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Kremer JL, Sanchez Ortega H, Souza-Siqueira T, Blanes Angeli C, Kei Iwai L, Palmisano G, Ferini Pacicco Lotfi C. Proteomic profiling of the extracellular matrix in the human adrenal cortex. Matrix Biol Plus 2024; 23:100158. [PMID: 39188294 PMCID: PMC11345916 DOI: 10.1016/j.mbplus.2024.100158] [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] [Received: 04/20/2024] [Revised: 07/09/2024] [Accepted: 07/25/2024] [Indexed: 08/28/2024] Open
Abstract
The extracellular matrix (ECM) comprises macromolecules that shape a complex three-dimensional network. Filling the intercellular space and playing a crucial role in the structure and function of tissues, ECM regulates essential cellular processes such as adhesion, differentiation, and cell signaling. In the human adrenal gland, composed of cortex and medulla surrounded by a capsule, the ECM has not yet been directly described, although its impact on the processes of proliferation and steroidogenesis of the adrenal cortex is recognized. This study analyzes the ECM of the adult human adrenal cortex, which was separated into outer fraction (OF) and inner fraction (IF), by comparing their proteomic profiles. The study discusses the composition, spatial distribution, and relevance of differentially expressed ECM signatures of the adrenal cortex matrisome on adrenal structure and function. The findings were validated through database analysis (cross-validation), histochemical, and immunohistochemical approaches. A total of 121 ECM proteins were identified and categorized into glycoproteins, collagens, ECM regulators, proteoglycans, ECM-affiliated proteins, and secreted factors. Thirty-one ECM proteins were identified only in OF, nine only in IF, and 81 were identified in common with both fractions. Additionally, 106 ECM proteins were reported in the Human matrisome DB 2.0, and the proteins differentially expressed in OF and IF, were identified. This study provides significant insights into the composition and regulation of the ECM in the human adrenal cortex, shedding light on the adrenal microenvironment and its role in the functioning, maintenance, and renewal of the adrenal gland.
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Affiliation(s)
- Jean Lucas Kremer
- Laboratory of Cellular Structure and Function, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Henrique Sanchez Ortega
- Laboratory of Cellular Structure and Function, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Talita Souza-Siqueira
- Department of Clinical Medicine, Laboratory of Cellular, Genetic and Molecular Nephrology, University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Claudia Blanes Angeli
- Glycoproteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Brazil
| | - Leo Kei Iwai
- Laboratory of Applied Toxicology, Center of Toxins, Immune-response and Cell Signaling LETA/CeTICS Laboratory, Butantan Institute, São Paulo, Brazil
| | - Giuseppe Palmisano
- Glycoproteomics Laboratory, Department of Parasitology, ICB, University of São Paulo, Brazil
- School of Natural Science, Macquarie University, Sydney, Australia
| | - Claudimara Ferini Pacicco Lotfi
- Laboratory of Cellular Structure and Function, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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2
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Faktor J, Kote S, Bienkowski M, Hupp TR, Marek-Trzonkowska N. Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker. Commun Biol 2024; 7:708. [PMID: 38851810 PMCID: PMC11162451 DOI: 10.1038/s42003-024-06354-8] [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: 01/20/2023] [Accepted: 05/20/2024] [Indexed: 06/10/2024] Open
Abstract
Robotically assisted proteomics provides insights into the regulation of multiple proteins achieving excellent spatial resolution. However, developing an effective method for spatially resolved quantitative proteomics of formalin fixed paraffin embedded tissue (FFPE) in an accessible and economical manner remains challenging. We introduce non-robotic In-insert FFPE proteomics approach, combining glass insert FFPE tissue processing with spatial quantitative data-independent mass spectrometry (DIA). In-insert approach identifies 450 proteins from a 5 µm thick breast FFPE tissue voxel with 50 µm lateral dimensions covering several tens of cells. Furthermore, In-insert approach associated a keratin series and moesin (MOES) with prolactin-induced protein (PIP) indicating their prolactin and/or estrogen regulation. Our data suggest that PIP is a spatial biomarker for hormonally triggered cytoskeletal remodeling, potentially useful for screening hormonally affected hotspots in breast tissue. In-insert proteomics represents an alternative FFPE processing method, requiring minimal laboratory equipment and skills to generate spatial proteotype repositories from FFPE tissue.
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Affiliation(s)
- Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Michal Bienkowski
- Medical University of Gdansk, University of Gdansk, Mariana Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Ted R Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
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3
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Darville LNF, Lockhart JH, Putty Reddy S, Fang B, Izumi V, Boyle TA, Haura EB, Flores ER, Koomen JM. A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues. Methods Mol Biol 2024; 2823:193-223. [PMID: 39052222 DOI: 10.1007/978-1-0716-3922-1_13] [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] [Indexed: 07/27/2024]
Abstract
Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the cross-linking and pre-analytical variables, these samples have utility for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients' medical histories. Proteomics of formalin-fixed paraffin-embedded (FFPE) tissues also integrates with histological evaluation and molecular pathology strategies, so that additional collection of research biopsies or resected tumor aliquots is not needed. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the protein extraction and proteomics sample preparation from FFPE samples can be onerous, particularly for small (i.e., limited or precious) samples. Therefore, we provide a protocol for a recently introduced kit-based EasyPep method with benchmarking against a modified version of the well-established filter-aided sample preparation strategy using laser-capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables while also supporting the development of methods for spatial proteomics to examine intratumoral heterogeneity. Data are posted in ProteomeXchange (PXD045879).
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Affiliation(s)
| | | | | | - Bin Fang
- H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | | | - John M Koomen
- H. Lee Moffitt Cancer Center, Tampa, FL, USA.
- Molecular Oncology/Pathology, Moffitt Cancer Center, Tampa, FL, USA.
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4
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Brady A, Sheneman KR, Pulsifer AR, Price SL, Garrison TM, Maddipati KR, Bodduluri SR, Pan J, Boyd NL, Zheng JJ, Rai SN, Hellmann J, Haribabu B, Uriarte SM, Lawrenz MB. Type 3 secretion system induced leukotriene B4 synthesis by leukocytes is actively inhibited by Yersinia pestis to evade early immune recognition. PLoS Pathog 2024; 20:e1011280. [PMID: 38271464 PMCID: PMC10846697 DOI: 10.1371/journal.ppat.1011280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 02/06/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Subverting the host immune response to inhibit inflammation is a key virulence strategy of Yersinia pestis. The inflammatory cascade is tightly controlled via the sequential action of lipid and protein mediators of inflammation. Because delayed inflammation is essential for Y. pestis to cause lethal infection, defining the Y. pestis mechanisms to manipulate the inflammatory cascade is necessary to understand this pathogen's virulence. While previous studies have established that Y. pestis actively inhibits the expression of host proteins that mediate inflammation, there is currently a gap in our understanding of the inflammatory lipid mediator response during plague. Here we used the murine model to define the kinetics of the synthesis of leukotriene B4 (LTB4), a pro-inflammatory lipid chemoattractant and immune cell activator, within the lungs during pneumonic plague. Furthermore, we demonstrated that exogenous administration of LTB4 prior to infection limited bacterial proliferation, suggesting that the absence of LTB4 synthesis during plague contributes to Y. pestis immune evasion. Using primary leukocytes from mice and humans further revealed that Y. pestis actively inhibits the synthesis of LTB4. Finally, using Y. pestis mutants in the Ysc type 3 secretion system (T3SS) and Yersinia outer protein (Yop) effectors, we demonstrate that leukocytes recognize the T3SS to initiate the rapid synthesis of LTB4. However, several Yop effectors secreted through the T3SS effectively inhibit this host response. Together, these data demonstrate that Y. pestis actively inhibits the synthesis of the inflammatory lipid LTB4 contributing to the delay in the inflammatory cascade required for rapid recruitment of leukocytes to sites of infection.
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Affiliation(s)
- Amanda Brady
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Katelyn R. Sheneman
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Amanda R. Pulsifer
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Sarah L. Price
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Taylor M. Garrison
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Krishna Rao Maddipati
- Department of Pathology, Lipidomics Core Facility, Wayne State University, Detroit, Michigan, United States of America
| | - Sobha R. Bodduluri
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Jianmin Pan
- Biostatistics and Bioinformatics Facility, Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Nolan L. Boyd
- Center for Cardiometabolic Science, Christina Lee Brown Environment Institute, Division of Environmental Medicine, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Jing-Juan Zheng
- Center for Cardiometabolic Science, Christina Lee Brown Environment Institute, Division of Environmental Medicine, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Shesh N. Rai
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Jason Hellmann
- Center for Cardiometabolic Science, Christina Lee Brown Environment Institute, Division of Environmental Medicine, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Bodduluri Haribabu
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
| | - Silvia M. Uriarte
- Deptartment of Oral Immunology & Infectious Diseases, University of Louisville, Louisville, Kentucky, United States of America
| | - Matthew B. Lawrenz
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky, United States of America
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, Louisville, Kentucky, United States of America
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5
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Elnagdy M, Wang Y, Rodriguez W, Zhang J, Bauer P, Wilkey DW, Merchant M, Pan J, Farooqui Z, Cannon R, Rai S, Maldonado C, Barve S, McClain CJ, Gobejishvili L. Increased expression of phosphodiesterase 4 in activated hepatic stellate cells promotes cytoskeleton remodeling and cell migration. J Pathol 2023; 261:361-371. [PMID: 37735782 PMCID: PMC10653049 DOI: 10.1002/path.6194] [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: 02/12/2023] [Revised: 06/24/2023] [Accepted: 07/30/2023] [Indexed: 09/23/2023]
Abstract
Activation and transdifferentiation of hepatic stellate cells (HSC) into migratory myofibroblasts is a key process in liver fibrogenesis. Cell migration requires an active remodeling of the cytoskeleton, which is a tightly regulated process coordinated by Rho-specific guanine nucleotide exchange factors (GEFs) and the Rho family of small GTPases. Rho-associated kinase (ROCK) promotes assembly of focal adhesions and actin stress fibers by regulating cytoskeleton organization. GEF exchange protein directly activated by cAMP 1 (EPAC1) has been implicated in modulating TGFβ1 and Rho signaling; however, its role in HSC migration has never been examined. The aim of this study was to evaluate the role of cAMP-degrading phosphodiesterase 4 (PDE4) enzymes in regulating EPAC1 signaling, HSC migration, and fibrogenesis. We show that PDE4 protein expression is increased in activated HSCs expressing alpha smooth muscle actin and active myosin light chain (MLC) in fibrotic tissues of human nonalcoholic steatohepatitis cirrhosis livers and mouse livers exposed to carbon tetrachloride. In human livers, TGFβ1 levels were highly correlated with PDE4 expression. TGFβ1 treatment of LX2 HSCs decreased levels of cAMP and EPAC1 and increased PDE4D expression. PDE4 specific inhibitor, rolipram, and an EPAC-specific agonist decreased TGFβ1-mediated cell migration in vitro. In vivo, targeted delivery of rolipram to the liver prevented fibrogenesis and collagen deposition and decreased the expression of several fibrosis-related genes, and HSC activation. Proteomic analysis of mouse liver tissues identified the regulation of actin cytoskeleton by the kinase effectors of Rho GTPases as a major pathway impacted by rolipram. Western blot analyses confirmed that PDE4 inhibition decreased active MLC and endothelin 1 levels, key proteins involved in cytoskeleton remodeling and contractility. The current study, for the first time, demonstrates that PDE4 enzymes are expressed in hepatic myofibroblasts and promote cytoskeleton remodeling and HSC migration. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Mohamed Elnagdy
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Kentucky, USA
| | - Yali Wang
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
| | - Walter Rodriguez
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
| | - JingWen Zhang
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
| | - Philip Bauer
- Department of Physiology, School of Medicine, University of Louisville, Kentucky, USA
- EndoProtech, Inc., Louisville, Kentucky, USA
| | - Daniel W. Wilkey
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
| | - Michael Merchant
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Kentucky, USA
| | - Jianmin Pan
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Kentucky, USA
| | - Zainab Farooqui
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
| | - Robert Cannon
- Department of Surgery, School of Medicine, University of Louisville, Kentucky, USA
| | - Shesh Rai
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Kentucky, USA
| | - Claudio Maldonado
- Department of Physiology, School of Medicine, University of Louisville, Kentucky, USA
- EndoProtech, Inc., Louisville, Kentucky, USA
| | - Shirish Barve
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Kentucky, USA
| | - Craig J. McClain
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Kentucky, USA
- Robley Rex VA Medical Center, Louisville, Kentucky, USA
| | - Leila Gobejishvili
- University of Louisville Alcohol Research Center, University of Louisville, Kentucky, USA
- Hepatobiology and Toxicology Center, University of Louisville, Kentucky, USA
- Department of Medicine, School of Medicine, University of Louisville, Kentucky, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Kentucky, USA
- Department of Physiology, School of Medicine, University of Louisville, Kentucky, USA
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6
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Piell KM, Petri BJ, Head KZ, Wahlang B, Xu R, Zhang X, Pan J, Rai SN, de Silva K, Chariker JH, Rouchka EC, Tan M, Li Y, Cave MC, Klinge CM. Disruption of the mouse liver epitranscriptome by long-term aroclor 1260 exposure. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 100:104138. [PMID: 37137421 PMCID: PMC10330322 DOI: 10.1016/j.etap.2023.104138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/05/2023]
Abstract
Chronic environmental exposure to polychlorinated biphenyls (PCBs) is associated with non-alcoholic fatty liver disease (NAFLD) and exacerbated by a high fat diet (HFD). Here, chronic (34 wks.) exposure of low fat diet (LFD)-fed male mice to Aroclor 1260 (Ar1260), a non-dioxin-like (NDL) mixture of PCBs, resulted in steatohepatitis and NAFLD. Twelve hepatic RNA modifications were altered with Ar1260 exposure including reduced abundance of 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A), in contrast to increased Am in the livers of HFD-fed, Ar1260-exposed mice reported previously. Differences in 13 RNA modifications between LFD- and HFD- fed mice, suggest that diet regulates the liver epitranscriptome. Integrated network analysis of epitranscriptomic modifications identified a NRF2 (Nfe2l2) pathway in the chronic, LFD, Ar1260-exposed livers and an NFATC4 (Nfatc4) pathway for LFD- vs. HFD-fed mice. Changes in protein abundance were validated. The results demonstrate that diet and Ar1260 exposure alter the liver epitranscriptome in pathways associated with NAFLD.
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Affiliation(s)
- Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Kimberly Z Head
- University of Louisville Hepatobiology and Toxicology Center, USA
| | - Banrida Wahlang
- University of Louisville Hepatobiology and Toxicology Center, USA
| | - Raobo Xu
- University of Louisville Hepatobiology and Toxicology Center, USA; Department of Chemistry, University of Louisville College of Arts and Sciences, USA
| | - Xiang Zhang
- University of Louisville Hepatobiology and Toxicology Center, USA; Department of Chemistry, University of Louisville College of Arts and Sciences, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA
| | - Jianmin Pan
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; Cancer Data Science Center, Biostatistics and Informatics Shared Resource, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Shesh N Rai
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; Cancer Data Science Center, Biostatistics and Informatics Shared Resource, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Kalpani de Silva
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA; Department of Neuroscience Training, University of Louisville, Louisville, KY 40292, USA
| | - Julia H Chariker
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA; Department of Neuroscience Training, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Min Tan
- Division of Surgical Oncology, Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Yan Li
- Division of Surgical Oncology, Department of Surgery, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Matthew C Cave
- University of Louisville Hepatobiology and Toxicology Center, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA; The University of Louisville Superfund Research Center, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA.
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7
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An Optimized Comparative Proteomic Approach as a Tool in Neurodegenerative Disease Research. Cells 2022; 11:cells11172653. [PMID: 36078061 PMCID: PMC9454658 DOI: 10.3390/cells11172653] [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: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Recent advances in proteomic technologies now allow unparalleled assessment of the molecular composition of a wide range of sample types. However, the application of such technologies and techniques should not be undertaken lightly. Here, we describe why the design of a proteomics experiment itself is only the first step in yielding high-quality, translatable results. Indeed, the effectiveness and/or impact of the majority of contemporary proteomics screens are hindered not by commonly considered technical limitations such as low proteome coverage but rather by insufficient analyses. Proteomic experimentation requires a careful methodological selection to account for variables from sample collection, through to database searches for peptide identification to standardised post-mass spectrometry options directed analysis workflow, which should be adjusted for each study, from determining when and how to filter proteomic data to choosing holistic versus trend-wise analyses for biologically relevant patterns. Finally, we highlight and discuss the difficulties inherent in the modelling and study of the majority of progressive neurodegenerative conditions. We provide evidence (in the context of neurodegenerative research) for the benefit of undertaking a comparative approach through the application of the above considerations in the alignment of publicly available pre-existing data sets to identify potential novel regulators of neuronal stability.
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8
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Petri BJ, Piell KM, Wahlang B, Head KZ, Andreeva K, Rouchka EC, Pan J, Rai SN, Cave MC, Klinge CM. Multiomics analysis of the impact of polychlorinated biphenyls on environmental liver disease in a mouse model. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 94:103928. [PMID: 35803474 DOI: 10.1016/j.etap.2022.103928] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/27/2022] [Accepted: 07/03/2022] [Indexed: 06/15/2023]
Abstract
Exposure to high fat diet (HFD) and persistent organic pollutants including polychlorinated biphenyls (PCBs) is associated with liver injury in human populations and non-alcoholic fatty liver disease (NAFLD) and steatohepatitis (NASH) in animal models. Previously, exposure of HFD-fed male mice to the non-dioxin-like (NDL) PCB mixture Aroclor1260, dioxin-like (DL) PCB126, or Aroclor1260 + PCB126 co-exposure caused toxicant-associated steatohepatitis (TASH) and differentially altered the liver proteome. Here unbiased mRNA and miRNA sequencing (mRNA- and miRNA- seq) was used to identify biological pathways altered in these liver samples. Fewer transcripts and miRs were up- or down- regulated by PCB126 or Aroclor1260 compared to the combination, suggesting that crosstalk between the receptors activated by these PCBs amplifies changes in the transcriptome. Pathway enrichment analysis identified "positive regulation of Wnt/β-catenin signaling" and "role of miRNAs in cell migration, survival, and angiogenesis" for differentially expressed mRNAs and miRNAs, respectively. We evaluated the five miRNAs increased in human plasma with PCB exposure and suspected TASH and found that miR-192-5p was increased with PCB exposure in mouse liver. Although we observed little overlap between differentially expressed mRNA transcripts and proteins, biological pathway-relevant PCB-induced miRNA-mRNA and miRNA-protein inverse relationships were identified that may explain protein changes. These results provide novel insights into miRNA and mRNA transcriptome changes playing direct and indirect roles in the functional protein pathways in PCB-related hepatic lipid accumulation, inflammation, and fibrosis in a mouse model of TASH and its relevance to human liver disease in exposed populations.
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Affiliation(s)
- Belinda J Petri
- Department of Biochemistry & Molecular Genetics, Center for Genetics and Molecular Medicine University of Louisville, Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, Center for Genetics and Molecular Medicine University of Louisville, Louisville, KY 40292, USA
| | - Banrida Wahlang
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Kimberly Z Head
- University of Louisville Hepatobiology and Toxicology Center, USA
| | | | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, Center for Genetics and Molecular Medicine University of Louisville, Louisville, KY 40292, USA; KY INBRE Bioinformatics Core, University of Louisville, USA
| | - Jianmin Pan
- Biostatistics and Bioinformatics Facility, Brown Cancer Center, USA
| | - Shesh N Rai
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; Biostatistics and Bioinformatics Facility, Brown Cancer Center, USA
| | - Matthew C Cave
- Department of Biochemistry & Molecular Genetics, Center for Genetics and Molecular Medicine University of Louisville, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, Center for Genetics and Molecular Medicine University of Louisville, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA.
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9
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Jin J, Wahlang B, Thapa M, Head KZ, Hardesty JE, Srivastava S, Merchant ML, Rai SN, Prough RA, Cave MC. Proteomics and metabolic phenotyping define principal roles for the aryl hydrocarbon receptor in mouse liver. Acta Pharm Sin B 2021; 11:3806-3819. [PMID: 35024308 PMCID: PMC8727924 DOI: 10.1016/j.apsb.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/20/2022] Open
Abstract
Dioxin-like molecules have been associated with endocrine disruption and liver disease. To better understand aryl hydrocarbon receptor (AHR) biology, metabolic phenotyping and liver proteomics were performed in mice following ligand-activation or whole-body genetic ablation of this receptor. Male wild type (WT) and Ahr–/– mice (Taconic) were fed a control diet and exposed to 3,3′,4,4′,5-pentachlorobiphenyl (PCB126) (61 nmol/kg by gavage) or vehicle for two weeks. PCB126 increased expression of canonical AHR targets (Cyp1a1 and Cyp1a2) in WT but not Ahr–/–. Knockouts had increased adiposity with decreased glucose tolerance; smaller livers with increased steatosis and perilipin-2; and paradoxically decreased blood lipids. PCB126 was associated with increased hepatic triglycerides in Ahr–/–. The liver proteome was impacted more so by Ahr–/– genotype than ligand-activation, but top gene ontology (GO) processes were similar. The PCB126-associated liver proteome was Ahr-dependent. Ahr principally regulated liver metabolism (e.g., lipids, xenobiotics, organic acids) and bioenergetics, but it also impacted liver endocrine response (e.g., the insulin receptor) and function, including the production of steroids, hepatokines, and pheromone binding proteins. These effects could have been indirectly mediated by interacting transcription factors or microRNAs. The biologic roles of the AHR and its ligands warrant more research in liver metabolic health and disease.
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Key Words
- AHR
- AHR, aryl hydrocarbon receptor
- ALT, alanine transaminase
- ANOVA, analysis of variance
- AST, aspartate transaminase
- AUC, area under the curve
- CAR, constitutive androstane receptor
- CD36, cluster of differentiation 36
- CYP, cytochrome P450
- EPF, enrichment by protein function
- Endocrine disruption
- Environmental liver disease
- FDR, false discovery rate
- FGF21, fibroblast growth factor 21
- GCR, glucocorticoid receptor
- GO, gene ontology
- H&E, hematoxylin-eosin
- HDL, high-density lipoprotein
- HFD, high fat diet
- IGF1, insulin-like growth factor 1
- IL-6, interleukin 6
- IPF, interaction by protein function
- LDL, low-density lipoprotein
- MCP-1, monocyte chemoattractant protein-1
- MUP, major urinary protein
- NAFLD, non-alcoholic fatty liver disease
- NFKBIA, nuclear factor kappa-inhibitor alpha
- Nonalcoholic fatty liver disease
- PAI-1, plasminogen activator inhibitor-1
- PCB, polychlorinated biphenyl
- PCB126
- PLIN2, perilipin-2
- PNPLA3, patatin-like phospholipase domain-containing protein 3
- PPARα, peroxisome proliferator-activated receptor alpha
- PXR, pregnane-xenobiotic receptor
- Perilipin-2
- Pheromones
- SGK1, serum/glucocorticoid regulated kinase
- TAFLD, toxicant-associated fatty liver disease
- TASH, toxicant-associated steatohepatitis
- TAT, tyrosine aminotransferase
- TMT, tandem mass tag
- VLDL, very low-density lipoprotein
- WT, wild type
- ZFP125, zinc finger protein 125
- miR, microRNA
- nHDLc, non-HDL cholesterol
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10
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Klinge CM, Piell KM, Petri BJ, He L, Zhang X, Pan J, Rai SN, Andreeva K, Rouchka EC, Wahlang B, Beier JI, Cave MC. Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab008. [PMID: 34548932 PMCID: PMC8448424 DOI: 10.1093/eep/dvab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/10/2021] [Indexed: 05/30/2023]
Abstract
Exposure to a single dose of polychlorinated biphenyls (PCBs) and a 12-week high-fat diet (HFD) results in nonalcoholic steatohepatitis (NASH) in mice by altering intracellular signaling and inhibiting epidermal growth factor receptor signaling. Post-transcriptional chemical modification (PTM) of RNA regulates biological processes, but the contribution of epitranscriptomics to PCB-induced steatosis remains unknown. This study tested the hypothesis that PCB and HFD exposure alters the global RNA epitranscriptome in male mouse liver. C57BL/6J male mice were fed a HFD for 12 weeks and exposed to a single dose of Aroclor 1260 (20 mg/kg), PCB 126 (20 µg/kg), both Aroclor 1260 and PCB 126 or vehicle control after 2 weeks on HFD. Chemical RNA modifications were identified at the nucleoside level by liquid chromatography-mass spectrometry. From 22 PTM global RNA modifications, we identified 10 significant changes in RNA modifications in liver with HFD and PCB 126 exposure. Only two modifications were significantly different from HFD control liver in all three PCB exposure groups: 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A). Exposure to HFD + PCB 126 + Aroclor 1260 increased the abundance of N(6), O(2)-dimethyladenosine (m6Am), which is associated with the largest number of transcript changes. Increased m6Am and pseudouridine were associated with increased protein expression of the writers of these modifications: Phosphorylated CTD Interacting Factor 1 (PCIF1) and Pseudouridine Synthase 10 (PUS10), respectively, in HFD + PCB 126- + Aroclor 1260-exposed mouse liver. Increased N1-methyladenosine (m1A) and m6A were associated with increased transcript levels of the readers of these modifications: YTH N6-Methyladenosine RNA Binding Protein 2 (YTHDF2), YTH Domain Containing 2 (YTHDC2), and reader FMRP Translational Regulator 1 (FMR1) transcript and protein abundance. The results demonstrate that PCB exposure alters the global epitranscriptome in a mouse model of NASH; however, the mechanism for these changes requires further investigation.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Liqing He
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
| | - Jianmin Pan
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Shesh N Rai
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- Department of Bioinformatics and Biostatistics, University of Louisville School of Public Health and Information Sciences, Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
| | - Kalina Andreeva
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, JB Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Juliane I Beier
- Department of Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of Pittsburgh, Louisville, KY 40292, USA
- Pittsburgh Liver Research Center (PLRC), Louisville, KY 40292, USA
- Department of Environmental and Occupational Health Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew C Cave
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA
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11
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García-Vence M, Chantada-Vazquez MDP, Sosa-Fajardo A, Agra R, Barcia de la Iglesia A, Otero-Glez A, García-González M, Cameselle-Teijeiro JM, Nuñez C, Bravo JJ, Bravo SB. Protein Extraction From FFPE Kidney Tissue Samples: A Review of the Literature and Characterization of Techniques. Front Med (Lausanne) 2021; 8:657313. [PMID: 34055835 PMCID: PMC8158658 DOI: 10.3389/fmed.2021.657313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Most tissue biopsies from patients in hospital environments are formalin-fixed and paraffin-embedded (FFPE) for long-term storage. This fixation process produces a modification in the proteins called “crosslinks”, which improves protein stability necessary for their conservation. Currently, these samples are mainly used in clinical practice for performing immunohistochemical analysis, since these modifications do not suppose a drawback for this technique; however, crosslinks difficult the protein extraction process. Accordingly, these modifications make the development of a good protein extraction protocol necessary. Due to the specific characteristics of each tissue, the same extraction buffers or deparaffinization protocols are not equally effective in all cases. Therefore, it is necessary to obtain a specific protocol for each tissue. The present work aims to establish a deparaffinization and protein extraction protocol from FFPE kidney samples to obtain protein enough of high quality for the subsequent proteomic analysis. Different deparaffination, protocols and protein extraction buffers will be tested in FFPE kidney samples. The optimized conditions will be applied in the identification by LC-MS/MS analysis of proteins extracted from 5, 10, and 15 glomeruli obtained through the microdissection of FFPE renal samples.
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Affiliation(s)
- Maria García-Vence
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Maria Del Pilar Chantada-Vazquez
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain.,Research Unit, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain
| | - Ana Sosa-Fajardo
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit, Brussels, Belgium
| | - Rebeca Agra
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Ana Barcia de la Iglesia
- Nephrology Laboratory, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Alfonso Otero-Glez
- Nephrology Service, University Clinical Hospital of Ourense (CHOU), Orense, Spain
| | - Miguel García-González
- Nephrology Laboratory, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - José M Cameselle-Teijeiro
- Department of Pathology, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Santiago, Spain
| | - Cristina Nuñez
- Research Unit, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain
| | - Juan J Bravo
- Nephrology Service, University Clinical Hospital of Vigo (Alvaro Cunqueiro-CHUVI), Vigo, Spain
| | - Susana B Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
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12
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Morgenstern D, Barzilay R, Levin Y. RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control Tool. J Proteome Res 2021; 20:2098-2104. [PMID: 33657803 PMCID: PMC8041395 DOI: 10.1021/acs.jproteome.0c00956] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Every laboratory performing mass-spectrometry-based
proteomics
strives to generate high-quality data. Among the many factors that
impact the outcome of any experiment in proteomics is the LC–MS
system performance, which should be monitored within each specific
experiment and also long term. This process is termed quality control
(QC). We present an easy-to-use tool that rapidly produces a visual,
HTML-based report that includes the key parameters needed to monitor
the LC–MS system performance, with a focus on monitoring the
performance within an experiment. The tool, named RawBeans, generates
a report for individual files or for a set of samples from a whole
experiment. We anticipate that it will help proteomics users and experts
evaluate raw data quality independent of data processing. The tool
is available at https://bitbucket.org/incpm/prot-qc/downloads. The mass-spectrometry proteomics data have been deposited to the
ProteomeXchange Consortium via the PRIDE partner repository with the
data set identifier PXD022816.
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Affiliation(s)
- David Morgenstern
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Barzilay
- Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
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13
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Jin J, Wahlang B, Shi H, Hardesty JE, Falkner KC, Head KZ, Srivastava S, Merchant ML, Rai SN, Cave MC, Prough RA. Dioxin-like and non-dioxin-like PCBs differentially regulate the hepatic proteome and modify diet-induced nonalcoholic fatty liver disease severity. Med Chem Res 2020; 29:1247-1263. [PMID: 32831531 PMCID: PMC7440142 DOI: 10.1007/s00044-020-02581-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/30/2020] [Indexed: 02/06/2023]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants associated with metabolic disruption and non-alcoholic fatty liver disease (NAFLD). Based on their ability to activate the aryl hydrocarbon receptor (AhR), PCBs are subdivided into two classes: dioxin-like (DL) and non-dioxin-like (NDL) PCBs. Previously, we demonstrated that NDL PCBs compromised the liver to promote more severe diet-induced NAFLD. Here, the hepatic effects and potential mechanisms (by untargeted liver proteomics) of DL PCBs, NDL PCBs or co-exposure to both in diet-induced NAFLD are investigated. Male C57Bl/6 mice were fed a 42% fat diet and exposed to vehicle control; Aroclor1260 (20 mg/kg, NDL PCB mixture); PCB126 (20 μg/kg, DL PCB congener); or a mixture of Aroclor1260 (20 mg/kg)+PCB126 (20 μg/kg) for 12 weeks. Each exposure was associated with a distinct hepatic proteome. Phenotypic and proteomic analyses revealed increased hepatic inflammation and phosphoprotein signaling disruption by Aroclor1260. PCB126 decreased hepatic inflammation and fibrosis at the molecular level; while altering cytoskeletal remodeling, metal homeostasis, and intermediary/xenobiotic metabolism. PCB126 attenuated Aroclor1260-induced hepatic inflammation but increased hepatic free fatty acids in the co-exposure group. Aroclor1260+PCB126 exposure was strongly associated with multiple epigenetic processes, and these could potentially explain the observed non-additive effects of the exposures on the hepatic proteome. Taken together, the results demonstrated that PCB exposures differentially regulated the hepatic proteome and the histologic severity of diet-induced NAFLD. Future research is warranted to determine the AhR-dependence of the observed effects including metal homeostasis and the epigenetic regulation of gene expression.
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Affiliation(s)
- Jian Jin
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Banrida Wahlang
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- UofL Superfund Research Center, University of Louisville, Louisville, KY, 40202, USA
| | - Hongxue Shi
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Josiah E. Hardesty
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - K. Cameron Falkner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Kimberly Z. Head
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Sudhir Srivastava
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, 40202, USA
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Michael L. Merchant
- UofL Superfund Research Center, University of Louisville, Louisville, KY, 40202, USA
- Division of Nephrology and Hypertension, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Shesh N. Rai
- UofL Superfund Research Center, University of Louisville, Louisville, KY, 40202, USA
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, 40202, USA
| | - Matthew C. Cave
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- UofL Superfund Research Center, University of Louisville, Louisville, KY, 40202, USA
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
- Robley Rex Veterans Affairs Medical Center, Louisville, KY, 40206, USA
| | - Russell A. Prough
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40202, USA
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14
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Merchant ML, Barati MT, Caster DJ, Hata JL, Hobeika L, Coventry S, Brier ME, Wilkey DW, Li M, Rood IM, Deegens JK, Wetzels JF, Larsen CP, Troost JP, Hodgin JB, Mariani LH, Kretzler M, Klein JB, McLeish KR. Proteomic Analysis Identifies Distinct Glomerular Extracellular Matrix in Collapsing Focal Segmental Glomerulosclerosis. J Am Soc Nephrol 2020; 31:1883-1904. [PMID: 32561683 DOI: 10.1681/asn.2019070696] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 04/13/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The mechanisms leading to extracellular matrix (ECM) replacement of areas of glomerular capillaries in histologic variants of FSGS are unknown. This study used proteomics to test the hypothesis that glomerular ECM composition in collapsing FSGS (cFSGS) differs from that of other variants. METHODS ECM proteins in glomeruli from biopsy specimens of patients with FSGS not otherwise specified (FSGS-NOS) or cFSGS and from normal controls were distinguished and quantified using mass spectrometry, verified and localized using immunohistochemistry (IHC) and confocal microscopy, and assessed for gene expression. The analysis also quantified urinary excretion of ECM proteins and peptides. RESULTS Of 58 ECM proteins that differed in abundance between cFSGS and FSGS-NOS, 41 were more abundant in cFSGS and 17 in FSGS-NOS. IHC showed that glomerular tuft staining for cathepsin B, cathepsin C, and annexin A3 in cFSGS was significantly greater than in other FSGS variants, in minimal change disease, or in membranous nephropathy. Annexin A3 colocalized with cathepsin B and C, claudin-1, phosphorylated ERK1/2, and CD44, but not with synaptopodin, in parietal epithelial cells (PECs) infiltrating cFSGS glomeruli. Transcripts for cathepsins B and C were increased in FSGS glomeruli compared with normal controls, and urinary excretion of both cathepsins was significantly greater in cFSGS compared with FSGS-NOS. Urinary excretion of ECM-derived peptides was enhanced in cFSGS, although in silico analysis did not identify enhanced excretion of peptides derived from cathepsin B or C. CONCLUSIONS ECM differences suggest that glomerular sclerosis in cFSGS differs from that in other FSGS variants. Infiltration of activated PECs may disrupt ECM remodeling in cFSGS. These cells and their cathepsins may be therapeutic targets.
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Affiliation(s)
- Michael L Merchant
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Michelle T Barati
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Dawn J Caster
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Jessica L Hata
- Pathology Department, Norton Children's Hospital, Louisville, Kentucky
| | - Liliane Hobeika
- Division of Nephrology, Department of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Susan Coventry
- Pathology Department, Norton Children's Hospital, Louisville, Kentucky
| | - Michael E Brier
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Daniel W Wilkey
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Ming Li
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Ilse M Rood
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen K Deegens
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jack F Wetzels
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Jonathan P Troost
- Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor, Michigan
| | - Jeffrey B Hodgin
- Division of Pathology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Laura H Mariani
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Jon B Klein
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky.,Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky
| | - Kenneth R McLeish
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky
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15
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Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations. Genes Dis 2019; 8:215-223. [PMID: 33997168 PMCID: PMC8099687 DOI: 10.1016/j.gendis.2019.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/14/2019] [Indexed: 11/28/2022] Open
Abstract
Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational tools. The Quantitative Insights into Microbial Ecology Version 2 (QIIME2) has been widely used for 16S rRNA data analysis. While many articles have demonstrated the use of QIIME2 with suitable datasets, the application to pre-clinical data has rarely been talked about. The issues involved in the pre-clinical data include the low-quality score and small sample size that should be addressed properly during analysis. In addition, there are few articles that discuss the detailed statistical methods behind those alpha and beta diversity significance tests that researchers are eager to find. Running the program without knowing the logic behind it is extremely risky. In this article, we first provide a guideline for analyzing 16S rRNA data using QIIME2. Then we will talk about issues in pre-clinical data, and how they could impact the outcome. Finally, we provide brief explanations of statistical methods such as group significance tests and sample size calculation.
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16
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Interactive Web Tool for Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry Data. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2019; 12:85-88. [PMID: 32148360 PMCID: PMC7059686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
INTRODUCTION The proteomics experiments involve several steps and there are many choices available for each step in the workflow. Therefore, standardization of proteomics workflow is an essential task for design of proteomics experiments. However, there are challenges associated with the quantitative measurements based on liquid chromatography-mass spectrometry such as heterogeneity due to technical variability and missing values. METHODS We introduce a web application, Proteomics Workflow Standardization Tool (PWST) to standardize the proteomics workflow. The tool will be helpful in deciding the most suitable choice for each step of the experimentation. This is based on identifying steps/choices with least variability such as comparing Coefficient of Variation (CV). We demonstrate the tool on data with categorical and continuous variables. We have used the special cases of general linear model, analysis of covariance and analysis of variance with fixed effects to study the effects due to various sources of variability. We have provided various options that will aid in finding the contribution of sum of squares for each variable and the CV. The user can analyze the data variability at protein and peptide level even in the presence of missing values. AVAILABILITY AND IMPLEMENTATION The source code for "PWST" is written in R and implemented as shiny web application that can be accessed freely from https://ulbbf.shinyapps.io/pwst/.
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