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Thomas MA, Kim SY, Curran AM, Smith B, Antiochos B, Na CH, Darrah E. An unbiased proteomic analysis of PAD4 in human monocytes: novel substrates, binding partners and subcellular localizations. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220477. [PMID: 37778379 PMCID: PMC10542449 DOI: 10.1098/rstb.2022.0477] [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: 05/01/2023] [Accepted: 08/05/2023] [Indexed: 10/03/2023] Open
Abstract
Peptidylarginine deiminase IV (PAD4) post-translationally converts arginine residues in proteins to citrullines and is implicated in playing a central role in the pathogenesis of several diseases. Although PAD4 was historically thought to be a nuclear enzyme, recent evidence has revealed a more complex localization of PAD4 with evidence of additional cytosolic and cell surface localization and activity. However, the mechanisms by which PAD4, which lacks conventional secretory signal sequences, traffics to extranuclear localizations are unknown. In this study, we show that PAD4 was enriched in the organelle fraction of monocytes with evidence of citrullination of organelle proteins. We also demonstrated that PAD4 can bind to several cytosolic, nuclear and organelle proteins that may serve as binding partners for PAD4 to traffic intracellularly. Additionally, cell surface expression of PAD4 increased with monocyte differentiation into monocyte-derived dendritic cells and co-localized with several endocytic/autophagic and conventional secretory pathway markers, implicating the use of these pathways by PAD4 to traffic within the cell. Our results suggest that PAD4 is expressed in multiple subcellular localizations and may play previously unappreciated roles in physiological and pathological conditions. This article is part of the Theo Murphy meeting issue 'The virtues and vices of protein citrullination'.
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Affiliation(s)
- Mekha A. Thomas
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, 5200 Eastern Ave, Suite 5200, Baltimore, MD 21224, USA
| | - Seok-Young Kim
- Department of Neurology, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ashley M. Curran
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, 5200 Eastern Ave, Suite 5200, Baltimore, MD 21224, USA
| | - Barbara Smith
- Department of Cell Biology, Institute for Basic Biomedical Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Brendan Antiochos
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, 5200 Eastern Ave, Suite 5200, Baltimore, MD 21224, USA
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Erika Darrah
- Division of Rheumatology, Department of Medicine, School of Medicine, Johns Hopkins University, 5200 Eastern Ave, Suite 5200, Baltimore, MD 21224, USA
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Bejarano E, Whitcomb EA, Pfeiffer RL, Rose KL, Asensio MJ, Rodríguez-Navarro JA, Ponce-Mora A, Canto A, Almansa I, Schey KL, Jones BW, Taylor A, Rowan S. Unbalanced redox status network as an early pathological event in congenital cataracts. Redox Biol 2023; 66:102869. [PMID: 37677999 PMCID: PMC10495660 DOI: 10.1016/j.redox.2023.102869] [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: 06/21/2023] [Revised: 08/08/2023] [Accepted: 08/31/2023] [Indexed: 09/09/2023] Open
Abstract
The lens proteome undergoes dramatic composition changes during development and maturation. A defective developmental process leads to congenital cataracts that account for about 30% of cases of childhood blindness. Gene mutations are associated with approximately 50% of early-onset forms of lens opacity, with the remainder being of unknown etiology. To gain a better understanding of cataractogenesis, we utilized a transgenic mouse model expressing a mutant ubiquitin protein in the lens (K6W-Ub) that recapitulates most of the early pathological changes seen in human congenital cataracts. We performed mass spectrometry-based tandem-mass-tag quantitative proteomics in E15, P1, and P30 control or K6W-Ub lenses. Our analysis identified targets that are required for early normal differentiation steps and altered in cataractous lenses, particularly metabolic pathways involving glutathione and amino acids. Computational molecular phenotyping revealed that glutathione and taurine were spatially altered in the K6W-Ub cataractous lens. High-performance liquid chromatography revealed that both taurine and the ratio of reduced glutathione to oxidized glutathione, two indicators of redox status, were differentially compromised in lens biology. In sum, our research documents that dynamic proteome changes in a mouse model of congenital cataracts impact redox biology in lens. Our findings shed light on the molecular mechanisms associated with congenital cataracts and point out that unbalanced redox status due to reduced levels of taurine and glutathione, metabolites already linked to age-related cataract, could be a major underlying mechanism behind lens opacities that appear early in life.
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Affiliation(s)
- Eloy Bejarano
- JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA; School of Health Sciences and Veterinary School, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, Valencia, Spain
| | - Elizabeth A Whitcomb
- JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
| | - Rebecca L Pfeiffer
- Moran Eye Center, The University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Kristie L Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Maria José Asensio
- Servicio de Neurobiología, Departamento de Investigación, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
| | - José Antonio Rodríguez-Navarro
- Servicio de Neurobiología, Departamento de Investigación, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain; Department of Cell Biology, Complutense University of Madrid, Madrid, Spain
| | - Alejandro Ponce-Mora
- School of Health Sciences and Veterinary School, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, Valencia, Spain
| | - Antolín Canto
- School of Health Sciences and Veterinary School, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, Valencia, Spain
| | - Inma Almansa
- School of Health Sciences and Veterinary School, Universidad Cardenal Herrera-CEU, CEU Universities, Moncada, Valencia, Spain
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bryan W Jones
- Moran Eye Center, The University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Allen Taylor
- JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA; Friedman School of Nutrition and Science Policy, Tufts University, Boston, MA, USA.
| | - Sheldon Rowan
- JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA; Friedman School of Nutrition and Science Policy, Tufts University, Boston, MA, USA.
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Curran AM, Girgis AA, Jang Y, Crawford JD, Thomas MA, Kawalerski R, Coller J, Bingham CO, Na CH, Darrah E. Citrullination modulates antigen processing and presentation by revealing cryptic epitopes in rheumatoid arthritis. Nat Commun 2023; 14:1061. [PMID: 36828807 PMCID: PMC9958131 DOI: 10.1038/s41467-023-36620-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Abstract
Cryptic peptides, hidden from the immune system under physiologic conditions, are revealed by changes to MHC class II processing and hypothesized to drive the loss of immune tolerance to self-antigens in autoimmunity. Rheumatoid arthritis (RA) is an autoimmune disease characterized by immune responses to citrullinated self-antigens, in which arginine residues are converted to citrullines. Here, we investigate the hypothesis that citrullination exposes cryptic peptides by modifying protein structure and proteolytic cleavage. We show that citrullination alters processing and presentation of autoantigens, resulting in the generation of a unique citrullination-dependent repertoire composed primarily of native sequences. This repertoire stimulates T cells from RA patients with anti-citrullinated protein antibodies more robustly than controls. The generation of this unique repertoire is achieved through altered protease cleavage and protein destabilization, rather than direct presentation of citrulline-containing epitopes, suggesting a novel paradigm for the role of protein citrullination in the breach of immune tolerance in RA.
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Affiliation(s)
- Ashley M Curran
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexander A Girgis
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yura Jang
- Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunology, Office of Biotechnology Products, Center for Drugs Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Jonathan D Crawford
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mekha A Thomas
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan Kawalerski
- Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeff Coller
- Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Clifton O Bingham
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chan Hyun Na
- Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erika Darrah
- Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Jang Y, Pletnikova O, Troncoso JC, Pantelyat AY, Dawson TM, Rosenthal LS, Na CH. Mass Spectrometry-Based Proteomics Analysis of Human Substantia Nigra From Parkinson's Disease Patients Identifies Multiple Pathways Potentially Involved in the Disease. Mol Cell Proteomics 2023; 22:100452. [PMID: 36423813 PMCID: PMC9792365 DOI: 10.1016/j.mcpro.2022.100452] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 10/26/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra (SN) of the brain. Despite decades of studies, the precise pathogenic mechanism of PD is still elusive. An unbiased proteomic analysis of PD patient's brain allows the identification of critical proteins and molecular pathways that lead to dopamine cell death and α-synuclein deposition and the resulting devastating clinical symptoms. In this study, we conducted an in-depth proteome analysis of human SN tissues from 15 PD patients and 15 healthy control individuals combining Orbitrap mass spectrometry with the isobaric tandem mass tag-based multiplexing technology. We identified 10,040 proteins with 1140 differentially expressed proteins in the SN of PD patients. Pathway analysis showed that the ribosome pathway was the most enriched one, followed by gamma-aminobutyric acidergic synapse, retrograde endocannabinoid signaling, cell adhesion molecules, morphine addiction, Prion disease, and PD pathways. Strikingly, the majority of the proteins enriched in the ribosome pathway were mitochondrial ribosomal proteins (mitoribosomes). The subsequent protein-protein interaction analysis and the weighted gene coexpression network analysis confirmed that the mitoribosome is the most enriched protein cluster. Furthermore, the mitoribosome was also identified in our analysis of a replication set of ten PD and nine healthy control SN tissues. This study provides potential disease pathways involved in PD and paves the way to study further the pathogenic mechanism of PD.
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Affiliation(s)
- Yura Jang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Juan C Troncoso
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexander Y Pantelyat
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, Louisiana, USA; Diana Helis Henry Medical Research Foundation, New Orleans, Louisiana, USA.
| | - Liana S Rosenthal
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - Chan Hyun Na
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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Lee S, Ryu HG, Kweon SH, Kim H, Park H, Lee KH, Jang SM, Na CH, Kim S, Ko HS. c-Abl Regulates the Pathological Deposition of TDP-43 via Tyrosine 43 Phosphorylation. Cells 2022; 11:3972. [PMID: 36552734 PMCID: PMC9776721 DOI: 10.3390/cells11243972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Non-receptor tyrosine kinase, c-Abl plays a role in the pathogenesis of several neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Here, we found that TDP-43, which was one of the main proteins comprising pathological deposits in amyotrophic lateral sclerosis (ALS), is a novel substrate for c-Abl. The phosphorylation of tyrosine 43 of TDP-43 by c-Abl led to increased TDP-43 levels in the cytoplasm and increased the formation of G3BP1-positive stress granules in SH-SY5Y cells. The kinase-dead mutant of c-Abl had no effect on the cytoplasmic localization of TDP-43. The expression of phosphor-mimetic mutant Y43E of TDP-43 in primary cortical neurons accumulated the neurite granule. Furthermore, the phosphorylation of TDP-43 at tyrosine 43 by c-Abl promoted the aggregation of TDP-43 and increased neuronal cell death in primary cortical neurons, but not in c-Abl-deficient primary cortical neurons. Identification of c-Abl as the kinase of TDP43 provides new insight into the pathogenesis of ALS.
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Affiliation(s)
- Saebom Lee
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hye Guk Ryu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
- Department of Cosmetic Science and Technology, Daegu Haany University, Gyeongsan 38610, Republic of Korea
| | - Sin Ho Kweon
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyerynn Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Hyeonwoo Park
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Kyung-Ha Lee
- Department of Cosmetic Science and Technology, Daegu Haany University, Gyeongsan 38610, Republic of Korea
- Department of Molecular Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Sang-Min Jang
- Department of Biochemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Chan Hyun Na
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sangjune Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Han Seok Ko
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Li R, Bhandari S, Martinez-Zubiaurre I, Bruun JA, Urbarova I, Smedsrød B, Simón-Santamaría J, Sørensen KK. Changes in the proteome and secretome of rat liver sinusoidal endothelial cells during early primary culture and effects of dexamethasone. PLoS One 2022; 17:e0273843. [PMID: 36054185 PMCID: PMC9439253 DOI: 10.1371/journal.pone.0273843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 08/16/2022] [Indexed: 11/28/2022] Open
Abstract
Introduction Liver sinusoidal endothelial cells (LSECs) are specialized fenestrated scavenger endothelial cells involved in the elimination of modified plasma proteins and tissue turnover waste macromolecules from blood. LSECs also participate in liver immune responses. A challenge when studying LSEC biology is the rapid loss of the in vivo phenotype in culture. In this study, we have examined biological processes and pathways affected during early-stage primary culture of rat LSECs and checked for cell responses to the pro-inflammatory cytokine interleukin (IL)-1β and the anti-inflammatory drug dexamethasone. Methods LSECs from male Sprague Dawley rats were cultured on type I collagen in 5% oxygen atmosphere in DMEM with serum-free supplements for 2 and 24 h. Quantitative proteomics using tandem mass tag technology was used to examine proteins in cells and supernatants. Validation was done with qPCR, ELISA, multiplex immunoassay, and caspase 3/7 assay. Cell ultrastructure was examined by scanning electron microscopy, and scavenger function by quantitative endocytosis assays. Results LSECs cultured for 24 h showed a characteristic pro-inflammatory phenotype both in the presence and absence of IL-1β, with upregulation of cellular responses to cytokines and interferon-γ, cell-cell adhesion, and glycolysis, increased expression of fatty acid binding proteins (FABP4, FABP5), and downregulation of several membrane receptors (STAB1, STAB2, LYVE1, CLEC4G) and proteins in pyruvate metabolism, citric acid cycle, fatty acid elongation, amino acid metabolism, and oxidation-reduction processes. Dexamethasone inhibited apoptosis and improved LSEC viability in culture, repressed inflammatory and immune regulatory pathways and secretion of IL-1β and IL-6, and further upregulated FABP4 and FABP5 compared to time-matched controls. The LSEC porosity and endocytic activity were reduced at 24 h both with and without dexamethasone but the dexamethasone-treated cells showed a less stressed phenotype. Conclusion Rat LSECs become activated towards a pro-inflammatory phenotype during early culture. Dexamethasone represses LSEC activation, inhibits apoptosis, and improves cell viability.
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Affiliation(s)
- Ruomei Li
- Department of Medical Biology, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Sabin Bhandari
- Department of Medical Biology, UiT–The Arctic University of Norway, Tromsø, Norway
| | | | - Jack-Ansgar Bruun
- Department of Medical Biology, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Ilona Urbarova
- Department of Community Medicine, UiT–The Arctic University of Norway, Tromsø, Norway
| | - Bård Smedsrød
- Department of Medical Biology, UiT–The Arctic University of Norway, Tromsø, Norway
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Khan SY, Ali M, Kabir F, Na CH, Delannoy M, Ma Y, Qiu C, Costello MJ, Hejtmancik JF, Riazuddin SA. The role of FYCO1-dependent autophagy in lens fiber cell differentiation. Autophagy 2022; 18:2198-2215. [PMID: 35343376 PMCID: PMC9397473 DOI: 10.1080/15548627.2022.2025570] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 12/27/2021] [Accepted: 12/31/2021] [Indexed: 11/02/2022] Open
Abstract
FYCO1 (FYVE and coiled-coil domain containing 1) is an adaptor protein, expressed ubiquitously and required for microtubule-dependent, plus-end-directed transport of macroautophagic/autophagic vesicles. We have previously shown that loss-of-function mutations in FYCO1 cause cataracts with no other ocular and/or extra-ocular phenotype. Here, we show fyco1 homozygous knockout (fyco1-/-) mice recapitulate the cataract phenotype consistent with a critical role of FYCO1 and autophagy in lens morphogenesis. Transcriptome coupled with proteome and metabolome profiling identified many autophagy-associated genes, proteins, and lipids respectively perturbed in fyco1-/- mice lenses. Flow cytometry of FYCO1 (c.2206C>T) knock-in (KI) human lens epithelial cells revealed a decrease in autophagic flux and autophagic vesicles resulting from the loss of FYCO1. Transmission electron microscopy showed cellular organelles accumulated in FYCO1 (c.2206C>T) KI lens-like organoid structures and in fyco1-/- mice lenses. In summary, our data confirm the loss of FYCO1 function results in a diminished autophagic flux, impaired organelle removal, and cataractogenesis.Abbreviations: CC: congenital cataracts; DE: differentially expressed; ER: endoplasmic reticulum; FYCO1: FYVE and coiled-coil domain containing 1; hESC: human embryonic stem cell; KI: knock-in; OFZ: organelle-free zone; qRT-PCR: quantitative real-time PCR; PE: phosphatidylethanolamine; RNA-Seq: RNA sequencing; SD: standard deviation; sgRNA: single guide RNA; shRNA: shorthairpin RNA; TEM: transmission electron microscopy; WT: wild type.
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Affiliation(s)
- Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Delannoy
- Department of Cell Biology and Imaging Facility, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yinghong Ma
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Caihong Qiu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - M. Joseph Costello
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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8
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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9
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Examining the effects of cigarette smoke on mouse lens through a multi OMIC approach. Sci Rep 2021; 11:18801. [PMID: 34552108 PMCID: PMC8458305 DOI: 10.1038/s41598-021-95013-7] [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] [Received: 12/30/2020] [Accepted: 07/14/2021] [Indexed: 11/22/2022] Open
Abstract
Here, we report a multi OMIC (transcriptome, proteome, and metabolome) approach to investigate molecular changes in lens fiber cells (FC) of mice exposed to cigarette smoke (CS). Pregnant mice were placed in a whole-body smoke chamber and a few days later pups were born, which were exposed to CS for 5 hours/day, 5 days/week for a total of 3½ months. We examined the mice exposed to CS for CS-related cataractogenesis after completion of the CS exposure but no cataracts were observed. Lenses of CS-exposed and age-matched, untreated control mice were extracted and lens FC were subjected to multi OMIC profiling. We identified 348 genes, 130 proteins, and 14 metabolites exhibiting significant (p < 0.05) differential levels in lens FC of mice exposed to CS, corresponding to 3.6%, 4.3%, and 5.0% of the total genes, protein, and metabolites, respectively identified in this study. Our multi OMIC approach confirmed that only a small fraction of the transcriptome, the proteome, and the metabolome was perturbed in the lens FC of mice exposed to CS, which suggests that exposure of CS had a minimal effect on the mouse lens. It is worth noting that while our results confirm that CS exposure does not have a substantial impact on the molecular landscape of the mouse lens FC, we cannot rule out that CS exposure for longer durations and/or in combination with other morbidities or environmental factors would have a more robust effect and/or result in cataractogenesis.
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10
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Ali M, Khan SY, Jang Y, Na CH, Talbot CC, Gottsch JD, Handa JT, Riazuddin SA. Cigarette Smoke Triggers Loss of Corneal Endothelial Cells and Disruption of Descemet's Membrane Proteins in Mice. Invest Ophthalmol Vis Sci 2021; 62:3. [PMID: 33651877 PMCID: PMC7938020 DOI: 10.1167/iovs.62.3.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To investigate changes at a molecular level in the mouse corneal endothelium (CE) exposed to chronic cigarette smoke (CS). Methods Pregnant mice (gestation days 18–20) were placed in a whole-body exposure smoking chamber, and a few days later pups were born. After 3.5 months of CS exposure, a ConfoScan4 scanning microscope was used to examine the corneal endothelial cells (CECs) of CS-exposed and control (Ct) mice. The CE was peeled under a microscope and maintained as four biological replicates (two male and two female) for CS-exposed and Ct mice; each replicate consisted of 16 CEs. The proteome of the CE was investigated through mass spectrometry. Results The CE images of CS-exposed and Ct mice revealed a difference in the shape of CECs accompanied by a nearly 10% decrease in CEC density (P < 0.00003) following CS exposure. Proteome profiling identified a total of 524 proteins exhibiting statistically significant changes in CE from CS-exposed mice. Importantly, proteins associated with Descemet's membrane (DM), including COL4α1, COL4α2, COL4α3, COL4α4, COL4α5, COL4α6, COL8α1, COL8α2, and FN1, among others, exhibited diminished protein levels in the CE of CS-exposed mice. Conclusions Our data confirm that exposure to CS results in reduced CEC density accompanied by diminished levels of multiple collagen and extracellular matrix proteins associated with DM.
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Affiliation(s)
- Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Yura Jang
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Chan Hyun Na
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - John D Gottsch
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - James T Handa
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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11
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Chu HS, Peterson C, Jun A, Foster J. Targeting the integrated stress response in ophthalmology. Curr Eye Res 2021; 46:1075-1088. [PMID: 33474991 DOI: 10.1080/02713683.2020.1867748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Purpose: To summarize the Integrated Stress Response (ISR) in the context of ophthalmology, with special interest on the cornea and anterior segment. Results: The ISR is a powerful and conserved signaling pathway that allows for cells to respond to a diverse array of both intracellular and extracellular stressors. The pathway is classically responsible for coordination of the cellular response to amino acid starvation, ultraviolet light, heme dysregulation, viral infection, and unfolded protein. Under normal circumstances, it is considered pro-survival and a necessary mechanism through which protein translation is controlled. However, in cases of severe or prolonged stress the pathway can promote apoptosis, and loss of normal cellular phenotype. The activation of this pathway culminates in the global inhibition of cap-dependent protein translation and the canonical expression of the activating transcription factor 4 (ATF4). Conclusion:The eye is uniquely exposed to ISR responsive stressors due to its environmental exposure and relative isolation from the circulatory system which are necessary for its function. We will discuss how this pathway is critical for the proper function of the tissue, its role in development, as well as how targeting of the pathway could alleviate key aspects of diverse ophthalmic diseases.
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Affiliation(s)
- Hsiao-Sang Chu
- Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA.,Department of Ophthalmology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei City, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei City, Taiwan
| | - Cornelia Peterson
- Department of Molecular & Comparative Pathobiology, Johns Hopkins University, Baltimore, MD, USA
| | - Albert Jun
- Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA
| | - James Foster
- Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University, Baltimore, MD, USA
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12
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A missense allele of PEX5 is responsible for the defective import of PTS2 cargo proteins into peroxisomes. Hum Genet 2021; 140:649-666. [PMID: 33389129 DOI: 10.1007/s00439-020-02238-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/07/2020] [Indexed: 11/27/2022]
Abstract
Peroxisomes, single-membrane intracellular organelles, play an important role in various metabolic pathways. The translocation of proteins from the cytosol to peroxisomes depends on peroxisome import receptor proteins and defects in peroxisome transport result in a wide spectrum of peroxisomal disorders. Here, we report a large consanguineous family with autosomal recessive congenital cataracts and developmental defects. Genome-wide linkage analysis localized the critical interval to chromosome 12p with a maximum two-point LOD score of 4.2 (θ = 0). Next-generation exome sequencing identified a novel homozygous missense variant (c.653 T > C; p.F218S) in peroxisomal biogenesis factor 5 (PEX5), a peroxisome import receptor protein. This missense mutation was confirmed by bidirectional Sanger sequencing. It segregated with the disease phenotype in the family and was absent in ethnically matched control chromosomes. The lens-specific knockout mice of Pex5 recapitulated the cataractous phenotype. In vitro import assays revealed a normal capacity of the mutant PEX5 to enter the peroxisomal Docking/Translocation Module (DTM) in the presence of peroxisome targeting signal 1 (PTS1) cargo protein, be monoubiquitinated and exported back into the cytosol. Importantly, the mutant PEX5 protein was unable to form a stable trimeric complex with peroxisomal biogenesis factor 7 (PEX7) and a peroxisome targeting signal 2 (PTS2) cargo protein and, therefore, failed to promote the import of PTS2 cargo proteins into peroxisomes. In conclusion, we report a novel missense mutation in PEX5 responsible for the defective import of PTS2 cargo proteins into peroxisomes resulting in congenital cataracts and developmental defects.
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13
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Khan SY, Ali M, Riazuddin SA. Metabolome profiling of the developing murine lens. Exp Eye Res 2020; 202:108343. [PMID: 33159909 DOI: 10.1016/j.exer.2020.108343] [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: 06/10/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 01/27/2023]
Abstract
Metabolomics is a study of the entire repertoire of metabolites in a cell at a particular time point. Here, we investigate the mouse lens at multiple embryonic and postnatal time points to establish the metabolome profile during early lens development. The lenses were isolated at six time points including embryonic day 15 (E15) and E18 and postnatal day 0 (P0), P3, P6, and P9. A total of four biological replicates of each time point, each consisting of 25 mg of lens tissue were preserved. Sample preparation was performed by protein precipitation followed by centrifugation to remove proteins and recover metabolites. The resulting extract was subjected to reverse phase/ultra-performance liquid chromatography-tandem mass spectrometry. Metabolome profiling identified a total of 353 metabolites in mouse lens, marked with an abundance of collagen, antioxidant, glycosaminoglycans, lipid, amino acid, and energy-related metabolites. A comparative metabolome analysis identified >200 metabolites exhibiting increased levels (p < 0.05) at latter time points relative to E15. Principal component analysis revealed distinct metabolomic signatures running from E15 to P9 while random forest analysis categorized lipid-, amino acid-, and nucleotide-related metabolites contributing significantly to the separation of the time points. To the best of our knowledge, this is the first report investigating the mouse lens metabolome at multiple embryonic and postnatal time points.
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Affiliation(s)
- Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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14
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Yu SH, Kyriakidou P, Cox J. Isobaric Matching between Runs and Novel PSM-Level Normalization in MaxQuant Strongly Improve Reporter Ion-Based Quantification. J Proteome Res 2020; 19:3945-3954. [PMID: 32892627 PMCID: PMC7586393 DOI: 10.1021/acs.jproteome.0c00209] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
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Isobaric
labeling has the promise of combining high sample multiplexing
with precise quantification. However, normalization issues and the
missing value problem of complete n-plexes hamper
quantification across more than one n-plex. Here,
we introduce two novel algorithms implemented in MaxQuant that substantially
improve the data analysis with multiple n-plexes.
First, isobaric matching between runs makes use of the three-dimensional
MS1 features to transfer identifications from identified to unidentified
MS/MS spectra between liquid chromatography–mass spectrometry
runs in order to utilize reporter ion intensities in unidentified
spectra for quantification. On typical datasets, we observe a significant
gain in MS/MS spectra that can be used for quantification. Second,
we introduce a novel PSM-level normalization, applicable to data with
and without the common reference channel. It is a weighted median-based
method, in which the weights reflect the number of ions that were
used for fragmentation. On a typical dataset, we observe complete
removal of batch effects and dominance of the biological sample grouping
after normalization. Furthermore, we provide many novel processing
and normalization options in Perseus, the companion software for the
downstream analysis of quantitative proteomics results. All novel
tools and algorithms are available with the regular MaxQuant and Perseus
releases, which are downloadable at http://maxquant.org.
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Affiliation(s)
- Sung-Huan Yu
- Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Pelagia Kyriakidou
- Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Jürgen Cox
- Computational Systems Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany.,Department of Biological and Medical Psychology, University of Bergen, Jonas Liesvei 91, Bergen 5009, Norway
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15
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Ali M, Kabir F, Raskar S, Renuse S, Na CH, Delannoy M, Khan SY, Riazuddin SA. Generation and proteome profiling of PBMC-originated, iPSC-derived lentoid bodies. Stem Cell Res 2020; 46:101813. [PMID: 32474394 DOI: 10.1016/j.scr.2020.101813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/18/2020] [Accepted: 04/09/2020] [Indexed: 01/13/2023] Open
Abstract
Here, we report proteome profiling of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cell (iPSC)-derived, lens-like organoids termed lentoid bodies at two differentiation time points. A small aliquot of the blood sample was ascertained to collect PBMCs that were reprogrammed to iPSCs. The PBMC-originated, iPSCs were differentiated to lentoid bodies employing the "fried egg" method. Quantitative real-time PCR (qRT-PCR) analysis revealed increased expression levels of lens-associated markers in lentoid bodies while transmission electron microscopy identified closely packed lens epithelial- and differentiating fiber-like cells in lentoid bodies. Total cellular protein was extracted from lentoid bodies at differentiation day 25 and mass spectrometry identified a total of 9,473 proteins. The low counts of crystallin proteins at differentiation day 25 prompted us to re-examine the proteome at differentiation day 35 as we reasoned that 10 additional days of differentiation will increase the crystallin count. However, we did not detect any substantial increase in crystallin protein counts at differentiation day 35. In conclusion, we report generation and proteome profiles of PBMC-originated, iPSC-derived lentoid bodies at multiple differentiation time points.
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Affiliation(s)
- Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Snehal Raskar
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Santosh Renuse
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chan Hyun Na
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael Delannoy
- Department of Cell Biology and Imaging Facility, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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16
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Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies. Sci Rep 2019; 9:18552. [PMID: 31811247 PMCID: PMC6898283 DOI: 10.1038/s41598-019-54258-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/26/2019] [Indexed: 01/18/2023] Open
Abstract
The ocular lens serves as an excellent system to investigate the intricate details of development and differentiation. Generation of lentoid bodies or lens-like structures using pluripotent stem cells is important for understanding the processes critical for lens morphogenesis and the mechanism of cataractogenesis. We previously reported the generation of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cells (iPSCs). Here, we report generation of lentoid bodies from human embryonic stem cells (hESCs) and (PBMC)-originated, iPSCs employing the “fried egg” method with brief modifications. The ultrastructure analysis of hESC- and iPSC-derived lentoid bodies identified closely packed lens epithelial- and differentiating fiber-like cells. In addition, we performed RNA sequencing (RNA-Seq) based transcriptome profiling of hESC- and iPSC-derived lentoid bodies at differentiation day 25. Next-generation RNA sequencing (RNA-Seq) of hESC- and iPSC-derived lentoid bodies detected expression (≥0.659 RPKM) of 13,975 and 14,003 genes, respectively. Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies revealed 13,563 (>96%) genes common in both datasets. Among the genes common in both transcriptome datasets, 12,856 (~95%) exhibited a quantitatively similar expression profile. Next, we compared the mouse lens epithelial and fiber cell transcriptomes with hESC- and iPSC-derived lentoid bodies transcriptomes and identified > 96% overlap with lentoid body transcriptomes. In conclusion, we report first-time comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies at differentiation day 25.
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17
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Aryal S, Anand D, Hernandez FG, Weatherbee BAT, Huang H, Reddy AP, Wilmarth PA, David LL, Lachke SA. MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery: application to lens development and cataract. Hum Genet 2019; 139:151-184. [PMID: 31797049 DOI: 10.1007/s00439-019-02095-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 11/24/2019] [Indexed: 12/20/2022]
Abstract
While the bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery) effectively identifies human cataract-associated genes, it is currently based on just transcriptome data, and thus, it is necessary to include protein-level information to gain greater confidence in gene prioritization. Here, we expand iSyTE through development of a novel proteome-based resource on the lens and demonstrate its utility in cataract gene discovery. We applied high-throughput tandem mass spectrometry (MS/MS) to generate a global protein expression profile of mouse lens at embryonic day (E)14.5, which identified 2371 lens-expressed proteins. A major challenge of high-throughput expression profiling is identification of high-priority candidates among the thousands of expressed proteins. To address this problem, we generated new MS/MS proteome data on mouse whole embryonic body (WB). WB proteome was then used as a reference dataset for performing "in silico WB-subtraction" comparative analysis with the lens proteome, which effectively identified 422 proteins with lens-enriched expression at ≥ 2.5 average spectral counts, ≥ 2.0 fold enrichment (FDR < 0.01) cut-off. These top 20% candidates represent a rich pool of high-priority proteins in the lens including known human cataract-linked genes and many new potential regulators of lens development and homeostasis. This rich information is made publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/), which enables user-friendly visualization of promising candidates, thus making iSyTE a comprehensive tool for cataract gene discovery.
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Affiliation(s)
- Sandeep Aryal
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Francisco G Hernandez
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Bailey A T Weatherbee
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Larry L David
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, 97239, USA
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA.
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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18
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Ning M, Wei P, Shen H, Wan X, Jin M, Li X, Shi H, Qiao Y, Jiang G, Gu W, Wang W, Wang L, Meng Q. Proteomic and metabolomic responses in hepatopancreas of whiteleg shrimp Litopenaeus vannamei infected by microsporidian Enterocytozoon hepatopenaei. FISH & SHELLFISH IMMUNOLOGY 2019; 87:534-545. [PMID: 30721776 DOI: 10.1016/j.fsi.2019.01.051] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/25/2019] [Accepted: 01/30/2019] [Indexed: 05/14/2023]
Abstract
Enterocytozoon hepatopenaei (EHP) causes hepatopancreatic microsporidiosis (HPM) in shrimp. HPM is not normally associated with shrimp mortality, but is associated with significant growth retardation. In this study, the responses induced by EHP were investigated in hepatopancreas of shrimp Litopenaeus vannamei using proteomics and metabolomics. Among differential proteins identified, several (e.g., peritrophin-44-like protein, alpha2 macroglobulin isoform 2, prophenoloxidase-activating enzymes, ferritin, Rab11A and cathepsin C) were related to pathogen infection and host immunity. Other proteomic biomarkers (i.e., farnesoic acid o-methyltransferase, juvenile hormone esterase-like carboxylesterase 1 and ecdysteroid-regulated protein) resulted in a growth hormone disorder that prevented the shrimp from molting. Both proteomic KEGG pathway (e.g., "Glycolysis/gluconeogenesis" and "Glyoxylate and dicarboxylate metabolism") and metabolomic KEGG pathway (e.g., "Galactose metabolism" and "Biosynthesis of unsaturated fatty acids") data indicated that energy metabolism pathway was down-regulated in the hepatopancreas when infected by EHP. More importantly, the changes of hormone regulation and energy metabolism could provide much-needed insight into the underlying mechanisms of stunted growth in shrimp after EHP infection. Altogether, this study demonstrated that proteomics and metabolomics could provide an insightful view into the effects of microsporidial infection in the shrimp L. vannamei.
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Affiliation(s)
- Mingxiao Ning
- College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Panpan Wei
- College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Hui Shen
- Institute of Oceanology and Marine Fisheries, Jiangsu, Jiangsu, 226007, China
| | - Xihe Wan
- Institute of Oceanology and Marine Fisheries, Jiangsu, Jiangsu, 226007, China
| | - Mingjian Jin
- Rudong Center for Control and Prevention of Aquatic Animal Infectious Disease, 25# Changjiang Road, Rudong, 226400, China
| | - Xiangqian Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hao Shi
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Yi Qiao
- Institute of Oceanology and Marine Fisheries, Jiangsu, Jiangsu, 226007, China
| | - Ge Jiang
- Institute of Oceanology and Marine Fisheries, Jiangsu, Jiangsu, 226007, China
| | - Wei Gu
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China
| | - Wen Wang
- College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China
| | - Li Wang
- College of Life Science and Technology, Southwest Minzu University, Chengdu, 610041, China.
| | - Qingguo Meng
- Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu, 222005, China.
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19
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Zhao Y, Wilmarth PA, Cheng C, Limi S, Fowler VM, Zheng D, David LL, Cvekl A. Proteome-transcriptome analysis and proteome remodeling in mouse lens epithelium and fibers. Exp Eye Res 2019; 179:32-46. [PMID: 30359574 PMCID: PMC6360118 DOI: 10.1016/j.exer.2018.10.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 08/31/2018] [Accepted: 10/20/2018] [Indexed: 12/21/2022]
Abstract
Epithelial cells and differentiated fiber cells represent distinct compartments in the ocular lens. While previous studies have revealed proteins that are preferentially expressed in epithelial vs. fiber cells, a comprehensive proteomics library comparing the molecular compositions of epithelial vs. fiber cells is essential for understanding lens formation, function, disease and regenerative potential, and for efficient differentiation of pluripotent stem cells for modeling of lens development and pathology in vitro. To compare protein compositions between the lens epithelium and fibers, we employed tandem mass spectrometry (2D-LC/MS) analysis of microdissected mouse P0.5 lenses. Functional classifications of the top 525 identified proteins into gene ontology categories by molecular processes and subcellular localizations, were adapted for the lens. Expression levels of both epithelial and fiber proteomes were compared with whole lens proteome and mRNA levels using E14.5, E16.5, E18.5, and P0.5 RNA-Seq data sets. During this developmental time window, multiple complex biosynthetic and catabolic processes generate the molecular and structural foundation for lens transparency. As expected, crystallins showed a high correlation between their mRNA and protein levels. Comprehensive data analysis confirmed and/or predicted roles for transcription factors (TFs), RNA-binding proteins (e.g. Carhsp1), translational apparatus including ribosomal heterogeneity and initiation factors, microtubules, cytoskeletal [e.g. non-muscle myosin IIA heavy chain (Myh9) and βB2-spectrin (Sptbn2)] and membrane proteins in lens formation and maturation. Our data highlighted many proteins with unknown functions in the lens that were preferentially enriched in epithelium or fibers, setting the stage for future studies to further dissect the roles of these proteins in fiber cell differentiation vs. epithelial cell maintenance. In conclusion, the present proteomic datasets represent the first mouse lens epithelium and fiber cell proteomes, establish comparative analyses of protein and RNA-Seq data, and characterize the major proteome remodeling required to form the mature lens fiber cells.
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Affiliation(s)
- Yilin Zhao
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Phillip A Wilmarth
- Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Catherine Cheng
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Saima Limi
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Velia M Fowler
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Deyou Zheng
- Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Neurology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Neurosurgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Larry L David
- Department of Biochemistry & Molecular Biology, Oregon Health Sciences University, 3181 Southwest Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Ales Cvekl
- Departments Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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20
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Identification of novel transcripts and peptides in developing murine lens. Sci Rep 2018; 8:11162. [PMID: 30042402 PMCID: PMC6057992 DOI: 10.1038/s41598-018-28727-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/19/2018] [Indexed: 01/09/2023] Open
Abstract
We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9). Here, we extend our analyses to identify novel transcripts and peptides in developing mouse lens. We identified a total of 9,707 novel transcripts and 325 novel fusion genes in developing mouse lens. Additionally, we identified 13,281 novel alternative splicing (AS) events in mouse lens including 6,990 exon skipping (ES), 2,447 alternative 3' splice site (A3SS), 1,900 alternative 5' splice site (A5SS), 1,771 mutually exclusive exons (MXE), and 173 intron retention (IR). Finally, we integrated our OMIC (Transcriptome and Proteome) datasets identifying 20 novel peptides in mouse lens. All 20 peptides were validated through matching MS/MS spectra of synthetic peptides. To the best of our knowledge, this is the first report integrating OMIC datasets to identify novel peptides in developing murine lens.
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