens soluble protein, and their abundance dropped precipitously by adulthood. While 9 of the SUMO tagged crystallins were useful for purification of crystallins for structural studies, γA, γB, γC, and γD were resistant to cleavage by SUMO protease. The abundance of WT and N101D human αA in transgenic mouse lenses was approximately 40-fold lower than endogenous mouse αA, but the deamidation mimic human αA N101D was less soluble than human WT αA. The high content of αA and the transient abundance of βA2, βB3, and γA in young lens suggest these crystallins play a role in early lens development and growth. βB1 becoming the most abundant crystallin may result from its role in promoting higher order β-crystallin oligomerization in mature lens. The full set of human crystallin expression vectors in the Addgene repository should be a useful resource for future crystallin studies. 15N labeling of these crystallins will be useful to accurately quantify crystallins in lens anatomic regions, as well as measure the composition of insoluble light scattering crystallin aggregates. The standards will also be useful to measure the abundance of crystallins expressed in transgenic animal models.
Collapse
Affiliation(s)
- Kate A Halverson-Kolkind
- Department of Biomaterials and Biomedical Sciences, School of Dentistry, Oregon Health & Science University, Robertson Collaborative Life Sciences Building & Skourtes Tower, 2730 S Moody Ave, Portland, OR, 97239, USA.
| | - Nicholas Caputo
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
| | - Kirsten J Lampi
- Department of Biomaterials and Biomedical Sciences, School of Dentistry, Oregon Health & Science University, Robertson Collaborative Life Sciences Building & Skourtes Tower, 2730 S Moody Ave, Portland, OR, 97239, USA.
| | - Om Srivastava
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Henry Peters Building, 1716 University Blvd, Birmingham, AL, 35233, USA.
| | - Larry L David
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR, 97239, USA.
| |
Collapse
|
2
|
Wadood AA, Xiquan Z. Unraveling the mysteries of chicken proteomics: Insights into follicle development and reproduction. J Proteomics 2024; 308:105281. [PMID: 39154802 DOI: 10.1016/j.jprot.2024.105281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
Chicken proteomics is a valuable method for comprehending the many mechanisms involved in follicle growth and reproduction in birds. This study offers a thorough summary of the latest progress in chicken proteomics research, specifically highlighting the knowledge obtained regarding follicle development and reproductive physiology. Proteomic studies have revealed essential proteins and pathways that play a role in follicle development, including those that control oocyte size, maturation, and ovulation. Proteomic investigations have provided insight into the molecular pathways that govern reproductive processes. By utilizing advanced proteomic technologies, including mass spectrometry and protein microarray analysis, we have been able to identify and measure many proteins in chicken follicles at their different developmental stages. The utilization of proteomic methods has enabled the identification of previously unknown biomarkers for reproductive efficiency that expedited the creation of innovative diagnostic instruments for monitoring reproductive health in chicken. Chicken proteomics not only offers insights into follicle growth and reproduction but also uncovers the effects of environmental influences on reproductive function. This provides new opportunities for exploring the molecular pathways that cause these effects. The integration of current data with upcoming proteomic technologies offers the potential for innovative strategies to enhance chicken reproduction.
Collapse
Affiliation(s)
- Armughan Ahmed Wadood
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China
| | - Zhang Xiquan
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affair, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
3
|
Novy B, Dagunts A, Weishaar T, Holland EE, Adoff H, Hutchinson E, De Maria M, Kampmann M, Tsvetanova NG, Lobingier BT. An engineered trafficking biosensor reveals a role for DNAJC13 in DOR downregulation. Nat Chem Biol 2024:10.1038/s41589-024-01705-2. [PMID: 39223388 DOI: 10.1038/s41589-024-01705-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 07/17/2024] [Indexed: 09/04/2024]
Abstract
Trafficking of G protein-coupled receptors (GPCRs) through the endosomal-lysosomal pathway is critical to homeostatic regulation of GPCRs following activation with agonist. Identifying the genes involved in GPCR trafficking is challenging due to the complexity of sorting operations and the large number of cellular proteins involved in the process. Here, we developed a high-sensitivity biosensor for GPCR expression and agonist-induced trafficking to the lysosome by leveraging the ability of the engineered peroxidase APEX2 to activate the fluorogenic substrate Amplex UltraRed (AUR). We used the GPCR-APEX2/AUR assay to perform a genome-wide CRISPR interference screen focused on identifying genes regulating expression and trafficking of the δ-opioid receptor (DOR). We identified 492 genes consisting of both known and new regulators of DOR function. We demonstrate that one new regulator, DNAJC13, controls trafficking of multiple GPCRs, including DOR, through the endosomal-lysosomal pathway by regulating the composition of the endosomal proteome and endosomal homeostasis.
Collapse
Affiliation(s)
- Brandon Novy
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Aleksandra Dagunts
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Tatum Weishaar
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Emily E Holland
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Hayden Adoff
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Emily Hutchinson
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Monica De Maria
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Disease, University of California, San Francisco, San Francisco, CA, USA
| | | | - Braden T Lobingier
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA.
| |
Collapse
|
4
|
Harkness BM, Chen S, Kim K, Reddy AP, McFarland TJ, Hegarty DM, Everist SJ, Saugstad JA, Lapidus J, Galor A, Aicher SA. Tear Proteins Altered in Patients with Persistent Eye Pain after Refractive Surgery: Biomarker Candidate Discovery. J Proteome Res 2024; 23:2629-2640. [PMID: 38885176 DOI: 10.1021/acs.jproteome.4c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Some patients develop persistent eye pain after refractive surgery, but factors that cause or sustain pain are unknown. We tested whether tear proteins of patients with pain 3 months after surgery differ from those of patients without pain. Patients undergoing refractive surgery (laser in situ keratomileusis or photorefractive keratectomy ) were recruited from 2 clinics, and tears were collected 3 months after surgery. Participants rated their eye pain using a numerical rating scale (NRS, 0-10; no pain-worst pain) at baseline, 1 day, and 3 months after surgery. Using tandem mass tag proteomic analysis, we examined tears from patients with pain [NRS ≥ 3 at 3 months (n = 16)] and patients with no pain [NRS ≤ 1 at 3 months (n = 32)] after surgery. A subset of proteins (83 of 2748 detected, 3.0%) were associated with pain 3 months after surgery. High-dimensional statistical models showed that the magnitude of differential expression was not the only important factor in classifying tear samples from pain patients. Models utilizing 3 or 4 proteins had better classification performance than single proteins and represented differences in both directions (higher or lower in pain). Thus, patterns of protein differences may serve as biomarkers of postsurgical eye pain as well as potential therapeutic targets.
Collapse
Affiliation(s)
- Brooke M Harkness
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Siting Chen
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, Oregon 97239-4197, United States
- Biostatistics & Design Program, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Kilsun Kim
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Trevor J McFarland
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Deborah M Hegarty
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Steven J Everist
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Julie A Saugstad
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Jodi Lapidus
- School of Public Health, Oregon Health & Science University-Portland State University, Portland, Oregon 97239-4197, United States
- Biostatistics & Design Program, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami Health System, Miami, Florida 33146, United States
- Miami Veterans Affairs Hospital, Miami, Florida 33125-1624, United States
| | - Sue A Aicher
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, Oregon 97239-4197, United States
| |
Collapse
|
5
|
Kang Y, Lehmann KS, Vanegas J, Long H, Jefferson A, Freeman M, Clark S. Structural basis of bulk lipid transfer by bridge-like lipid transfer protein LPD-3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600134. [PMID: 38948693 PMCID: PMC11213131 DOI: 10.1101/2024.06.21.600134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Bridge-like lipid transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum (ER), to an acceptor membrane, such as a that of the cell or an organelle 1 . Despite the fundamental importance of BLTPs for cellular function, the architecture, composition, and lipid transfer mechanisms remain poorly characterized. Here, we present the subunit composition and the cryo-electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenic C. elegans . LPD-3 folds into an elongated, rod-shaped tunnel whose interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, here named "Intake" and "Spigot", both of which interact with the N-terminal end of LPD-3 where lipids enter the tunnel. Intake has three transmembrane helices, one of which borders the entrance to the tunnel; Spigot has one transmembrane helix and extends 80 Å along the cytosolic surface of LPD-3. Experiments in multiple model systems indicate that Spigot plays a conserved role in ER-PM contact site formation. Our LPD-3 complex structural data, together with molecular dynamics simulations of the transmembrane region in a lipid bilayer, reveal protein-lipid interactions that suggest a model for how the native LPD-3-complex mediates bulk lipid transport and provide a foundation for mechanistic studies of BLTPs.
Collapse
|
6
|
Toure MA, Motoyama K, Xiang Y, Urgiles J, Kabinger F, Koglin AS, Iyer RS, Gagnon K, Kumar A, Ojeda S, Harrison DA, Rees MG, Roth JA, Ott CJ, Schiavoni R, Whittaker CA, Levine SS, White FM, Calo E, Richters A, Koehler AN. Targeted Degradation of CDK9 Potently Disrupts the MYC Transcriptional Network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.593352. [PMID: 38952800 PMCID: PMC11216368 DOI: 10.1101/2024.05.14.593352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Cyclin-dependent kinase 9 (CDK9) coordinates signaling events that regulate RNA polymerase II (Pol II) pause-release states. It is an important co-factor for transcription factors, such as MYC, that drive aberrant cell proliferation when their expression is deregulated. CDK9 modulation offers an approach for attenuating dysregulation in such transcriptional programs. As a result, numerous drug development campaigns to inhibit CDK9 kinase activity have been pursued. More recently, targeted degradation has emerged as an attractive approach. However, comprehensive evaluation of degradation versus inhibition is still critically needed to assess the biological contexts in which degradation might offer superior therapeutic benefits. We validated that CDK9 inhibition triggers a compensatory mechanism that dampens its effect on MYC expression and found that this feedback mechanism was absent when the kinase is degraded. Importantly, CDK9 degradation is more effective than its inhibition for disrupting MYC transcriptional regulatory circuitry likely through the abrogation of both enzymatic and scaffolding functions of CDK9. Highlights - KI-CDK9d-32 is a highly potent and selective CDK9 degrader. - KI-CDK9d-32 leads to rapid downregulation of MYC protein and mRNA transcripts levels. - KI-CDK9d-32 represses canonical MYC pathways and leads to a destabilization of nucleolar homeostasis. - Multidrug resistance ABCB1 gene emerged as the strongest resistance marker for the CDK9 PROTAC degrader.
Collapse
|
7
|
Clark S, Jeong H, Posert R, Goehring A, Gouaux E. The structure of the Caenorhabditis elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction. Proc Natl Acad Sci U S A 2024; 121:e2314096121. [PMID: 38354260 PMCID: PMC10895266 DOI: 10.1073/pnas.2314096121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/21/2023] [Indexed: 02/16/2024] Open
Abstract
Mechanotransduction is the process by which a mechanical force, such as touch, is converted into an electrical signal. Transmembrane channel-like (TMC) proteins are an evolutionarily conserved family of membrane proteins whose function has been linked to a variety of mechanosensory processes, including hearing and balance sensation in vertebrates and locomotion in Drosophila. TMC1 and TMC2 are components of ion channel complexes, but the molecular features that tune these complexes to diverse mechanical stimuli are unknown. Caenorhabditis elegans express two TMC homologs, TMC-1 and TMC-2, both of which are the likely pore-forming subunits of mechanosensitive ion channels but differ in their expression pattern and functional role in the worm. Here, we present the single-particle cryo-electron microscopy structure of the native TMC-2 complex isolated from C. elegans. The complex is composed of two copies of the pore-forming TMC-2 subunit, the calcium and integrin binding protein CALM-1 and the transmembrane inner ear protein TMIE. Comparison of the TMC-2 complex to the recently published cryo-EM structure of the C. elegans TMC-1 complex highlights conserved protein-lipid interactions, as well as a π-helical structural motif in the pore-forming helices, that together suggest a mechanism for TMC-mediated mechanosensory transduction.
Collapse
Affiliation(s)
- Sarah Clark
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
| | - Hanbin Jeong
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
| | - Rich Posert
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
| | - April Goehring
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
- HHMI, Oregon Health and Science University, Portland, OR97239
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, OR97239
- HHMI, Oregon Health and Science University, Portland, OR97239
| |
Collapse
|
8
|
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] [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.
Collapse
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
| |
Collapse
|
9
|
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] [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.
Collapse
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.
| |
Collapse
|
10
|
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] [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.
Collapse
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.
| |
Collapse
|
11
|
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] [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.
Collapse
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.
| |
Collapse
|
12
|
Raghunathan V, Nartey A, Dhamodaran K, Baidouri H, Staverosky JA, Keller KE, Zientek K, Reddy A, Acott T, Vranka JA. Characterization of extracellular matrix deposited by segmental trabecular meshwork cells. Exp Eye Res 2023; 234:109605. [PMID: 37506755 PMCID: PMC11104015 DOI: 10.1016/j.exer.2023.109605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/14/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
PURPOSE Biophysical and biochemical attributes of the extracellular matrix are major determinants of cell fate in homeostasis and disease. Ocular hypertension and glaucoma are diseases where the trabecular meshwork tissue responsible for aqueous humor egress becomes stiffer accompanied by changes in its matrisome in a segmental manner with regions of high or low flow. Prior studies demonstrate these alterations in the matrix are dynamic in response to age and pressure changes. The underlying reason for segmentation or differential response to pressure and stiffening are unknown. This is largely due to a lack of appropriate models (in vitro or ex vivo) to study this phenomena. METHODS Primary trabecular meshwork cells were isolated from segmental flow regions, and cells were cultured for 4 weeks in the presence or absence or dexamethasone to obtain cell derived matrices (CDM). The biomechanical attributes of the CDM, composition of the matrisome, and incidence of crosslinks were determined by atomic force microscopy and mass spectrometry. RESULTS Data demonstrate that matrix deposited by cells from low flow regions are stiffer and exhibit a greater number of immature and mature crosslinks, and that these are exacerbated in the presence of steroid. We also show a differential response of high or low flow cells to steroid via changes observed in the matrix composition. However, no correlations were observed between elastic moduli and presence or absence of mature and immature crosslinks in the CDMs. CONCLUSION Regardless of a direct correlation between matrix stiffness and crosslinks, we observed distinct differences in the composition and mechanics of the matrices deposited by segmental flow cells. These results suggest distinct differences in cellular identify and likely a basis for mechanical memory post isolation and culture. Nevertheless, we conclude that although a mechanistic basis for matrix stiffness was undetermined in this study, it is a viable tool to study cell-matrix interactions and further our understanding of trabecular meshwork pathobiology.
Collapse
Affiliation(s)
| | - Andrews Nartey
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, TX, USA
| | - Kamesh Dhamodaran
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, TX, USA
| | - Hasna Baidouri
- Department of Basic Sciences, College of Optometry, University of Houston, Houston, TX, USA
| | | | - Kate E Keller
- Ophthalmology and Visual Sciences, Casey Eye Institute, USA
| | - Keith Zientek
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Ashok Reddy
- Proteomics Shared Resources, Oregon Health & Science University, Portland, OR, USA
| | - Ted Acott
- Ophthalmology and Visual Sciences, Casey Eye Institute, USA
| | | |
Collapse
|
13
|
Clark S, Jeong H, Posert R, Goehring A, Gouaux E. Structure of C. elegans TMC-2 complex suggests roles of lipid-mediated subunit contacts in mechanosensory transduction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553618. [PMID: 37645790 PMCID: PMC10462014 DOI: 10.1101/2023.08.16.553618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Mechanotransduction is the process by which a mechanical force, such as touch, is converted into an electrical signal. Transmembrane channel-like (TMC) proteins are an evolutionarily-conserved family of ion channels whose function has been linked to a variety of mechanosensory processes, including hearing and balance sensation in vertebrates and locomotion in Drosophila. The molecular features that tune homologous TMC ion channel complexes to diverse mechanical stimuli are unknown. Caenorhabditis elegans express two TMC homologs, TMC-1 and TMC-2, both of which are the likely pore-forming subunits of mechanosensitive ion channels but differ in their expression pattern and functional role in the worm. Here we present the single particle cryo-electron microscopy structure of the native TMC-2 complex isolated from C. elegans. The complex is composed of two copies each of the pore-forming TMC-2 subunit, the calcium and integrin binding protein CALM-1 and the transmembrane inner ear protein TMIE. Comparison of the TMC-2 complex to the recently published cryo-EM structure of the C. elegans TMC-1 complex reveals differences in subunit composition and highlights conserved protein-lipid interactions, as well as other structural features, that together suggest a mechanism for TMC-mediated mechanosensory transduction.
Collapse
Affiliation(s)
- Sarah Clark
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Hanbin Jeong
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Rich Posert
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - April Goehring
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| |
Collapse
|
14
|
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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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.
Collapse
|
15
|
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] [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.
Collapse
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.
| |
Collapse
|
16
|
Harkness BM, Hegarty DM, Saugstad JA, Behrens H, Betz J, David LL, Lapidus JA, Chen S, Stutzman R, Chamberlain W, Perez-Blanco M, Galor A, Aicher SA. Experimental design considerations for studies of human tear proteins. Ocul Surf 2023; 28:58-78. [PMID: 36764654 PMCID: PMC10409878 DOI: 10.1016/j.jtos.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
PURPOSE Human tears contain abundant, diverse sets of proteins that may serve as biomarkers of ocular surface health. There is a need for reproducible methods that consider multiple factors influencing the tear proteome, in addition to the variable of interest. Here we examined a workflow for proteomic analysis of tear proteins without the need to pool tear samples from multiple individuals, thus allowing for analyses based on individual factors, and increasing opportunities for protein biomarker discovery. METHODS Tears were collected by Schirmer strip following topical ocular anesthetic application then individually stored at -80 °C prior to processing for proteomics. Tear proteins were extracted from Schirmer strips, digested using suspension trapping spin columns (S-Trap), and labeled with high multiplicity tandem mass tags (TMT). Peptide digests were then extensively fractionated by two-dimensional chromatography and analyzed by mass spectrometry to identify and measure changes in protein abundance in each sample. Analysis of select samples was performed to test protocols and to compare the impact of clinically relevant parameters. To facilitate comparison of separate TMT experiments, common pool samples were included in each TMT instrument run and internal reference scaling (IRS) was performed. RESULTS Differences in subsets of tear proteins were noted for: geographic site of tear collection, contact lens use, and differences in tear fluid volume among individuals. CONCLUSION These findings demonstrate that proteomic analysis of human tear proteins can be performed without the need to pool samples, and that development of analytic workflows must consider factors that may affect outcomes in studies focused on diverse clinical samples.
Collapse
Affiliation(s)
- Brooke M Harkness
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Deborah M Hegarty
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Julie A Saugstad
- Department of Anesthesiology & Perioperative Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Hannah Behrens
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Jason Betz
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA
| | - Larry L David
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA; Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Jodi A Lapidus
- Biostatistics and Design Program, Oregon Health & Science University, USA; Oregon Health & Science University-Portland State University School of Public Health, USA
| | - Siting Chen
- Biostatistics and Design Program, Oregon Health & Science University, USA
| | - Richard Stutzman
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Maricarmen Perez-Blanco
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Surgical Services, Miami Veterans Administration Medical Center, Miami, FL, USA
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami, Miami, FL, USA; Surgical Services, Miami Veterans Administration Medical Center, Miami, FL, USA
| | - Sue A Aicher
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, USA.
| |
Collapse
|
17
|
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. RESEARCH SQUARE 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] [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.
Collapse
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
| |
Collapse
|
18
|
Raghunathan V, Nartey A, Dhamodaran K, Baidouri H, Staverosky JA, Keller KE, Zientek K, Reddy A, Acott T, Vranka JA. Characterization of extracellular matrix deposited by segmental trabecular meshwork cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.532242. [PMID: 36945588 PMCID: PMC10028995 DOI: 10.1101/2023.03.11.532242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Biophysical and biochemical attributes of the extracellular matrix are major determinants of cell fate in homeostasis and disease. Ocular hypertension and glaucoma are diseases where the trabecular meshwork tissue responsible for aqueous humor egress becomes stiffer accompanied by changes in its matrisome in a segmental manner with regions of high or low flow. Prior studies demonstrate these alterations in the matrix are dynamic in response to age and pressure changes. The underlying reason for segmentation or differential response to pressure and stiffening are unknown. This is largely due to a lack of appropriate models ( in vitro or ex vivo ) to study this phenomena. In this study, we characterize the biomechanical attributes, matrisome, and incidence of crosslinks in the matrix deposited by primary cells isolated from segmental flow regions and when treated with glucocorticosteroid. Data demonstrate that matrix deposited by cells from low flow regions are stiffer and exhibit a greater number of immature and mature crosslinks, and that these are exacerbated in the presence of steroid. We also show a differential response of high or low flow cells to steroid via changes observed in the matrix composition. We conclude that although a mechanistic basis for matrix stiffness was undetermined in this study, it is a viable tool to study cell-matrix interactions and further our understanding of trabecular meshwork pathobiology.
Collapse
|
19
|
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 PMCID: PMC11349083 DOI: 10.1016/j.exer.2022.109303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
20
|
Li BX, David LL, Davis LE, Xiao X. Protein arginine methyltransferase 5 is essential for oncogene product EWSR1-ATF1-mediated gene transcription in clear cell sarcoma. J Biol Chem 2022; 298:102434. [PMID: 36041632 PMCID: PMC9513783 DOI: 10.1016/j.jbc.2022.102434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription dysregulation is common in sarcomas driven by oncogenic transcription factors. Clear cell sarcoma of soft tissue (CCSST) is a rare sarcoma with poor prognosis presently with no therapy. It is characterized by a balanced t(12;22) (q13;q12) chromosomal translocation, resulting in a fusion of the Ewing's sarcoma gene EWSR1 with activating transcription factor 1 (ATF1) to give an oncogene EWSR1-ATF1. Unlike normal ATF1, whose transcription activity is dependent on phosphorylation, EWSR1-ATF1 is constitutively active to drive ATF1-dependent gene transcription to cause tumorigenesis. No EWSR1-ATF1-targeted therapies have been identified due to the challenges in targeting intracellular transcription factors. Through proteomics screening to identify potential druggable targets for CCSST, we discovered protein arginine methyltransferase 5 (PRMT5) as a novel protein to interact with EWSR1-ATF1. PRMT5 is a type II protein arginine methyltransferase to symmetrically dimethylate arginine residues in substrate proteins to regulate a diverse range of activities including gene transcription, RNA splicing, and DNA repair. We found that PRMT5 enhances EWSR1-ATF1-mediated gene transcription to sustain CCSST cell proliferation. Genetic silencing of PRMT5 in CCSST cells resulted in severely impaired cell proliferation and EWSR1-ATF1-driven transcription. Furthermore, we demonstrate that the clinical-stage PRMT5 inhibitor JNJ-64619178 potently and efficaciously inhibited CCSST cell growth in vitro and in vivo. These results provide new insights into PRMT5 as a transcription regulator and warrant JNJ-64619178 for further clinical development to treat CCSST patients.
Collapse
Affiliation(s)
- Bingbing X Li
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, USA.
| | - Larry L David
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, USA
| | - Lara E Davis
- Knight Cancer Institute, Oregon Health & Science University, Portland, USA; Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, USA
| | - Xiangshu Xiao
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, USA.
| |
Collapse
|
21
|
He D, Feng H, Sundberg B, Yang J, Powers J, Christian AH, Wilkinson JE, Monnin C, Avizonis D, Thomas CJ, Friedman RA, Kluger MD, Hollingsworth MA, Grandgenett PM, Klute KA, Toste FD, Chang CJ, Chio IIC. Methionine oxidation activates pyruvate kinase M2 to promote pancreatic cancer metastasis. Mol Cell 2022; 82:3045-3060.e11. [PMID: 35752173 PMCID: PMC9391305 DOI: 10.1016/j.molcel.2022.06.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/06/2022] [Accepted: 06/02/2022] [Indexed: 02/07/2023]
Abstract
Cancer mortality is primarily a consequence of its metastatic spread. Here, we report that methionine sulfoxide reductase A (MSRA), which can reduce oxidized methionine residues, acts as a suppressor of pancreatic ductal adenocarcinoma (PDA) metastasis. MSRA expression is decreased in the metastatic tumors of PDA patients, whereas MSRA loss in primary PDA cells promotes migration and invasion. Chemoproteomic profiling of pancreatic organoids revealed that MSRA loss results in the selective oxidation of a methionine residue (M239) in pyruvate kinase M2 (PKM2). Moreover, M239 oxidation sustains PKM2 in an active tetrameric state to promote respiration, migration, and metastasis, whereas pharmacological activation of PKM2 increases cell migration and metastasis in vivo. These results demonstrate that methionine residues can act as reversible redox switches governing distinct signaling outcomes and that the MSRA-PKM2 axis serves as a regulatory nexus between redox biology and cancer metabolism to control tumor metastasis.
Collapse
Affiliation(s)
- Dan He
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Huijin Feng
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Belen Sundberg
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jiaxing Yang
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Justin Powers
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alec H Christian
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Cian Monnin
- Metabolomics Innovation Resource, Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Daina Avizonis
- Metabolomics Innovation Resource, Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA; Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard A Friedman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael D Kluger
- Division of Gastrointestinal & Endocrine Surgery, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Paul M Grandgenett
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kelsey A Klute
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Iok In Christine Chio
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
22
|
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] [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.
Collapse
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
| |
Collapse
|
23
|
Park D, Reddy AP, Wilmarth PA, Jensen JT, Han L. Mucus secretions from a conditionally reprogrammed primary endocervical cell culture. F&S SCIENCE 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] [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.
Collapse
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
| |
Collapse
|
24
|
Martín-Acosta P, Meng Q, Klimek J, Reddy AP, David L, Petrie SK, Li BX, Xiao X. A clickable photoaffinity probe of betulinic acid identifies tropomyosin as a target. Acta Pharm Sin B 2022; 12:2406-2416. [PMID: 35646545 PMCID: PMC9136574 DOI: 10.1016/j.apsb.2021.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/25/2021] [Accepted: 12/09/2021] [Indexed: 12/30/2022] Open
Abstract
Target identification of bioactive compounds is important for understanding their mechanisms of action and provides critical insights into their therapeutic utility. While it remains a challenge, unbiased chemoproteomics strategy using clickable photoaffinity probes is a useful and validated approach for target identification. One major limitation of this approach is the efficient synthesis of appropriately substituted clickable photoaffinity probes. Herein, we describe an efficient and consistent method to prepare such probes. We further employed this method to prepare a highly stereo-congested probe based on naturally occurring triterpenoid betulinic acid. With this photoaffinity probe, we identified tropomyosin as a novel target for betulinic acid that can account for the unique biological phenotype on cellular cytoskeleton induced by betulinic acid.
Collapse
Affiliation(s)
- Pedro Martín-Acosta
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Qianli Meng
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - John Klimek
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ashok P. Reddy
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR 97239, USA
| | - Larry David
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Stefanie Kaech Petrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Neurology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Bingbing X. Li
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xiangshu Xiao
- Program in Chemical Biology, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| |
Collapse
|
25
|
Ma Z, Chauss D, Disatham J, Jiao X, Brennan LA, Menko AS, Kantorow M, Hejtmancik JF. Patterns of Crystallin Gene Expression in Differentiation State Specific Regions of the Embryonic Chicken Lens. Invest Ophthalmol Vis Sci 2022; 63:8. [PMID: 35412582 PMCID: PMC9012887 DOI: 10.1167/iovs.63.4.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Transition from lens epithelial cells to lens fiber cell is accompanied by numerous changes in gene expression critical for lens transparency. We identify expression patterns of highly prevalent genes including ubiquitous and enzyme crystallins in the embryonic day 13 chicken lens. Methods Embryonic day 13 chicken lenses were dissected into central epithelial cell (EC), equatorial epithelial cell (EQ), cortical fiber cell (FP), and nuclear fiber cell (FC) compartments. Total RNA was prepared, subjected to high-throughput unidirectional mRNA sequencing, analyzed, mapped to the chicken genome, and functionally grouped. Results A total of 77,097 gene-specific transcripts covering 17,450 genes were expressed, of which 10,345 differed between two or more lens subregions. Ubiquitous crystallin gene expression increased from EC to EQ and was similar in FP and FC. Highly expressed crystallin genes fell into three coordinately expressed groups with R2 ≥ 0.93: CRYAA, CRYBB2, CRYAB, and CRYBA2; CRYBB1, CRYBA4, CRYGN, ASL1, and ASL; and CRYBB3 and CRYBA1. The highly expressed transcription factors YBX1, YBX3, PNRC1, and BASP1 were coordinately expressed with the second group of crystallins (r2 > 0.88). Conclusions Although it is well known that lens crystallin gene expression changes during the epithelial to fiber cell transition, these data identify for the first time three distinct patterns of expression for specific subsets of crystallin genes, each highly correlated with expression of specific transcription factors. The results provide a quantitative basis for designing functional experiments pinpointing the mechanisms governing the landscape of crystallin expression during fiber cell differentiation to attain lens transparency.
Collapse
Affiliation(s)
- Zhiwei Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Daniel Chauss
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States
| | - Joshua Disatham
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Lisa Ann Brennan
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States
| | - A Sue Menko
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States
| | - Marc Kantorow
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| |
Collapse
|
26
|
Buenafe AC, Dorrell C, Reddy AP, Klimek J, Marks DL. Proteomic analysis distinguishes extracellular vesicles produced by cancerous versus healthy pancreatic organoids. Sci Rep 2022; 12:3556. [PMID: 35241737 PMCID: PMC8894448 DOI: 10.1038/s41598-022-07451-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) are produced and released by both healthy and malignant cells and bear markers indicative of ongoing biological processes. In the present study we utilized high resolution flow cytometry to detect EVs in the plasma of patients with pancreatic ductal adenocarcinoma (PDAC) and in the supernatants of PDAC and healthy control (HC) pancreatic organoid cultures. Using ultrafiltration and size exclusion chromatography, PDAC and HC pancreatic organoid EVs were isolated for mass spectrometry analysis. Proteomic and functional protein network analysis showed a striking distinction in that EV proteins profiled in pancreatic cancer organoids were involved in vesicular transport and tumorigenesis while EV proteins in healthy organoids were involved in cellular homeostasis. Thus, the most abundant proteins identified in either case represented non-overlapping cellular programs. Tumor-promoting candidates LAMA5, SDCBP and TENA were consistently upregulated in PDAC EVs. Validation of specific markers for PDAC EVs versus healthy pancreatic EVs will provide the biomarkers and enhanced sensitivity necessary to monitor early disease or disease progression, with or without treatment. Moreover, disease-associated changes in EV protein profiles provide an opportunity to investigate alterations in cellular programming with disease progression.
Collapse
Affiliation(s)
- Abigail C Buenafe
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA.
| | - Craig Dorrell
- Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, USA
| | - John Klimek
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, USA
| | - Daniel L Marks
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
| |
Collapse
|
27
|
Jeong H, Clark S, Goehring A, Dehghani-Ghahnaviyeh S, Rasouli A, Tajkhorshid E, Gouaux E. Structures of the TMC-1 complex illuminate mechanosensory transduction. Nature 2022; 610:796-803. [PMID: 36224384 PMCID: PMC9605866 DOI: 10.1038/s41586-022-05314-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/02/2022] [Indexed: 02/05/2023]
Abstract
The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid-protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.
Collapse
Affiliation(s)
- Hanbin Jeong
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA
| | - Sarah Clark
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA
| | - April Goehring
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR USA
| | - Sepehr Dehghani-Ghahnaviyeh
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Ali Rasouli
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Emad Tajkhorshid
- grid.35403.310000 0004 1936 9991Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA ,grid.35403.310000 0004 1936 9991Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Eric Gouaux
- grid.433851.80000 0004 0608 3919Vollum Institute, Oregon Health and Science University, Portland, OR USA ,grid.5288.70000 0000 9758 5690Howard Hughes Medical Institute, Oregon Health and Science University, Portland, OR USA
| |
Collapse
|
28
|
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] [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.
Collapse
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
| |
Collapse
|
29
|
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] [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.
Collapse
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
| |
Collapse
|
30
|
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] [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.
Collapse
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.)
| |
Collapse
|
31
|
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] [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.
Collapse
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
| |
Collapse
|
32
|
Ryu H, Sun XX, Chen Y, Li Y, Wang X, Dai RS, Zhu HM, Klimek J, David L, Fedorov LM, Azuma Y, Sears RC, Dai MS. The deubiquitinase USP36 promotes snoRNP group SUMOylation and is essential for ribosome biogenesis. EMBO Rep 2021; 22:e50684. [PMID: 33852194 DOI: 10.15252/embr.202050684] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 12/21/2022] Open
Abstract
SUMOylation plays a crucial role in regulating diverse cellular processes including ribosome biogenesis. Proteomic analyses and experimental evidence showed that a number of nucleolar proteins involved in ribosome biogenesis are modified by SUMO. However, how these proteins are SUMOylated in cells is less understood. Here, we report that USP36, a nucleolar deubiquitinating enzyme (DUB), promotes nucleolar SUMOylation. Overexpression of USP36 enhances nucleolar SUMOylation, whereas its knockdown or genetic deletion reduces the levels of SUMOylation. USP36 interacts with SUMO2 and Ubc9 and directly mediates SUMOylation in cells and in vitro. We show that USP36 promotes the SUMOylation of the small nucleolar ribonucleoprotein (snoRNP) components Nop58 and Nhp2 in cells and in vitro and their binding to snoRNAs. It also promotes the SUMOylation of snoRNP components Nop56 and DKC1. Functionally, we show that knockdown of USP36 markedly impairs rRNA processing and translation. Thus, USP36 promotes snoRNP group SUMOylation and is critical for ribosome biogenesis and protein translation.
Collapse
Affiliation(s)
- Hyunju Ryu
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Xiao-Xin Sun
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Yingxiao Chen
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Yanping Li
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Xiaoyan Wang
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Roselyn S Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Hong-Ming Zhu
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - John Klimek
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.,OHSU Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Larry David
- Department of Chemical Physiology & Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, USA.,OHSU Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Lev M Fedorov
- OHSU Transgenic Mouse Models Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Rosalie C Sears
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Mu-Shui Dai
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
33
|
Melly GC, Stokas H, Davidson PM, Roma JS, Rhodes HL, Purdy GE. Identification of residues important for M. tuberculosis MmpL11 function reveals that function is modulated by phosphorylation in the C-terminal domain. Mol Microbiol 2021; 115:208-221. [PMID: 32985735 DOI: 10.1111/mmi.14611] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 11/26/2022]
Abstract
The Mycobacterium tuberculosis cell envelope is a critical interface between the host and pathogen and provides a protective barrier against the immune response and antibiotics. Cell envelope lipids are also mycobacterial virulence factors that influence the host immune response. The mycobacterial membrane protein large (MmpL) proteins transport cell envelope lipids and siderophores that are important for the basic physiology and pathogenesis of M. tuberculosis. We recently identified MmpL11 as a conserved transporter of mycolic acid-containing lipids including monomeromycolyl diacylglycerol (MMDAG), mycolate wax ester (MWE), and long-chain triacylglycerols (LC-TAGs). These lipids contribute to biofilm formation in M. tuberculosis and M. smegmatis, and non-replicating persistence in M. tuberculosis. In this report, we identified domains and residues that are essential for MmpL11TB lipid transporter activity. Specifically, we show that the D1 periplasmic loop and a conserved tyrosine are essential for the MmpL11 function. Intriguingly, we found that MmpL11 levels are regulated by the phosphorylation of threonine in the cytoplasmic C-terminal domain, providing the first direct evidence of the phospho-regulation of MmpL11 transporter activity in M. tuberculosis and M. smegmatis. Our results offer further insight into the function of MmpL transporters and regulation of mycobacterial cell envelope biogenesis.
Collapse
Affiliation(s)
- Geoff C Melly
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Haley Stokas
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Patrick M Davidson
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - José Santinni Roma
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Heather L Rhodes
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Georgiana E Purdy
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
34
|
Motor control and cognition deficits associated with protein carbamoylation in food (cassava) cyanogenic poisoning: Neurodegeneration and genomic perspectives. Food Chem Toxicol 2020; 148:111917. [PMID: 33296712 DOI: 10.1016/j.fct.2020.111917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/21/2022]
Abstract
A case-control design determined whether konzo, an upper motoneuron disease linked to food (cassava) toxicity was associated with protein carbamoylation and genetic variations. Exon sequences of thiosulfate sulfurtransferase (TST) or mercaptopyruvate sulfurtransferase (MPST), plasma cyanide detoxification rates, and 2D-LC-MS/MS albumin carbamoylation were assessed in 40 children [21 konzo-affected and 19 putatively healthy controls, mean (SD) age: 9.2 (3.0) years] subjected to cognition and motor testing using the Kaufman Assessment Battery and the Bruininks/Oseretsky Test, respectively. Konzo was significantly associated with higher levels of carbamoylated peptides 206-219 (LDELRDEGKASSAK, pep1) after adjusting for age, gender, albumin concentrations and BUN [regression coefficient: 0.03 (95%CI:0.02-0.05), p = 0.01]. Levels of pep1 negatively correlated with performance scores at all modalities of motor proficiency (r = 0.38 to 0.61; all p < 0.01) or sequential processing (memory)(r = - 0.59, p = 0.00) and overall cognitive performance (r = - 0.48, p = 0.00) but positively with time needed for cyanide detoxification in plasma (r = 0.33, p = 0.04). Rare potentially damaging TST p.Arg206Cys (rs61742280) and MPST p.His317Tyr (rs1038542246) heterozygous variants were identified but with no impact on subject phenotypes. Protein carbamoylation appears to be a reliable marker for cassava related neurodegeneration.
Collapse
|
35
|
Zaini PA, Feinberg NG, Grilo FS, Saxe HJ, Salemi MR, Phinney BS, Crisosto CH, Dandekar AM. Comparative Proteomic Analysis of Walnut ( Juglans regia L.) Pellicle Tissues Reveals the Regulation of Nut Quality Attributes. Life (Basel) 2020; 10:E314. [PMID: 33261033 PMCID: PMC7760677 DOI: 10.3390/life10120314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 11/16/2022] Open
Abstract
Walnuts (Juglans regia L.) are a valuable dietary source of polyphenols and lipids, with increasing worldwide consumption. California is a major producer, with 'Chandler' and 'Tulare' among the cultivars more widely grown. 'Chandler' produces kernels with extra light color at a higher frequency than other cultivars, gaining preference by growers and consumers. Here we performed a deep comparative proteome analysis of kernel pellicle tissue from these two valued genotypes at three harvest maturities, detecting a total of 4937 J. regia proteins. Late and early maturity stages were compared for each cultivar, revealing many developmental responses common or specific for each cultivar. Top protein biomarkers for each developmental stage were also selected based on larger fold-change differences and lower variance among replicates, including proteins for biosynthesis of lipids and phenols, defense-related proteins and desiccation stress-related proteins. Comparison between the genotypes also revealed the common and specific protein repertoires, totaling 321 pellicle proteins with differential abundance at harvest stage. The proteomics data provides clues on antioxidant, secondary, and hormonal metabolism that could be involved in the loss of quality in the pellicles during processing for commercialization.
Collapse
Affiliation(s)
- Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| | - Noah G. Feinberg
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| | - Filipa S. Grilo
- Department of Food Sciences and Technology, University of California, Davis, CA 95616, USA;
| | - Houston J. Saxe
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| | - Michelle R. Salemi
- Proteomics Core Facility, University of California, Davis, CA 95616, USA; (M.R.S.); (B.S.P.)
| | - Brett S. Phinney
- Proteomics Core Facility, University of California, Davis, CA 95616, USA; (M.R.S.); (B.S.P.)
| | - Carlos H. Crisosto
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (P.A.Z.); (N.G.F.); (H.J.S.); (C.H.C.)
| |
Collapse
|
36
|
Saitz TR, Ostrowski KA, Martinez Acevedo A, Bash JC, Klimek J, Fuchs EF, David LL, Hedges JC. The vasal fluid proteomic profile and microscopic sperm presence at time of vasectomy reversal. Transl Androl Urol 2020; 9:2000-2006. [PMID: 33209664 PMCID: PMC7658130 DOI: 10.21037/tau-20-703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background The microscopic characteristics of vasal fluid at time of vasectomy reversal (VR) guide operative decision making and predict fertility outcomes. The proteomic profile of this vasal fluid has not been described or correlated with the microscopic fluid appearance. To characterize the vasal fluid proteome at time of VR and evaluate the variation of the vasal fluid proteome with respect to microscopic presence of sperm. Methods A prospective cohort study was conducted enrolling twenty-five men undergoing VR for infertility and/or pain at a University-affiliated hospital. Vasal fluid samples obtained at time of VR were grouped based on presence of sperm on light microscopy at time of VR. Proteomic profiles were generated using liquid chromatography/ tandem mass spectrometry, and MS/MS protein spectral counts compared between individuals and treatment groups, controlling for less than 5% protein false discovery rate (FDR). Proteins were matched with the human swissprot database using the Comet search engine, and categorized by Gene Ontology (GO) terms. Results There was large variability between the 46 vasal fluid samples collected, with 1,692 unique proteins detected. The three most abundant proteins were Lactotransferrin, Cysteine-rich secretory protein 1, A-kinase anchor protein 4. There was no correlation between the proteome and microscopic sperm presence. Prevalent GO terms included viral process, signal transduction, innate immune response, protein folding and spermatogenesis. Conclusions We describe the proteome and the most common proteins in vasal fluid at time of VR. Numerable sperm, testis and epididymis specific proteins were present even in the absence of sperm on microscopy. Further evaluation is needed to determine if a protein biomarker may better guide operative decision making and predict VR fertility outcomes.
Collapse
Affiliation(s)
- Theodore R Saitz
- Department of Urology, Oregon Health & Science University, Portland, OR, USA.,Department of Surgery, Nellis Air Force Base Hospital, Uniformed Services University of the Health Sciences, Nellis AFB, NV, USA
| | - Kevin A Ostrowski
- Department of Urology, University of Washington School of Medicine, Health Sciences Building, Seattle, WA, USA
| | | | - Jasper C Bash
- Department of Urology, Oregon Health & Science University, Portland, OR, USA
| | - John Klimek
- Proteomics Shared Resource, Oregon Health & Sciences University, Portland, OR, USA
| | - Eugene F Fuchs
- Department of Urology, Oregon Health & Science University, Portland, OR, USA
| | - Larry L David
- Department of Chemical Physiology & Biochemistry, Oregon Health Sciences University, Portland, OR, USA
| | - Jason C Hedges
- Department of Urology, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
37
|
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] [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.
Collapse
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.)
| |
Collapse
|
38
|
Contreras-Llano LE, Meyer C, Liu Y, Sarker M, Lim S, Longo ML, Tan C. Holistic engineering of cell-free systems through proteome-reprogramming synthetic circuits. Nat Commun 2020; 11:3138. [PMID: 32561745 PMCID: PMC7305103 DOI: 10.1038/s41467-020-16900-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/27/2020] [Indexed: 11/09/2022] Open
Abstract
Synthetic biology has focused on engineering genetic modules that operate orthogonally from the host cells. A synthetic biological module, however, can be designed to reprogram the host proteome, which in turn enhances the function of the synthetic module. Here, we apply this holistic synthetic biology concept to the engineering of cell-free systems by exploiting the crosstalk between metabolic networks in cells, leading to a protein environment more favorable for protein synthesis. Specifically, we show that local modules expressing translation machinery can reprogram the bacterial proteome, changing the expression levels of more than 700 proteins. The resultant feedback generates a cell-free system that can synthesize fluorescent reporters, protein nanocages, and the gene-editing nuclease Cas9, with up to 5-fold higher expression level than classical cell-free systems. Our work demonstrates a holistic approach that integrates synthetic and systems biology concepts to achieve outcomes not possible by only local, orthogonal circuits.
Collapse
Affiliation(s)
- Luis E Contreras-Llano
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Conary Meyer
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Yao Liu
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Mridul Sarker
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Block N1.3, Singapore, 637457, Singapore
| | - Sierin Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Block N1.3, Singapore, 637457, Singapore
| | - Marjorie L Longo
- Department of Chemical Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA.
| |
Collapse
|
39
|
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] [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.
Collapse
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.
| |
Collapse
|
40
|
Melly GC, Stokas H, Dunaj JL, Hsu FF, Rajavel M, Su CC, Yu EW, Purdy GE. Structural and functional evidence that lipoprotein LpqN supports cell envelope biogenesis in Mycobacterium tuberculosis. J Biol Chem 2019; 294:15711-15723. [PMID: 31471317 PMCID: PMC6816100 DOI: 10.1074/jbc.ra119.008781] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 08/27/2019] [Indexed: 01/07/2023] Open
Abstract
The mycobacterial cell envelope is crucial to host-pathogen interactions as a barrier against antibiotics and the host immune response. In addition, cell envelope lipids are mycobacterial virulence factors. Cell envelope lipid biosynthesis is the target of a number of frontline tuberculosis treatments and has been the focus of much research. However, the transport mechanisms by which these lipids reach the mycomembrane remain poorly understood. Many envelope lipids are exported from the cytoplasm to the periplasmic space via the mycobacterial membrane protein large (MmpL) family of proteins. In other bacteria, lipoproteins can contribute to outer membrane biogenesis through direct binding of substrates and/or protein-protein associations with extracytoplasmic biosynthetic enzymes. In this report, we investigate whether the lipoprotein LpqN plays a similar role in mycobacteria. Using a genetic two-hybrid approach, we demonstrate that LpqN interacts with periplasmic loop domains of the MmpL3 and MmpL11 transporters that export mycolic acid-containing cell envelope lipids. We observe that LpqN also interacts with secreted cell envelope biosynthetic enzymes such as Ag85A via pulldown assays. The X-ray crystal structures of LpqN and LpqN bound to dodecyl-trehalose suggest that LpqN directly binds trehalose monomycolate, the MmpL3 and Ag85A substrate. Finally, we observe altered lipid profiles of the ΔlpqN mutant during biofilm maturation, pointing toward a possible physiological role for the protein. The results of this study suggest that LpqN may act as a membrane fusion protein, connecting MmpL transporters with periplasmic proteins, and provide general insight into the role of lipoproteins in Mycobacterium tuberculosis cell envelope biogenesis.
Collapse
Affiliation(s)
- Geoff C. Melly
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239
| | - Haley Stokas
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239
| | - Jennifer L. Dunaj
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239
| | - Fong Fu Hsu
- Department of Internal Medicine, Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | | | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Georgiana E. Purdy
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, Oregon 97239, To whom correspondence should be addressed. Tel.:
503-346-0767; E-mail:
| |
Collapse
|
41
|
Puy C, Ngo ATP, Pang J, Keshari RS, Hagen MW, Hinds MT, Gailani D, Gruber A, Lupu F, McCarty OJT. Endothelial PAI-1 (Plasminogen Activator Inhibitor-1) Blocks the Intrinsic Pathway of Coagulation, Inducing the Clearance and Degradation of FXIa (Activated Factor XI). Arterioscler Thromb Vasc Biol 2019; 39:1390-1401. [PMID: 31242030 DOI: 10.1161/atvbaha.119.312619] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective- Activation of coagulation FXI (factor XI) by FXIIa (activated factor XII) is a prothrombotic process. The endothelium is known to play an antithrombotic role by limiting thrombin generation and platelet activation. It is unknown whether the antithrombotic role of the endothelium includes sequestration of FXIa (activated factor XI) activity. This study aims to determine the role of endothelial cells (ECs) in the regulation of the intrinsic pathway of coagulation. Approach and Results- Using a chromogenic assay, we observed that human umbilical veins ECs selectively blocked FXIa yet supported kallikrein and FXIIa activity. Western blotting and mass spectrometry analyses revealed that FXIa formed a complex with endothelial PAI-1 (plasminogen activator inhibitor-1). Blocking endothelial PAI-1 increased the cleavage of a chromogenic substrate by FXIa and the capacity of FXIa to promote fibrin formation in plasma. Western blot and immunofluorescence analyses showed that FXIa-PAI-1 complexes were either released into the media or trafficked to the early and late endosomes and lysosomes of ECs. When baboons were challenged with Staphylococcus aureus to induce a prothrombotic phenotype, an increase in circulating FXIa-PAI-1 complex levels was detected by ELISA within 2 to 8 hours postchallenge. Conclusions- PAI-1 forms a complex with FXIa on ECs, blocking its activity and inducing the clearance and degradation of FXIa. Circulating FXIa-PAI-1 complexes were detected in a baboon model of S. aureus sepsis. Although ECs support kallikrein and FXIIa activity, inhibition of FXIa by ECs may promote the clearance of intravascular FXIa. Visual Overview- An online visual overview is available for this article.
Collapse
Affiliation(s)
- Cristina Puy
- From the Department of Biomedical Engineering (C.P., A.T.P.N., J.P., M.W.H., M.T.H., A.G., Q.J.T.M.), School of Medicine, Oregon Health & Science University, Portland.,Division of Hematology/Medical Oncology (C.P., A.G., O.J.T.M.), School of Medicine, Oregon Health & Science University, Portland
| | - Anh T P Ngo
- From the Department of Biomedical Engineering (C.P., A.T.P.N., J.P., M.W.H., M.T.H., A.G., Q.J.T.M.), School of Medicine, Oregon Health & Science University, Portland
| | - Jiaqing Pang
- From the Department of Biomedical Engineering (C.P., A.T.P.N., J.P., M.W.H., M.T.H., A.G., Q.J.T.M.), School of Medicine, Oregon Health & Science University, Portland
| | - Ravi S Keshari
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City (R.S.K., F.L.)
| | - Matthew W Hagen
- From the Department of Biomedical Engineering (C.P., A.T.P.N., J.P., M.W.H., M.T.H., A.G., Q.J.T.M.), School of Medicine, Oregon Health & Science University, Portland
| | - Monica T Hinds
- From the Department of Biomedical Engineering (C.P., A.T.P.N., J.P., M.W.H., M.T.H., A.G., Q.J.T.M.), School of Medicine, Oregon Health & Science University, Portland
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN (D.G.)
| | - András Gruber
- From the Department of Biomedical Engineering (C.P., A.T.P.N., J.P., M.W.H., M.T.H., A.G., Q.J.T.M.), School of Medicine, Oregon Health & Science University, Portland.,Division of Hematology/Medical Oncology (C.P., A.G., O.J.T.M.), School of Medicine, Oregon Health & Science University, Portland
| | - Florea Lupu
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City (R.S.K., F.L.)
| | - Owen J T McCarty
- From the Department of Biomedical Engineering (C.P., A.T.P.N., J.P., M.W.H., M.T.H., A.G., Q.J.T.M.), School of Medicine, Oregon Health & Science University, Portland.,Division of Hematology/Medical Oncology (C.P., A.G., O.J.T.M.), School of Medicine, Oregon Health & Science University, Portland
| |
Collapse
|
42
|
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] [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.
Collapse
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.
| |
Collapse
|
43
|
Meacham KA, Cortés MP, Wiggins EM, Maass A, Latorre M, Ralle M, Burkhead JL. Altered zinc balance in the Atp7b -/- mouse reveals a mechanism of copper toxicity in Wilson disease. Metallomics 2018; 10:1595-1606. [PMID: 30277246 PMCID: PMC6310031 DOI: 10.1039/c8mt00199e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Wilson disease (WD) is an autosomal recessive disorder caused by mutation in the ATP7B gene that affects copper transport in the body. ATP7B mutation damages copper transporter function, ultimately resulting in excessive copper accumulation and subsequent toxicity in both the liver and brain. Mechanisms of copper toxicity, however, are not well defined. The Atp7b-/- mouse model is well-characterized and presents a hepatic phenotype consistent with WD. In this study, we found that the untreated Atp7b-/- mice accumulate approximately 2-fold excess hepatic zinc compared to the wild type. We used targeted transcriptomics and proteomics to analyze the molecular events associated with zinc and copper accumulation in the Atp7b-/- mouse liver. Altered gene expression of Zip5 and ZnT1 zinc transporters indicated a transcriptional homeostatic response, while increased copper/zinc ratios associated with high levels of metallothioneins 1 and 2, indicated altered Zn availability in cells. These data suggest that copper toxicity in Wilson disease includes effects on zinc-dependent proteins. Transcriptional network analysis of RNA-seq data reveals an interconnected network of transcriptional activators with over-representation of zinc-dependent and zinc-responsive transcription factors. In the context of previous research, these observations support the hypothesis that mechanisms of copper toxicity include disruption of intracellular zinc distribution in liver cells. The translational significance of this work lies in oral zinc supplementation in treatment for WD, which is thought to mediate protective effects through the induction of metallothionein synthesis in the intestine. This work indicates broader impacts of altered zinc-copper balance in WD, including global transcriptional responses and altered zinc balance in the liver.
Collapse
Affiliation(s)
- Kelsey A Meacham
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, USA.
| | | | | | | | | | | | | |
Collapse
|
44
|
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] [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.
Collapse
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
| |
Collapse
|
45
|
Abstract
Cataract is a major cause of blindness worldwide. It is characterized by lens opacification and is accompanied by extensive posttranslational modifications (PTMs) in various proteins. PTMs play an essential role in lens opacification. Several PTMs have been described in proteins isolated from relatively old human lenses, including phosphorylation, deamidation, racemization, truncation, acetylation, and methylation. An overwhelming majority of previous cataract proteomic studies have exclusively focused on crystallin proteins, which are the most abundant proteome components of the lens. To investigate the proteome of cataract markers, this chapter focuses on the proteomic research on the functional relevance of the major PTMs in crystallins of human cataractous lenses. Elucidating the role of these modifications in cataract formation has been a challenging task because they are among the most difficult PTMs to study analytically. The proteomic status of some amides presents similar properties in normal aged and cataractous lenses, whereas some may undergo greater PTMs in cataract. Therefore, it is of great importance to review the current proteomic research on crystallins, the major protein markers in different types of cataract, to elucidate the pathogenesis of this major human-blinding condition.
Collapse
Affiliation(s)
- Keke Zhang
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Department of Ophthalmology, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Myopia, Ministry of Health PR China, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiangjia Zhu
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Department of Ophthalmology, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Myopia, Ministry of Health PR China, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Lu
- Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Department of Ophthalmology, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China; Key Laboratory of Myopia, Ministry of Health PR China, Shanghai, China; Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
46
|
Ritchie C, Mack A, Harper L, Alfadhli A, Stork PJS, Nan X, Barklis E. Analysis of K-Ras Interactions by Biotin Ligase Tagging. Cancer Genomics Proteomics 2018. [PMID: 28647697 DOI: 10.21873/cgp.20034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Mutations of the human K-Ras 4B (K-Ras) G protein are associated with a significant proportion of all human cancers. Despite this fact, a comprehensive analysis of K-Ras interactions is lacking. Our investigations focus on characterization of the K-Ras interaction network. MATERIALS AND METHODS We employed a biotin ligase-tagging approach, in which tagged K-Ras proteins biotinylate neighbor proteins in a proximity-dependent fashion, and proteins are identified via mass spectrometry (MS) sequencing. RESULTS In transfected cells, a total of 748 biotinylated proteins were identified from cells expressing biotin ligase-tagged K-Ras variants. Significant differences were observed between membrane-associated variants and a farnesylation-defective mutant. In pancreatic cancer cells, 56 K-Ras interaction partners were identified. Most of these were cytoskeletal or plasma membrane proteins, and many have been identified previously as potential cancer biomarkers. CONCLUSION Biotin ligase tagging offers a rapid and convenient approach to the characterization of K-Ras interaction networks.
Collapse
Affiliation(s)
- Christopher Ritchie
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Andrew Mack
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Logan Harper
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Philip J S Stork
- Department of Vollum Institute, Oregon Health & Science University, Portland, OR, U.S.A
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, U.S.A
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A.
| |
Collapse
|
47
|
Morgan CP, Zhao H, LeMasurier M, Xiong W, Pan B, Kazmierczak P, Avenarius MR, Bateschell M, Larisch R, Ricci AJ, Müller U, Barr-Gillespie PG. TRPV6, TRPM6 and TRPM7 Do Not Contribute to Hair-Cell Mechanotransduction. Front Cell Neurosci 2018; 12:41. [PMID: 29515374 PMCID: PMC5826258 DOI: 10.3389/fncel.2018.00041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/01/2018] [Indexed: 12/02/2022] Open
Abstract
Hair cells of the inner ear transduce mechanical stimuli like sound or head movements into electrical signals, which are propagated to the central nervous system. The hair-cell mechanotransduction channel remains unidentified. We tested whether three transient receptor channel (TRP) family members, TRPV6, TRPM6 and TRPM7, were necessary for transduction. TRPV6 interacted with USH1C (harmonin), a scaffolding protein that participates in transduction. Using a cysteine-substitution knock-in mouse line and methanethiosulfonate (MTS) reagents selective for this allele, we found that inhibition of TRPV6 had no effect on transduction in mouse cochlear hair cells. TRPM6 and TRPM7 each interacted with the tip-link component PCDH15 in cultured eukaryotic cells, which suggested they might be part of the transduction complex. Cochlear hair cell transduction was not affected by manipulations of Mg2+, however, which normally perturbs TRPM6 and TRPM7. To definitively examine the role of these two channels in transduction, we showed that deletion of either or both of their genes selectively in hair cells had no effect on auditory function. We suggest that TRPV6, TRPM6 and TRPM7 are unlikely to be the pore-forming subunit of the hair-cell transduction channel.
Collapse
Affiliation(s)
- Clive P. Morgan
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - Hongyu Zhao
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - Meredith LeMasurier
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - Wei Xiong
- Department of Neuroscience, Scripps Research Institute, La Jolla, CA, United States
| | - Bifeng Pan
- Department of Otolaryngology, Stanford University, Stanford, CA, United States
| | - Piotr Kazmierczak
- Department of Neuroscience, Scripps Research Institute, La Jolla, CA, United States
| | - Matthew R. Avenarius
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - Michael Bateschell
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - Ruby Larisch
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| | - Anthony J. Ricci
- Department of Otolaryngology, Stanford University, Stanford, CA, United States
| | - Ulrich Müller
- Department of Neuroscience, Scripps Research Institute, La Jolla, CA, United States
| | - Peter G. Barr-Gillespie
- Oregon Hearing Research Center & Vollum Institute, Oregon Health & Science University, Portland, OR, United States
| |
Collapse
|
48
|
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] [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.
Collapse
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
| |
Collapse
|
49
|
De Maria A, Wilmarth PA, David LL, Bassnett S. Proteomic Analysis of the Bovine and Human Ciliary Zonule. Invest Ophthalmol Vis Sci 2017; 58:573-585. [PMID: 28125844 PMCID: PMC5283081 DOI: 10.1167/iovs.16-20866] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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.
Collapse
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
| |
Collapse
|
50
|
Rauch BJ, Klimek J, David L, Perona JJ. Persulfide Formation Mediates Cysteine and Homocysteine Biosynthesis in Methanosarcina acetivorans. Biochemistry 2017; 56:1051-1061. [PMID: 28165724 DOI: 10.1021/acs.biochem.6b00931] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The mechanisms of sulfur uptake and trafficking in methanogens inhabiting sulfidic environments are highly distinctive. In aerobes, sulfur transfers between proteins occur via persulfide relay, but direct evidence for persulfides in methanogens has been lacking. Here, we use mass spectrometry to analyze tryptic peptides of the Methanosarcina acetivorans SepCysS and MA1821 proteins purified anaerobically from methanogen cells. These enzymes insert sulfide into phosphoseryl(Sep)-tRNACys and aspartate semialdehyde, respectively, to form Cys-tRNACys and homocysteine. A high frequency of persulfidation at conserved cysteines of each protein was identified, while the substantial presence of persulfides in peptides from other cellular proteins suggests that this modification plays a general physiological role in the organism. Purified native SepCysS containing persulfide at conserved Cys260 generates Cys-tRNACys in anaerobic single-turnover reactions without exogenously added sulfur, directly linking active-site persulfide formation in vivo with catalytic activity.
Collapse
Affiliation(s)
- Benjamin J Rauch
- Department of Chemistry, Portland State University , P.O. Box 751, Portland, Oregon 97207, United States.,Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - John Klimek
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Larry David
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - John J Perona
- Department of Chemistry, Portland State University , P.O. Box 751, Portland, Oregon 97207, United States.,Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| |
Collapse
|