1
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Piell KM, Petri BJ, Xu J, Cai L, Rai SN, Li M, Wilkey DW, Merchant ML, Cave MC, Klinge CM. Chronic Aroclor 1260 exposure alters the mouse liver proteome, selenoproteins, and metals in steatotic liver disease. Environ Toxicol Pharmacol 2024; 107:104430. [PMID: 38552755 DOI: 10.1016/j.etap.2024.104430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/09/2024]
Abstract
The prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) continues to increase due in part to the obesity epidemic and to environmental exposures to metabolism disrupting chemicals. A single gavage exposure of male mice to Aroclor 1260 (Ar1260), an environmentally relevant mixture of non-dioxin-like polychlorinated biphenyls (PCBs), resulted in steatohepatitis and altered RNA modifications in selenocysteine tRNA 34 weeks post-exposure. Unbiased approaches identified the liver proteome, selenoproteins, and levels of 25 metals. Ar1260 altered the abundance of 128 proteins. Enrichment analysis of the liver Ar1260 proteome included glutathione metabolism and translation of selenoproteins. Hepatic glutathione peroxidase 4 (GPX4) and Selenoprotein O (SELENOO) were increased and Selenoprotein F (SELENOF), Selenoprotein S (SELENOS), Selenium binding protein 2 (SELENBP2) were decreased with Ar1260 exposure. Increased copper, selenium (Se), and zinc and reduced iron levels were detected. These data demonstrate that Ar1260 exposure alters the (seleno)proteome, Se, and metals in MASLD-associated pathways.
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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; Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA
| | - Jason Xu
- Pediatric Research Institute, Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Lu Cai
- Pediatric Research Institute, Department of Pediatrics, University of Louisville School of Medicine, Louisville, KY 40292, USA; Departments of Radiation Oncology, Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, 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
| | - Ming Li
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Daniel W Wilkey
- University of Louisville Hepatobiology and Toxicology Center; University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Michael L Merchant
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA; Division of Nephrology & Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; University of Louisville Hepatobiology and Toxicology Center; University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Matthew C Cave
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), University of Louisville, Louisville, KY 40292, USA; University of Louisville Hepatobiology and Toxicology Center; University of Louisville School of Medicine, Louisville, KY 40202, 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, University of Louisville School of Medicine, Louisville, KY 40292, 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), University of Louisville, Louisville, KY 40292, USA.
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2
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Sayed K, Dolin CE, Wilkey DW, Li J, Sato T, Beier JI, Argemi J, Bataller R, Wahed AS, Merchant ML, Benos PV, Arteel GE. A plasma peptidomic signature reveals extracellular matrix remodeling and predicts prognosis in alcohol-related hepatitis. medRxiv 2023:2023.12.13.23299905. [PMID: 38168372 PMCID: PMC10760272 DOI: 10.1101/2023.12.13.23299905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Alcohol-related hepatitis (AH) is plagued with high mortality and difficulty in identifying at-risk patients. The extracellular matrix undergoes significant remodeling during inflammatory liver injury that can be detected in biological fluids and potentially used for mortality prediction. EDTA plasma samples were collected from AH patients (n= 62); Model for End-Stage Liver Disease (MELD) score defined AH severity as moderate (12-20; n=28) and severe (>20; n=34). The peptidome data was collected by high resolution, high mass accuracy UPLC-MS. Univariate and multivariate analyses identified differentially abundant peptides, which were used for Gene Ontology, parent protein matrisomal composition and protease involvement. Machine learning methods were used on patient-specific peptidome and clinical data to develop mortality predictors. Analysis of plasma peptides from AH patients and healthy controls identified over 1,600 significant peptide features corresponding to 130 proteins. These were enriched for ECM fragments in AH samples, likely related to turnover of hepatic-derived proteins. Analysis of moderate versus severe AH peptidomes showed a shift in abundance of peptides from collagen 1A1 and fibrinogen A proteins. The dominant proteases for the AH peptidome spectrum appear to be CAPN1 and MMP12. Increase in hepatic expression of these proteases was orthogonally-validated in RNA-seq data of livers from AH patients. Causal graphical modeling identified four peptides directly linked to 90-day mortality in >90% of the learned graphs. These peptides improved the accuracy of mortality prediction over MELD score and were used to create a clinically applicable mortality prediction assay. A signature based on plasma peptidome is a novel, non-invasive method for prognosis stratification in AH patients. Our results could also lead to new mechanistic and/or surrogate biomarkers to identify new AH mechanisms. Lay summary We used degraded proteins found the blood of alcohol-related hepatitis patients to identify new potential mechanisms of injury and to predict 90 day mortality.
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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4
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Li J, Sato T, Hernández-Tejero M, Beier JI, Sayed K, Benos PV, Wilkey DW, Humar A, Merchant ML, Duarte-Rojo A, Arteel GE. The plasma degradome reflects later development of NASH fibrosis after liver transplant. Sci Rep 2023; 13:9965. [PMID: 37340062 PMCID: PMC10282030 DOI: 10.1038/s41598-023-36867-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
Although liver transplantation (LT) is an effective therapy for cirrhosis, the risk of post-LT NASH is alarmingly high and is associated with accelerated progression to fibrosis/cirrhosis, cardiovascular disease and decreased survival. Lack of risk stratification strategies hampers early intervention against development of post-LT NASH fibrosis. The liver undergoes significant remodeling during inflammatory injury. During such remodeling, degraded peptide fragments (i.e., 'degradome') of the ECM and other proteins increase in plasma, making it a useful diagnostic/prognostic tool in chronic liver disease. To investigate whether liver injury caused by post-LT NASH would yield a unique degradome profile that is predictive of severe post-LT NASH fibrosis, a retrospective analysis of 22 biobanked samples from the Starzl Transplantation Institute (12 with post-LT NASH after 5 years and 10 without) was performed. Total plasma peptides were isolated and analyzed by 1D-LC-MS/MS analysis using a Proxeon EASY-nLC 1000 UHPLC and nanoelectrospray ionization into an Orbitrap Elite mass spectrometer. Qualitative and quantitative peptide features data were developed from MSn datasets using PEAKS Studio X (v10). LC-MS/MS yielded ~ 2700 identifiable peptide features based on the results from Peaks Studio analysis. Several peptides were significantly altered in patients that later developed fibrosis and heatmap analysis of the top 25 most significantly changed peptides, most of which were ECM-derived, clustered the 2 patient groups well. Supervised modeling of the dataset indicated that a fraction of the total peptide signal (~ 15%) could explain the differences between the groups, indicating a strong potential for representative biomarker selection. A similar degradome profile was observed when the plasma degradome patterns were compared being obesity sensitive (C57Bl6/J) and insensitive (AJ) mouse strains. The plasma degradome profile of post-LT patients yielded stark difference based on later development of post-LT NASH fibrosis. This approach could yield new "fingerprints" that can serve as minimally-invasive biomarkers of negative outcomes post-LT.
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Affiliation(s)
- Jiang Li
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Toshifumi Sato
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - María Hernández-Tejero
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Juliane I Beier
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering and Computer Science, University of New Haven, New Haven, CT, USA
| | | | - Daniel W Wilkey
- Department of Medicine, University of Louisville, Louisville, KY, USA
| | - Abhinav Humar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Andres Duarte-Rojo
- Division of Gastroenterology and Hepatology, Northwestern Medicine and Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Comprehensive Transplant Center, Northwestern Medicine and Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gavin E Arteel
- Department of Medicine, University of Pittsburgh, Thomas E. Starzl Biomedical Science Tower, West 1143, 200 Lothrop Street, Pittsburgh, PA, 15213, USA.
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA.
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5
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Li J, Sato T, Hernández-Tejero M, Beier JI, Sayed K, Benos PV, Wilkey DW, Humar A, Merchant ML, Duarte-Rojo A, Arteel GE. The plasma degradome reflects later development of NASH fibrosis after liver transplant. bioRxiv 2023:2023.01.30.526241. [PMID: 36778394 PMCID: PMC9915514 DOI: 10.1101/2023.01.30.526241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Although liver transplantation (LT) is an effective therapy for cirrhosis, the risk of post-LT NASH is alarmingly high and is associated with accelerated progression to fibrosis/cirrhosis, cardiovascular disease, and decreased survival. Lack of risk stratification strategies hamper liver undergoes significant remodeling during inflammatory injury. During such remodeling, degraded peptide fragments (i.e., 'degradome') of the ECM and other proteins increase in plasma, making it a useful diagnostic/prognostic tool in chronic liver disease. To investigate whether inflammatory liver injury caused by post-LT NASH would yield a unique degradome profile, predictive of severe post-LT NASH fibrosis, we performed a retrospective analysis of 22 biobanked samples from the Starzl Transplantation Institute (12 with post-LT NASH after 5 years and 10 without). Total plasma peptides were isolated and analyzed by 1D-LC-MS/MS analysis using a Proxeon EASY-nLC 1000 UHPLC and nanoelectrospray ionization into an Orbitrap Elite mass spectrometer. Qualitative and quantitative peptide features data were developed from MSn datasets using PEAKS Studio X (v10). LC-MS/MS yielded ∼2700 identifiable peptide features based on the results from Peaks Studio analysis. Several peptides were significantly altered in patients that later developed fibrosis and heatmap analysis of the top 25 most significantly-changed peptides, most of which were ECM-derived, clustered the 2 patient groups well. Supervised modeling of the dataset indicated that a fraction of the total peptide signal (∼15%) could explain the differences between the groups, indicating a strong potential for representative biomarker selection. A similar degradome profile was observed when the plasma degradome patterns were compared being obesity sensitive (C57Bl6/J) and insensitive (AJ) mouse strains. Both The plasma degradome profile of post-LT patients yields stark difference based on later development of post-LT NASH fibrosis. This approach could yield new "fingerprints" that can serve as minimally-invasive biomarkers of negative outcomes post-LT.
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6
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Hong KU, Gardner JQ, Doll MA, Stepp MW, Wilkey DW, Benz FW, Cai J, Merchant ML, Hein DW. Dataset for proteomic analysis of arylamine N-acetyltransferase 1 knockout MDA-MB-231 breast cancer cells. Data Brief 2022; 45:108634. [PMID: 36426076 PMCID: PMC9679541 DOI: 10.1016/j.dib.2022.108634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 01/22/2023] Open
Abstract
Arylamine N-acetyltransferase 1 (NAT1) is frequently upregulated in breast cancer. An unbiased analysis of proteomes of parental MDA-MB-231 breast cancer cells and two separate NAT1 knockout (KO) cell lines were performed. Among 4,890 proteins identified, 737 and 651 proteins were found significantly (p < 0.01) upregulated and downregulated, respectively, in NAT1 KO cells, compared to the parental cells. Each set of proteins was analyzed to identify Gene Ontology biological processes, molecular functions, and cellular components that were enriched in the set. Among the proteins upregulated in NAT1 KO cells, processes associated with MHC major histocompatibility complex I-mediated antigen presentation were significantly enriched. Multiple processes involved in mitochondrial functions were collectively downregulated in NAT1 KO cells, including multiple subunits of mitochondrial ATP synthase (Complex V of the electron transport chain). This was accompanied by a reduction in cell cycle-associated proteins and an increase in pro-apoptotic pathways in NAT1 KO cells. The current dataset contains additional representations of the biological processes and components that are differentially enriched in NAT1 KO MDA-MB-231 cells and will serve as a basis for generating novel hypotheses regarding the role of NAT1 in breast cancer. Data are available via ProteomeXchange with identifier PXD035953.
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Affiliation(s)
- Kyung U. Hong
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Jonathan Q. Gardner
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Mark A. Doll
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Marcus W. Stepp
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Daniel W. Wilkey
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Frederick W. Benz
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Jian Cai
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Michael L. Merchant
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - David W. Hein
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, USA,Corresponding author.
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7
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Hong KU, Gardner JQ, Doll MA, Stepp MW, Wilkey DW, Benz FW, Cai J, Merchant ML, Hein DW. Proteomic analysis of arylamine N-acetyltransferase 1 knockout breast cancer cells: Implications in immune evasion and mitochondrial biogenesis. Toxicol Rep 2022; 9:1566-1573. [PMID: 36158865 PMCID: PMC9500399 DOI: 10.1016/j.toxrep.2022.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/13/2022] [Accepted: 07/16/2022] [Indexed: 02/08/2023] Open
Abstract
Previous studies have shown that inhibition or depletion of N-acetyltransferase 1 (NAT1) in breast cancer cell lines leads to growth retardation both in vitro and in vivo, suggesting that NAT1 contributes to rapid growth of breast cancer cells. To understand molecular and cellular processes that NAT1 contributes to and generate novel hypotheses in regard to NAT1's role in breast cancer, we performed an unbiased analysis of proteomes of parental MDA-MB-231 breast cancer cells and two separate NAT1 knockout (KO) cell lines. Among 4890 proteins identified, 737 proteins were found significantly (p < 0.01) upregulated, and 651 proteins were significantly (p < 0.01) downregulated in both NAT1 KO cell lines. We performed enrichment analyses to identify Gene Ontology biological processes, molecular functions, and cellular components that were enriched in each data set. Among the proteins upregulated in NAT1 KO cells, pathways associated with MHC (major histocompatibility complex) I-mediated antigen presentation were significantly enriched. This raises an interesting and new hypothesis that upregulation of NAT1 in breast cancer cells may aid them evade immune detection. Multiple pathways involved in mitochondrial functions were collectively downregulated in NAT1 KO cells, including multiple subunits of mitochondrial ATP synthase (Complex V of the electron transport chain). This was accompanied by a reduction in cell cycle-associated proteins and an increase in pro-apoptotic pathways in NAT1 KO cells, consistent with reported observations that NAT1 KO cells exhibit a slower growth rate both in vitro and in vivo. Thus, mitochondrial dysfunction in NAT1 KO cells likely contributes to growth retardation.
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Affiliation(s)
- Kyung U. Hong
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Jonathan Q. Gardner
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Mark A. Doll
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Marcus W. Stepp
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Daniel W. Wilkey
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Frederick W. Benz
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Jian Cai
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Michael L. Merchant
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
| | - David W. Hein
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA,Correspondence to: Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, 505 S. Hancock Street, CTR Rm 303, Louisville, KY 40202, USA.
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Cummins TD, Powell DW, Wilkey DW, Brady MP, Benz FW, Barati MT, Caster DJ, Klein JB, Merchant ML. Quantitative Mass Spectrometry Normalization in Urine Biomarker Analysis in Nephrotic Syndrome. Glomerular Dis 2022; 2:121-131. [PMID: 36199623 PMCID: PMC9529004 DOI: 10.1159/000522217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chronic kidney disease (CKD) affects 30 million adults, costs ~$79 billion dollars (2016) in Medicare expenditures, and is the ninth leading cause of death in the United States. The disease is silent or undiagnosed in almost half of people with severely reduced kidney function. Urine provides an ideal biofluid that is accessible to high-sensitivity mass spectrometry-based proteomic interrogation and is an indicator of renal homeostasis. While the accurate and precise diagnosis and better disease management of CKD can be aided using urine biomarkers, their discovery in excessive protein or nephrotic urine samples can present challenges. In this work we present a mass spectrometry-based method utilizing multiplex tandem mass tag (TMT) quantification and improved protein quantification using reporter ion normalization to urinary creatinine to analyze urinary proteins from patients with a form of nephrotic syndrome (FSGS). A comparative analysis was performed for urine from patients in remission versus active disease flare. Two-dimensional LC-MS/MS TMT quantitative analysis identified over 1058 urine proteins, 580 proteins with 2 peptides or greater and quantifiable. Normalization of TMT abundance values to creatinine per ml of urine concentrated reduced variability in 2D-TMT-LC-MS/MS experiments. Univariate and multivariate analyses showed that 27 proteins were significantly increased in proteinuric disease flare. Hierarchical heatmap clustering showed that SERPINA1 and ORM1 were >1.5 fold increased in active disease versus remission urine samples. ELISA validation of SERPINA1 and ORM1 abundance agreed with our quantitative TMT proteomics analysis. These findings provide support for the utility of this method for identification of novel diagnostic markers of CKD and identify SERPINA1 and ORM1 as promising candidate diagnostic markers for FSGS.
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Affiliation(s)
- Timothy D. Cummins
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA,*Timothy D. Cummins,
| | - David W. Powell
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Daniel W. Wilkey
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Makayla P. Brady
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Fredrick W. Benz
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Michelle T. Barati
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Dawn J. Caster
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Jon B. Klein
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Michael L. Merchant
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville School of Medicine, Louisville, Kentucky, USA,Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky, USA
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9
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Ferragut Cardoso AP, Banerjee M, Al-Eryani L, Sayed M, Wilkey DW, Merchant ML, Park JW, States JC. Temporal Modulation of Differential Alternative Splicing in HaCaT Human Keratinocyte Cell Line Chronically Exposed to Arsenic for up to 28 Wk. Environ Health Perspect 2022; 130:17011. [PMID: 35072517 PMCID: PMC8785870 DOI: 10.1289/ehp9676] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND Chronic arsenic exposure via drinking water is associated with an increased risk of developing cancer and noncancer chronic diseases. Pre-mRNAs are often subject to alternative splicing, generating mRNA isoforms encoding functionally distinct protein isoforms. The resulting imbalance in isoform species can result in pathogenic changes in critical signaling pathways. Alternative splicing as a mechanism of arsenic-induced toxicity and carcinogenicity is understudied. OBJECTIVE This study aimed to accurately profile differential alternative splicing events in human keratinocytes induced by chronic arsenic exposure that might play a role in carcinogenesis. METHODS Independent quadruplicate cultures of immortalized human keratinocytes (HaCaT) were maintained continuously for 28 wk with 0 or 100 nM sodium arsenite. RNA-sequencing (RNA-Seq) was performed with poly(A) RNA isolated from cells harvested at 7, 19, and 28 wk with subsequent replicate multivariate analysis of transcript splicing (rMATS) analysis to detect and quantify differential alternative splicing events. Reverse transcriptase-polymerase chain reaction (RT-PCR) for selected alternative splicing events was performed to validate RNA-Seq predictions. Functional enrichment was performed by gene ontology (GO) analysis of the differential alternative splicing event data set at each time point. RESULTS At least 600 differential alternative splicing events were detected at each time point tested, comprising all the five main types of alternative splicing and occurring in both open reading frames (ORFs) and untranslated regions (UTRs). Based on functional relevance ELK4, SHC1, and XRRA1 were selected for validation of predicted alternative splicing events at 7 wk by RT-PCR. Densitometric analysis of RT-PCR data corroborated the rMATS predicted alternative splicing for all three events. Protein expression validation of the selected alternative splicing events was challenging given that very few isoform-specific antibodies are available. GO analysis demonstrated that the enriched terms in differential alternatively spliced mRNAs changed dynamically with the time of exposure. Notably, RNA metabolism and splicing regulation pathways were enriched at the 7-wk time point, when the greatest number of differentially alternatively spliced mRNAs are detected. Our preliminary proteomic analysis demonstrated that the expression of the canonical isoforms of the splice regulators DDX42, RMB25, and SRRM2 were induced upon chronic arsenic exposure, corroborating the splicing predictions. DISCUSSION These results using cultures of HaCaT cells suggest that arsenic exposure disrupted an alternative splice factor network and induced time-dependent genome-wide differential alternative splicing that likely contributed to the changing proteomic landscape in arsenic-induced carcinogenesis. However, significant challenges remain in corroborating alternative splicing data at the proteomic level. https://doi.org/10.1289/EHP9676.
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Affiliation(s)
- Ana P. Ferragut Cardoso
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Mayukh Banerjee
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Laila Al-Eryani
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Mohammed Sayed
- Computer Science and Engineering, University of Louisville, Louisville, Kentucky, USA
| | - Daniel W. Wilkey
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Michael L. Merchant
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Juw W. Park
- Computer Science and Engineering, University of Louisville, Louisville, Kentucky, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, Kentucky, USA
| | - J. Christopher States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
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10
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Schneider G, Kaliappan A, Nguyen TQ, Buscaglia R, Brock GN, Hall MB, DeSpirito C, Wilkey DW, Merchant ML, Klein JB, Wiese TA, Rivas-Perez HL, Kloecker GH, Garbett NC. The Utility of Differential Scanning Calorimetry Curves of Blood Plasma for Diagnosis, Subtype Differentiation and Predicted Survival in Lung Cancer. Cancers (Basel) 2021; 13:5326. [PMID: 34771491 PMCID: PMC8582427 DOI: 10.3390/cancers13215326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Early detection of lung cancer (LC) significantly increases the likelihood of successful treatment and improves LC survival rates. Currently, screening (mainly low-dose CT scans) is recommended for individuals at high risk. However, the recent increase in the number of LC cases unrelated to the well-known risk factors, and the high false-positive rate of low-dose CT, indicate a need to develop new, non-invasive methods for LC detection. Therefore, we evaluated the use of differential scanning calorimetry (DSC) for LC patients' diagnosis and predicted survival. Additionally, by applying mass spectrometry, we investigated whether changes in O- and N-glycosylation of plasma proteins could be an underlying mechanism responsible for observed differences in DSC curves of LC and control subjects. Our results indicate selected DSC curve features could be useful for differentiation of LC patients from controls with some capable of distinction between subtypes and stages of LC. DSC curve features also correlate with LC patients' overall/progression free survival. Moreover, the development of classification models combining patients' DSC curves with selected plasma protein glycosylation levels that changed in the presence of LC could improve the sensitivity and specificity of the detection of LC. With further optimization and development of the classification method, DSC could provide an accurate, non-invasive, radiation-free strategy for LC screening and diagnosis.
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Affiliation(s)
- Gabriela Schneider
- UofL Health—Brown Cancer Center and Division of Medical Oncology and Hematology, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (G.S.); (A.K.); (T.Q.N.); (M.B.H.); (G.H.K.)
| | - Alagammai Kaliappan
- UofL Health—Brown Cancer Center and Division of Medical Oncology and Hematology, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (G.S.); (A.K.); (T.Q.N.); (M.B.H.); (G.H.K.)
| | - Taylor Q. Nguyen
- UofL Health—Brown Cancer Center and Division of Medical Oncology and Hematology, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (G.S.); (A.K.); (T.Q.N.); (M.B.H.); (G.H.K.)
| | - Robert Buscaglia
- Department of Mathematics and Statistics, Northern Arizona University, Flagstaff, AZ 86011, USA;
| | - Guy N. Brock
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Melissa Barousse Hall
- UofL Health—Brown Cancer Center and Division of Medical Oncology and Hematology, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (G.S.); (A.K.); (T.Q.N.); (M.B.H.); (G.H.K.)
| | - Crissie DeSpirito
- Division of Pulmonary, Critical Care and Sleep Disorders Medicine, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (C.D.); (T.A.W.); (H.L.R.-P.)
| | - Daniel W. Wilkey
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (D.W.W.); (M.L.M.); (J.B.K.)
| | - Michael L. Merchant
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (D.W.W.); (M.L.M.); (J.B.K.)
| | - Jon B. Klein
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (D.W.W.); (M.L.M.); (J.B.K.)
- Robley Rex Veterans Affairs Medical Center, Louisville, KY 40202, USA
| | - Tanya A. Wiese
- Division of Pulmonary, Critical Care and Sleep Disorders Medicine, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (C.D.); (T.A.W.); (H.L.R.-P.)
| | - Hiram L. Rivas-Perez
- Division of Pulmonary, Critical Care and Sleep Disorders Medicine, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (C.D.); (T.A.W.); (H.L.R.-P.)
| | - Goetz H. Kloecker
- UofL Health—Brown Cancer Center and Division of Medical Oncology and Hematology, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (G.S.); (A.K.); (T.Q.N.); (M.B.H.); (G.H.K.)
| | - Nichola C. Garbett
- UofL Health—Brown Cancer Center and Division of Medical Oncology and Hematology, Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (G.S.); (A.K.); (T.Q.N.); (M.B.H.); (G.H.K.)
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11
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Biyik-Sit R, Kruer T, Dougherty S, Bradley JA, Wilkey DW, Merchant ML, Trent JO, Clem BF. Nuclear Pyruvate Kinase M2 (PKM2) Contributes to Phosphoserine Aminotransferase 1 (PSAT1)-Mediated Cell Migration in EGFR-Activated Lung Cancer Cells. Cancers (Basel) 2021; 13:cancers13163938. [PMID: 34439090 PMCID: PMC8391706 DOI: 10.3390/cancers13163938] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary Alternative functions for metabolic proteins have recently been shown to drive cancer growth. These may include differential enzymatic activity or novel protein associations. Phosphoserine aminotransferase 1 (PSAT1) participates in cellular serine synthesis and has been observed to be elevated in different tumor types. In this study, we aimed to identify new putative PSAT1 activities and determine their contribution to lung tumor progression. We found a direct association for PSAT1 with another enzyme, pyruvate kinase M2. While this appears not to affect PKM2’s metabolic activity, PSAT1 is required for the specific cellular localization of PKM2 upon tumorigenic signaling. Further, the depletion of PSAT1 suppresses lung cancer cell movement that can be partially restored by the compartment expression of PKM2. These findings reveal a novel mechanism that is able to promote the spread of this deadly disease. Abstract An elevated expression of phosphoserine aminotransferase 1 (PSAT1) has been observed in multiple tumor types and is associated with poorer clinical outcomes. Although PSAT1 is postulated to promote tumor growth through its enzymatic function within the serine synthesis pathway (SSP), its role in cancer progression has not been fully characterized. Here, we explore a putative non-canonical function of PSAT1 that contributes to lung tumor progression. Biochemical studies found that PSAT1 selectively interacts with pyruvate kinase M2 (PKM2). Amino acid mutations within a PKM2-unique region significantly reduced this interaction. While PSAT1 loss had no effect on cellular pyruvate kinase activity and PKM2 expression in non-small-cell lung cancer (NSCLC) cells, fractionation studies demonstrated that the silencing of PSAT1 in epidermal growth factor receptor (EGFR)-mutant PC9 or EGF-stimulated A549 cells decreased PKM2 nuclear translocation. Further, PSAT1 suppression abrogated cell migration in these two cell types whereas PSAT1 restoration or overexpression induced cell migration along with an elevated nuclear PKM2 expression. Lastly, the nuclear re-expression of the acetyl-mimetic mutant of PKM2 (K433Q), but not the wild-type, partially restored cell migration in PSAT1-silenced cells. Therefore, we conclude that, in response to EGFR activation, PSAT1 contributes to lung cancer cell migration, in part, by promoting nuclear PKM2 translocation.
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Affiliation(s)
- Rumeysa Biyik-Sit
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA; (R.B.-S.); (T.K.); (S.D.); (J.A.B.)
| | - Traci Kruer
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA; (R.B.-S.); (T.K.); (S.D.); (J.A.B.)
| | - Susan Dougherty
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA; (R.B.-S.); (T.K.); (S.D.); (J.A.B.)
| | - James A. Bradley
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA; (R.B.-S.); (T.K.); (S.D.); (J.A.B.)
| | - Daniel W. Wilkey
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, KY 40202, USA; (D.W.W.); (M.L.M.)
| | - Michael L. Merchant
- Department of Medicine, Division of Nephrology and Hypertension, University of Louisville School of Medicine, Louisville, KY 40202, USA; (D.W.W.); (M.L.M.)
| | - John O. Trent
- Department of Medicine, Division of Hematology and Oncology, University of Louisville School of Medicine, Louisville, KY 40202, USA;
- Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Brian F. Clem
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA; (R.B.-S.); (T.K.); (S.D.); (J.A.B.)
- Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Correspondence: ; Tel.: +1-502-852-8427
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12
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Perpich JD, Yakoumatos L, Johns P, Stocke KS, Fitzsimonds ZR, Wilkey DW, Merchant ML, Miller DP, Lamont RJ. Identification and characterization of a UbK family kinase in Porphyromonas gingivalis that phosphorylates the RprY response regulator. Mol Oral Microbiol 2021; 36:258-266. [PMID: 34241965 DOI: 10.1111/omi.12347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/03/2023]
Abstract
Phosphorylation of proteins is a key component of bacterial signaling systems that can control important functions such as community development and virulence. We report here the identification of a Ubiquitous bacterial Kinase (UbK) family member, designated UbK1, in the anaerobic periodontal pathogen, Porphyromonas gingivalis. UbK1 contains conserved SPT/S, Hanks-type HxDxYR, EW, and Walker A motifs, and a mutation analysis established the Walker A domain and the Hanks-type domain as required for both autophosphorylation and transphosphorylation. UbK1 autophosphorylates on the proximal serine in the SPT/S domain as well as the tyrosine residue within the HxDxYR domain and the tyrosine residue immediately proximal, indicating both serine/threonine and tyrosine specificity. The orphan two-component system response regulator (RR) RprY was phosphorylated on Y41 in the receiver domain by UbK1. The ubk1 gene is essential in P. gingivalis; however, overexpression of UbK1 showed that UbK1-mediated phosphorylation of RprY functions predominantly to augment its properties as a transcriptional enhancer. These results establish that P. gingivalis possesses an active UbK kinase in addition to a previously described Bacterial Tyrosine family kinase. The RR RprY is identified as the first transcriptional regulator controlled by a UbK enzyme.
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Affiliation(s)
- John D Perpich
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA.,Department of Pharmaceutical Sciences, Sullivan University College of Pharmacy and Health Sciences, Louisville, Kentucky, USA
| | - Lan Yakoumatos
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Parker Johns
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Kendall S Stocke
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Zackary R Fitzsimonds
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Daniel W Wilkey
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Michael L Merchant
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Daniel P Miller
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, Kentucky, USA
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13
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Al-Rabadi LF, Caza T, Trivin-Avillach C, Rodan AR, Andeen N, Hayashi N, Williams B, Revelo MP, Clayton F, Abraham J, Lin E, Liou W, Zou CJ, Ramkumar N, Cummins T, Wilkey DW, Kawalit I, Herzog C, Storey A, Edmondson R, Sjoberg R, Yang T, Chien J, Merchant M, Arthur J, Klein J, Larsen C, Beck LH. Serine Protease HTRA1 as a Novel Target Antigen in Primary Membranous Nephropathy. J Am Soc Nephrol 2021; 32:1666-1681. [PMID: 33952630 PMCID: PMC8425645 DOI: 10.1681/asn.2020101395] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/21/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Identification of target antigens PLA2R, THSD7A, NELL1, or Semaphorin-3B can explain the majority of cases of primary membranous nephropathy (MN). However, target antigens remain unidentified in 15%-20% of patients. METHODS A multipronged approach, using traditional and modern technologies, converged on a novel target antigen, and capitalized on the temporal variation in autoantibody titer for biomarker discovery. Immunoblotting of human glomerular proteins followed by differential immunoprecipitation and mass spectrometric analysis was complemented by laser-capture microdissection followed by mass spectrometry, elution of immune complexes from renal biopsy specimen tissue, and autoimmune profiling on a protein fragment microarray. RESULTS These approaches identified serine protease HTRA1 as a novel podocyte antigen in a subset of patients with primary MN. Sera from two patients reacted by immunoblotting with a 51-kD protein within glomerular extract and with recombinant human HTRA1, under reducing and nonreducing conditions. Longitudinal serum samples from these patients seemed to correlate with clinical disease activity. As in PLA2R- and THSD7A- associated MN, anti-HTRA1 antibodies were predominantly IgG4, suggesting a primary etiology. Analysis of sera collected during active disease versus remission on protein fragment microarrays detected significantly higher titers of anti-HTRA1 antibody in active disease. HTRA1 was specifically detected within immune deposits of HTRA1-associated MN in 14 patients identified among three cohorts. Screening of 118 "quadruple-negative" (PLA2R-, THSD7A-, NELL1-, EXT2-negative) patients in a large repository of MN biopsy specimens revealed a prevalence of 4.2%. CONCLUSIONS Conventional and more modern techniques converged to identify serine protease HTRA1 as a target antigen in MN.
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Affiliation(s)
- Laith Farah Al-Rabadi
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah
| | | | - Claire Trivin-Avillach
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts
| | - Aylin R. Rodan
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah,Molecular Medicine Program, University of Utah Health, Salt Lake City, Utah,Department of Human Genetics, University of Utah Health, Salt Lake City, Utah,Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah
| | - Nicole Andeen
- Department of Pathology, Oregon Health and Science University, Portland, Oregon
| | - Norifumi Hayashi
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts,Kanazawa Medical University, Ishikawa, Japan
| | - Brandi Williams
- Moran Eye Center, University of Utah Health, Salt Lake City, Utah
| | - Monica P. Revelo
- Department of Pathology, University of Utah Health, Salt Lake City, Utah
| | - Fred Clayton
- Department of Pathology, University of Utah Health, Salt Lake City, Utah
| | - Jo Abraham
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah
| | - Edwin Lin
- Department of Human Genetics, University of Utah Health, Salt Lake City, Utah
| | - Willisa Liou
- Department of Pathology, University of Utah Health, Salt Lake City, Utah
| | - Chang-Jiang Zou
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah
| | - Nirupama Ramkumar
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah
| | - Tim Cummins
- Clinical Proteomics Laboratory, Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Daniel W. Wilkey
- Clinical Proteomics Laboratory, Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Issa Kawalit
- International Renal Care Association, Amman, Jordan
| | - Christian Herzog
- Nephrology Division, Internal Medicine Department, University of Arkansas for Medical Science, Little Rock, Arkansas
| | - Aaron Storey
- Nephrology Division, Internal Medicine Department, University of Arkansas for Medical Science, Little Rock, Arkansas
| | - Rick Edmondson
- Nephrology Division, Internal Medicine Department, University of Arkansas for Medical Science, Little Rock, Arkansas
| | - Ronald Sjoberg
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Tianxin Yang
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah,Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah
| | - Jeremy Chien
- Department of Biochemistry and Molecular Medicine, University of California Davis Health, Davis, California
| | - Michael Merchant
- Clinical Proteomics Laboratory, Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - John Arthur
- Nephrology Division, Internal Medicine Department, University of Arkansas for Medical Science, Little Rock, Arkansas
| | - Jon Klein
- Clinical Proteomics Laboratory, Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky,Robley Rex Veterans Administration Medical Center, Louisville, Kentucky
| | | | - Laurence H. Beck
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts
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14
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Gu Z, Li F, Liu Y, Jiang M, Zhang L, He L, Wilkey DW, Merchant M, Zhang X, Deng Z, Chen S, Barve S, McClain CJ, Feng W. Exosome-Like Nanoparticles From Lactobacillus rhamnosusGG Protect Against Alcohol-Associated Liver Disease Through Intestinal Aryl Hydrocarbon Receptor in Mice. Hepatol Commun 2021; 5:846-864. [PMID: 34027273 PMCID: PMC8122379 DOI: 10.1002/hep4.1679] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 12/24/2020] [Indexed: 12/14/2022] Open
Abstract
Alcohol-associated liver disease (ALD) is a major cause of mortality. Gut barrier dysfunction-induced bacterial translocation and endotoxin release contribute to the pathogenesis of ALD. Probiotic Lactobacillus rhamnosus GG (LGG) is known to be beneficial on experimental ALD by reinforcing the intestinal barrier function. In this study, we aim to investigate whether the protective effects of LGG on intestinal barrier function is mediated by exosome-like nanoparticles (ELNPs) released by LGG. Intestinal epithelial cells and macrophages were treated with LGG-derived ELNPs (LDNPs) isolated from LGG culture. LDNPs increased tight junction protein expression in epithelial cells and protected from the lipopolysaccharide-induced inflammatory response in macrophages. Three-day oral application of LDNPs protected the intestine from alcohol-induced barrier dysfunction and the liver from steatosis and injury in an animal model of ALD. Co-administration of an aryl hydrocarbon receptor (AhR) inhibitor abolished the protective effects of LDNPs, indicating that the effects are mediated, at least in part, by intestinal AhR signaling. We further demonstrated that LDNP administration increased intestinal interleukin-22-Reg3 and nuclear factor erythroid 2-related factor 2 (Nrf2)-tight junction signaling pathways, leading to the inhibition of bacterial translocation and endotoxin release in ALD mice. This protective effect was associated with LDNP enrichment of bacterial tryptophan metabolites that are AhR agonists. Conclusions: Our results suggest that the beneficial effects of LGG and their supernatant in ALD are likely mediated by bacterial AhR ligand-enriched LDNPs that increase Reg3 and Nrf2 expression, leading to the improved barrier function. These findings provide a strategy for the treatment of ALD and other gut barrier dysfunction-associated diseases.
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Affiliation(s)
- Zelin Gu
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
| | - Fengyuan Li
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
| | - Yunhuan Liu
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
| | - Mengwei Jiang
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
| | - Lihua Zhang
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
| | - Liqing He
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of ChemistryUniversity of LouisvilleKYUSA
- Hepatobiology & Toxicology CenterUniversity of LouisvilleLouisvilleKYUSA
| | | | - Michael Merchant
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
- Hepatobiology & Toxicology CenterUniversity of LouisvilleLouisvilleKYUSA
| | - Xiang Zhang
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of ChemistryUniversity of LouisvilleKYUSA
- Hepatobiology & Toxicology CenterUniversity of LouisvilleLouisvilleKYUSA
| | - Zhong‐Bin Deng
- Hepatobiology & Toxicology CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of SurgeryUniversity of LouisvilleLouisvilleKYUSA
| | - Shao‐Yu Chen
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
| | - Shirish Barve
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
- Hepatobiology & Toxicology CenterUniversity of LouisvilleLouisvilleKYUSA
| | - Craig J. McClain
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
- Hepatobiology & Toxicology CenterUniversity of LouisvilleLouisvilleKYUSA
- Robley Rex VA Medical CenterLouisvilleKYUSA
| | - Wenke Feng
- Department of MedicineUniversity of LouisvilleLouisvilleKYUSA
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA
- Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
- Hepatobiology & Toxicology CenterUniversity of LouisvilleLouisvilleKYUSA
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15
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Caster DJ, Korte EA, Merchant ML, Klein JB, Barati MT, Joglekar A, Wilkey DW, Coventry S, Hata J, Rovin BH, Harley JB, Namjou-Khales B, McLeish KR, Powell DW. Patients with Proliferative Lupus Nephritis Have Autoantibodies That React to Moesin and Demonstrate Increased Glomerular Moesin Expression. J Clin Med 2021; 10:jcm10040793. [PMID: 33669337 PMCID: PMC7920286 DOI: 10.3390/jcm10040793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Kidney involvement in systemic lupus erythematosus (SLE)—termed lupus nephritis (LN)—is a severe manifestation of SLE that can lead to end-stage kidney disease (ESKD). LN is characterized by immune complex deposition and inflammation in the glomerulus. We tested the hypothesis that autoantibodies targeting podocyte and glomerular cell proteins contribute to the development of immune complex formation in LN. We used Western blotting with SLE sera from patients with and without LN to identify target antigens in human glomerular and cultured human-derived podocyte membrane proteins. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified the proteins in the gel regions corresponding to reactive bands observed with sera from LN patients. We identified 102 proteins that were present in both the podocyte and glomerular samples. We identified 10 high-probability candidates, including moesin, using bioinformatic analysis. Confirmation of moesin as a target antigen was conducted using immunohistochemical analysis (IHC) of kidney biopsy tissue and enzyme-linked immunosorbent assay (ELISA) to detect circulating antibodies. By IHC, biopsies from patients with proliferative lupus nephritis (PLN, class III/IV) demonstrated significantly increased glomerular expression of moesin (p < 0.01). By ELISA, patients with proliferative LN demonstrated significantly increased antibodies against moesin (p < 0.01). This suggests that moesin is a target glomerular antigen in lupus nephritis.
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Affiliation(s)
- Dawn J. Caster
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
- Correspondence: ; Tel.: +1-502-852-5757
| | - Erik A. Korte
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Michael L. Merchant
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Jon B. Klein
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
- Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, USA
| | - Michelle T. Barati
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Ami Joglekar
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Daniel W. Wilkey
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - Susan Coventry
- Pathology Department, Norton Children’s Hospital, Louisville, KY 40202, USA; (S.C.); (J.H.)
| | - Jessica Hata
- Pathology Department, Norton Children’s Hospital, Louisville, KY 40202, USA; (S.C.); (J.H.)
| | - Brad H. Rovin
- Department of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.B.H.); (B.N.-K.)
- US Department of Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
| | - Bahram Namjou-Khales
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.B.H.); (B.N.-K.)
| | - Kenneth R. McLeish
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
| | - David W. Powell
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA; (E.A.K.); (M.L.M.); (J.B.K.); (M.T.B.); (A.J.); (D.W.W.); (K.R.M.); (D.W.P.)
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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: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Banerjee M, Ferragut Cardoso AP, Lykoudi A, Wilkey DW, Pan J, Watson WH, Garbett NC, Rai SN, Merchant ML, States JC. Arsenite Exposure Displaces Zinc from ZRANB2 Leading to Altered Splicing. Chem Res Toxicol 2020; 33:1403-1417. [PMID: 32274925 DOI: 10.1021/acs.chemrestox.9b00515] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exposure to arsenic, a class I carcinogen, affects 200 million people globally. Skin is the major target organ, but the molecular etiology of arsenic-induced skin carcinogenesis remains unclear. Arsenite (As3+)-induced disruption of alternative splicing could be involved, but the mechanism is unknown. Zinc finger proteins play key roles in alternative splicing. As3+ can displace zinc (Zn2+) from C3H1 and C4 zinc finger motifs (zfm's), affecting protein function. ZRANB2, an alternative splicing regulator with two C4 zfm's integral to its structure and splicing function, was chosen as a candidate for this study. We hypothesized that As3+ could displace Zn2+ from ZRANB2, altering its structure, expression, and splicing function. As3+/Zn2+ binding and mutual displacement experiments were performed with synthetic apo-peptides corresponding to each ZRANB2 zfm, employing a combination of intrinsic fluorescence, ultraviolet spectrophotometry, zinc colorimetric assay, and liquid chromatography-tandem mass spectrometry. ZRANB2 expression in HaCaT cells acutely exposed to As3+ (0 or 5 μM, 0-72 h; or 0-5 μM, 6 h) was examined by RT-qPCR and immunoblotting. ZRANB2-dependent splicing of TRA2B mRNA, a known ZRANB2 target, was monitored by reverse transcription-polymerase chain reaction. As3+ bound to, as well as displaced Zn2+ from, each zfm. Also, Zn2+ displaced As3+ from As3+-bound zfm's acutely, albeit transiently. As3+ exposure induced ZRANB2 protein expression between 3 and 24 h and at all exposures tested but not ZRANB2 mRNA expression. ZRANB2-directed TRA2B splicing was impaired between 3 and 24 h post-exposure. Furthermore, ZRANB2 splicing function was also compromised at all As3+ exposures, starting at 100 nm. We conclude that As3+ exposure displaces Zn2+ from ZRANB2 zfm's, changing its structure and compromising splicing of its targets, and increases ZRANB2 protein expression as a homeostatic response both at environmental/toxicological exposures and therapeutically relevant doses.
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Affiliation(s)
- Mayukh Banerjee
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, United States
| | - Ana P Ferragut Cardoso
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, United States
| | - Angeliki Lykoudi
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, United States
| | - Daniel W Wilkey
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky 40202, United States
| | - Jianmin Pan
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, United States
| | - Walter H Watson
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, United States.,Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Louisville, Louisville, Kentucky 40202, United States
| | - Nichola C Garbett
- Division of Medical Oncology and Hematology, Department of Medicine, University of Louisville, Louisville, Kentucky 40202, United States.,James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, United States
| | - Shesh N Rai
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, United States.,Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky 40202, United States
| | - Michael L Merchant
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, United States.,Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky 40202, United States
| | - J Christopher States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40202, United States
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18
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Agrawal S, Merchant ML, Kino J, Li M, Wilkey DW, Gaweda AE, Brier ME, Chanley MA, Gooding JR, Sumner SJ, Klein JB, Smoyer WE. Predicting and Defining Steroid Resistance in Pediatric Nephrotic Syndrome Using Plasma Proteomics. Kidney Int Rep 2020; 5:66-80. [PMID: 31922062 PMCID: PMC6943770 DOI: 10.1016/j.ekir.2019.09.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/09/2019] [Indexed: 02/03/2023] Open
Abstract
INTRODUCTION Nephrotic syndrome (NS) is a characterized by massive proteinuria, edema, hypoalbuminemia, and dyslipidemia. Glucocorticoids (GCs), the primary therapy for >60 years, are ineffective in approximately 50% of adults and approximately 20% of children. Unfortunately, there are no validated biomarkers able to predict steroid-resistant NS (SRNS) or to define the pathways regulating SRNS. METHODS We performed proteomic analyses on paired pediatric NS patient plasma samples obtained both at disease presentation before glucocorticoid initiation and after approximately 7 weeks of GC therapy to identify candidate biomarkers able to either predict steroid resistance before treatment or define critical molecular pathways/targets regulating steroid resistance. RESULTS Proteomic analyses of 15 paired NS patient samples identified 215 prevalent proteins, including 13 candidate biomarkers that predicted SRNS before GC treatment, and 66 candidate biomarkers that mechanistically differentiated steroid-sensitive NS (SSNS) from SRNS. Ingenuity Pathway Analyses and protein networking pathways approaches further identified proteins and pathways associated with SRNS. Validation using 37 NS patient samples (24 SSNS/13 SRNS) confirmed vitamin D binding protein (VDB) and APOL1 as strong predictive candidate biomarkers for SRNS, and VDB, hemopexin (HPX), adiponectin (ADIPOQ), sex hormone-binding globulin (SHBG), and APOL1 as strong candidate biomarkers to mechanistically distinguish SRNS from SSNS. Logistic regression analysis identified a candidate biomarker panel (VDB, ADIPOQ, and matrix metalloproteinase 2 [MMP-2]) with significant ability to predict SRNS at disease presentation (P = 0.003; area under the receiver operating characteristic curve = 0.78). CONCLUSION Plasma proteomic analyses and immunoblotting of serial samples in childhood NS identified a candidate biomarker panel able to predict SRNS at disease presentation, as well as candidate molecular targets/pathways associated with clinical steroid resistance.
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Affiliation(s)
- Shipra Agrawal
- The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
- The Ohio State University, Columbus, Ohio, USA
| | | | - Jiro Kino
- The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Ming Li
- Kidney Disease Program, University of Louisville, Louisville, Kentucky, USA
| | - Daniel W. Wilkey
- Kidney Disease Program, University of Louisville, Louisville, Kentucky, USA
| | - Adam E. Gaweda
- Kidney Disease Program, University of Louisville, Louisville, Kentucky, USA
| | - Michael E. Brier
- Kidney Disease Program, University of Louisville, Louisville, Kentucky, USA
| | - Melinda A. Chanley
- The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Jessica R. Gooding
- National Institutes of Health Eastern Regional Comprehensive Metabolomics Resource Core at UNC, Chapel Hill, North Carolina, USA
- Discovery, Science and Technology, RTI International, Research Triangle Park, North Carolina, USA
| | - Susan J. Sumner
- National Institutes of Health Eastern Regional Comprehensive Metabolomics Resource Core at UNC, Chapel Hill, North Carolina, USA
- Nutrition Research Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jon B. Klein
- Kidney Disease Program, University of Louisville, Louisville, Kentucky, USA
- Robley Rex VA Medical Center, Louisville, Kentucky, USA
| | - William E. Smoyer
- The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
- The Ohio State University, Columbus, Ohio, USA
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Mouapi KN, Wagner LJ, Stephens CA, Hindi MM, Wilkey DW, Merchant ML, Maurer MC. Evaluating the Effects of Fibrinogen αC Mutations on the Ability of Factor XIII to Crosslink the Reactive αC Glutamines (Q237, Q328, Q366). Thromb Haemost 2019; 119:1048-1057. [PMID: 31055797 DOI: 10.1055/s-0039-1687875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Fibrinogen (Fbg) levels and extent of fibrin polymerization have been associated with various pathological conditions such as cardiovascular disease, arteriosclerosis, and coagulation disorders. Activated factor XIII (FXIIIa) introduces γ-glutamyl-ε-lysinyl isopeptide bonds between reactive glutamines and lysines in the fibrin network to form a blood clot resistant to fibrinolysis. FXIIIa crosslinks the γ-chains and at multiple sites in the αC region of Fbg. Fbg αC contains a FXIII binding site involving αC (389-402) that is located near three glutamines whose reactivities rank Q237 >> Q366 ≈ Q328. Mass spectrometry and two-dimensional heteronuclear single-quantum correlation nuclear magnetic resonance assays were used to probe the anchoring role that αC E396 may play in controlling FXIII function and characterize the effects of Q237 on the reactivities of Q328 and Q366. Studies with αC (233-425) revealed that the E396A mutation does not prevent the transglutaminase function of FXIII A2 or A2B2. Other residues must play a compensatory role in targeting FXIII to αC. Unlike full Fbg, Fbg αC (233-425) did not promote thrombin cleavage of FXIII, an event contributing to activation. With the αC (233-425) E396A mutant, Q237 exhibited slower reactivities compared with αC wild-type (WT) consistent with difficulties in directing this N-terminal segment toward an anchored FXIII interacting at a weaker binding region. Q328 and Q366 became less reactive when Q237 was replaced with inactive N237. Q237 crosslinking is proposed to promote targeting of Q328 and Q366 to the FXIII active site. FXIII thus uses Fbg αC anchoring sites and distinct Q environments to regulate substrate specificity.
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Affiliation(s)
- Kelly Njine Mouapi
- Chemistry Department, University of Louisville, Louisville, Kentucky, United States
| | - Lucille J Wagner
- Chemistry Department, University of Louisville, Louisville, Kentucky, United States
| | - Chad A Stephens
- Chemistry Department, University of Louisville, Louisville, Kentucky, United States
| | - Mohammed M Hindi
- Chemistry Department, University of Louisville, Louisville, Kentucky, United States
| | - Daniel W Wilkey
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Kentucky, United States
| | - Michael L Merchant
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Kentucky, United States
| | - Muriel C Maurer
- Chemistry Department, University of Louisville, Louisville, Kentucky, United States
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Hardesty JE, Wahlang B, Falkner KC, Shi H, Jin J, Zhou Y, Wilkey DW, Merchant ML, Watson CT, Feng W, Morris AJ, Hennig B, Prough RA, Cave MC. Proteomic Analysis Reveals Novel Mechanisms by Which Polychlorinated Biphenyls Compromise the Liver Promoting Diet-Induced Steatohepatitis. J Proteome Res 2019; 18:1582-1594. [PMID: 30807179 DOI: 10.1021/acs.jproteome.8b00886] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Environmental pollution contributes to fatty liver disease pathogenesis. Polychlorinated biphenyl (PCB) exposures have been associated with liver enzyme elevation and suspected steatohepatitis in cohort studies. Male mice treated with the commercial PCB mixture, Aroclor 1260 (20 mg/kg), and fed high fat diet (HFD) for 12 weeks developed steatohepatitis. Receptor-based modes of action including inhibition of the epidermal growth factor (EGF) receptor were previously proposed, but other mechanisms likely exist. Objectives were to identify and validate the pathways, transcription factors, and mechanisms responsible for the steatohepatitis associated with PCB and HFD coexposures. Comparative proteomics analysis was performed in archived mouse liver samples from the aforementioned chronic exposure study. Pathway and transcription factor analysis (TFA) was performed, and selected results were validated. Liver proteomics detected 1103 unique proteins. Aroclor 1260 upregulated 154 and downregulated 93 of these. Aroclor 1260 + HFD coexposures affected 55 pathways including glutathione metabolism, intermediary metabolism, and cytoskeletal remodeling. TFA of Aroclor 1260 treatment demonstrated alterations in the function of 42 transcription factors including downregulation of NRF2 and key nuclear receptors previously demonstrated to protect against steatohepatitis (e.g., HNF4α, FXR, PPARα/δ/γ, etc.). Validation studies demonstrated that Aroclor 1260 significantly reduced HNF4α protein levels, while Aroclor 1260 + HFD reduced expression of the HNF4α target gene, albumin, in vivo. Aroclor 1260 attenuated EGF-dependent HNF4α phosphorylation and target gene activation in vitro. Aroclor 1260 reduced levels of NRF2, its target genes, and glutathione in vivo. Aroclor 1260 attenuated EGF-dependent NRF2 upregulation, in vitro. Aroclor 1260 indirectly activated hepatic stellate cells in vitro via induction of hepatocyte-derived TGFβ. PCB exposures adversely impacted transcription factors regulating liver protection, function, and fibrosis. PCBs, thus, compromised the liver by reducing its protective responses against nutritional stress to promote diet-induced steatohepatitis. The identified mechanisms by which environmental pollutants influence fatty liver disease pathogenesis require confirmation in humans.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Andrew J Morris
- Superfund Research Center , University of Kentucky , Lexington , Kentucky 40536 , United States
| | - Bernhard Hennig
- Superfund Research Center , University of Kentucky , Lexington , Kentucky 40536 , United States
| | | | - Matthew C Cave
- The Robley Rex Veterans Affairs Medical Center , Louisville , Kentucky 40206 , United States.,The Jewish Hospital Liver Transplant Program , Louisville , Kentucky 40202 , United States
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Gosney JA, Wilkey DW, Merchant ML, Ceresa BP. Proteomics reveals novel protein associations with early endosomes in an epidermal growth factor-dependent manner. J Biol Chem 2018. [PMID: 29523688 DOI: 10.1074/jbc.ra117.000632] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that is an integral component of proliferative signaling. EGFRs on the cell surface become activated upon EGF binding and have an increased rate of endocytosis. Once in the cytoplasm, the EGF·EGFR complex is trafficked to the lysosome for degradation, and signaling is terminated. During trafficking, the EGFR kinase domain remains active, and the internalized EGFR can continue signaling to downstream effectors. Although effector activity varies based on the EGFR's endocytic location, it is not clear how this occurs. In an effort to identify proteins that uniquely associate with the internalized, liganded EGFR in the early endosome, we developed an early endosome isolation strategy to analyze their protein composition. Post-nuclear supernatant from HeLa cells stimulated with and without EGF were separated on an isotonic 17% Percoll gradient. The gradient was fractionated, and early endosomal fractions were pooled and immunoisolated with an EEA1 mAb. The isolated endosomes were validated by immunoblot using antibodies against organelle-specific marker proteins and transmission EM. These early endosomes were also subjected to LC-MS/MS for proteomic analysis. Five proteins were detected in endosomes in a ligand-dependent manner: EGFR, RUFY1, STOML2, PTPN23, and CCDC51. Knockdown of RUFY1 or PTPN23 by RNAi indicated that both proteins play a role in EGFR trafficking. These experiments indicate that endocytic trafficking of activated EGFR changes the protein composition, membrane trafficking, and signaling potential of the early endosome.
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Affiliation(s)
| | - Daniel W Wilkey
- Medicine, University of Louisville, Louisville, Kentucky 40202
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Atay S, Wilkey DW, Milhem M, Merchant M, Godwin AK. Insights into the Proteome of Gastrointestinal Stromal Tumors-Derived Exosomes Reveals New Potential Diagnostic Biomarkers. Mol Cell Proteomics 2017; 17:495-515. [PMID: 29242380 DOI: 10.1074/mcp.ra117.000267] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/21/2017] [Indexed: 12/13/2022] Open
Abstract
Developing tumors continuously release nano-sized vesicles that represent circulating "fingerprints" of the tumor's identity. In gastrointestinal stromal tumor (GIST), we have previously reported that these tumors release "oncosomes" carrying the constitutively activated tyrosine kinase (TK) receptor KIT. Despite the clinical utility of TK inhibitors, such as imatinib mesylate (IM), recurrence and metastasis are clinical problems that urge the need to identify new tumor-derived molecules. To this aim, we performed the first high quality proteomic study of GIST-derived exosomes (GDEs) and identified 1,060 proteins composing the core GDE proteome (cGDEp). The cGDEp was enriched in diagnostic markers (e.g. KIT, CD34, ANO1, PROM1, PRKCQ, and ENG), as well as proteins encoded by genes previously reported expressed in GIST (e.g. DPP4, FHL1, CDH11, and KCTD12). Many of these proteins were validated using cell lines, patient-derived KIT+ exosomes, and GIST tissues. We further show that in vitro and in vivo-derived GDE, carry proteins associated with IM response, such as Sprouty homolog 4 (SPRY4), surfeit 4 (SURF4), ALIX, and the cGMP-dependent 3',5'-cyclic phosphodiesterase 2A (PDE2A). Additionally, we report that the total exosome levels and exosome-associated KIT and SPRY4 protein levels have therapeutic values. In fact, molecular characterization of in vivo-derived KIT+ exosomes indicate significant sorting of p-KITTyr719, total KIT, and SPRY4 after IM-treatment of metastatic patients as compared with the pre-IM levels. Our data suggest that analysis of circulating exosomes levels and molecular markers of IM response in GIST patients with primary and metastatic disease is suitable to develop liquid based biopsies for the diagnosis, prognosis, and monitoring of response to treatment of these tumors. In summary, these findings provide the first insight into the proteome of GIST-derived oncosomes and offers a unique opportunity to further understand their oncogenic elements which contribute to tumorigenesis and drug resistance. Data are available via ProteomeXchange with identifier PXD007997.
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Affiliation(s)
- Safinur Atay
- From the ‡Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd., 4005 WHE, MS3040, Kansas City, Kansas 66160;
| | - Daniel W Wilkey
- §University of Louisville Room 209, Donald Baxter Research Building, 570 S. Preston Street, Louisville, Kentucky 40202
| | - Mohammed Milhem
- ¶Division of Hematology, Oncology, Blood and Marrow Transplantation 200 Hawkins Drive, C32 GH Iowa City, Iowa 52242
| | - Michael Merchant
- §University of Louisville Room 209, Donald Baxter Research Building, 570 S. Preston Street, Louisville, Kentucky 40202
| | - Andrew K Godwin
- From the ‡Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd., 4005 WHE, MS3040, Kansas City, Kansas 66160.,‖University of Kansas Cancer Center, 3901 Rainbow Blvd., 4005 WHE, MS3040, Kansas City, Kansas 66160
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23
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Larsen CP, Trivin-Avillach C, Coles P, Collins AB, Merchant M, Ma H, Wilkey DW, Ambruzs JM, Messias NC, Cossey LN, Rosales IA, Wooldridge T, Walker PD, Colvin RB, Klein J, Salant DJ, Beck LH. LDL Receptor-Related Protein 2 (Megalin) as a Target Antigen in Human Kidney Anti-Brush Border Antibody Disease. J Am Soc Nephrol 2017; 29:644-653. [PMID: 29074737 DOI: 10.1681/asn.2017060664] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
Primary renal tubulointerstitial disease resulting from proximal tubule antigen-specific antibodies and immune complex formation has not been well characterized in humans. We report a cohort of patients with a distinct, underappreciated kidney disease characterized by kidney antibrush border antibodies and renal failure (ABBA disease). We identified ten patients with ABBA disease who had a combination of proximal tubule damage, IgG-positive immune deposits in the tubular basement membrane, and circulating antibodies reactive with normal human kidney proximal tubular brush border. All but one of the patients also had segmental glomerular deposits on renal biopsy specimen. Patients with ABBA disease were elderly and presented with AKI and subnephrotic proteinuria. Serum from all patients but not controls recognized a high molecular weight protein in renal tubular protein extracts that we identified as LDL receptor-related protein 2 (LRP2), also known as megalin, by immunoprecipitation and mass spectrometry. Immunostaining revealed that LRP2 specifically colocalized with IgG in the tubular immune deposits on the ABBA biopsy specimen but not the control specimen analyzed. Finally, ABBA serum samples but not control samples showed reactivity against recombinantly expressed N-terminal LRP2 fragments on Western blots and immunoprecipitated the recombinantly expressed N-terminal region of LRP2. This case series details the clinicopathologic findings of patients with ABBA disease and shows that the antigenic target of these autoantibodies is LRP2. Future studies are needed to determine the disease prevalence, stimulus for ABBA, and optimal treatment.
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Affiliation(s)
| | - Claire Trivin-Avillach
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Paige Coles
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - A Bernard Collins
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michael Merchant
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky; and
| | - Hong Ma
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Daniel W Wilkey
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky; and
| | | | | | | | - Ivy A Rosales
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | - Robert B Colvin
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jon Klein
- Division of Nephrology & Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky; and
| | - David J Salant
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Laurence H Beck
- Renal Section, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts;
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24
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Dent LL, Mandape SN, Pratap S, Dong J, Davis J, Gaddy JA, Amoah K, Damo S, Marshall DR, Jones J, Brandt T, Diaz G, Wang Q, Gary T, Yenamandra A, Ghattas MZ, Elrakaiby M, Aziz RK, Zedan HH, Elmassry M, ElRakaiby M, Aziz RK, Lotfy M, Elmassry M, Marcel J, Khattab RA, Abdelfattah MM, Gilbert JA, Aziz RK, Dini P, Loux SC, Scoggin KE, Esteller-Vico A, Squires EL, Troedsson MHT, Daels P, Ball BA, De Silva K, Bailey E, Stephens JC, Kalbfleisch TS, Dolin CE, Poole LG, Wilkey DW, Rouchka EC, Arteel GE, Barati MT, Merchant ML, Higashi RM, Fan TWM, Moseley H, Lane AN. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: proceedings. BMC Proc 2017. [PMCID: PMC5667591 DOI: 10.1186/s12919-017-0078-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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25
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Shields KM, Tooley JG, Petkowski JJ, Wilkey DW, Garbett NC, Merchant ML, Cheng A, Schaner Tooley CE. Select human cancer mutants of NRMT1 alter its catalytic activity and decrease N-terminal trimethylation. Protein Sci 2017; 26:1639-1652. [PMID: 28556566 DOI: 10.1002/pro.3202] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 01/01/2023]
Abstract
A subset of B-cell lymphoma patients have dominant mutations in the histone H3 lysine 27 (H3K27) methyltransferase EZH2, which change it from a monomethylase to a trimethylase. These mutations occur in aromatic resides surrounding the active site and increase growth and alter transcription. We study the N-terminal trimethylase NRMT1 and the N-terminal monomethylase NRMT2. They are 50% identical, but differ in key aromatic residues in their active site. Given how these residues affect EZH2 activity, we tested whether they are responsible for the distinct catalytic activities of NRMT1/2. Additionally, NRMT1 acts as a tumor suppressor in breast cancer cells. Its loss promotes oncogenic phenotypes but sensitizes cells to DNA damage. Mutations of NRMT1 naturally occur in human cancers, and we tested a select group for altered activity. While directed mutation of the aromatic residues had minimal catalytic effect, NRMT1 mutants N209I (endometrial cancer) and P211S (lung cancer) displayed decreased trimethylase and increased monomethylase/dimethylase activity. Both mutations are located in the peptide-binding channel and indicate a second structural region impacting enzyme specificity. The NRMT1 mutants demonstrated a slower rate of trimethylation and a requirement for higher substrate concentration. Expression of the mutants in wild type NRMT backgrounds showed no change in N-terminal methylation levels or growth rates, demonstrating they are not acting as dominant negatives. Expression of the mutants in cells lacking endogenous NRMT1 resulted in minimal accumulation of N-terminal trimethylation, indicating homozygosity could help drive oncogenesis or serve as a marker for sensitivity to DNA damaging chemotherapeutics or γ-irradiation.
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Affiliation(s)
- Kaitlyn M Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, 40202
| | - John G Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, 14214
| | - Janusz J Petkowski
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Daniel W Wilkey
- Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky, 40202
| | - Nichola C Garbett
- Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky, 40202
| | - Michael L Merchant
- Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky, 40202
| | - Alan Cheng
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, Kentucky, 40202
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, 14214
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26
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Massey VL, Dolin CE, Poole LG, Hudson SV, Siow DL, Brock GN, Merchant ML, Wilkey DW, Arteel GE. The hepatic "matrisome" responds dynamically to injury: Characterization of transitional changes to the extracellular matrix in mice. Hepatology 2017; 65:969-982. [PMID: 28035785 PMCID: PMC5319876 DOI: 10.1002/hep.28918] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/14/2016] [Accepted: 10/16/2016] [Indexed: 12/13/2022]
Abstract
UNLABELLED The extracellular matrix (ECM) consists of diverse components that work bidirectionally with surrounding cells to create a responsive microenvironment. In some contexts (e.g., hepatic fibrosis), changes to the ECM are well recognized and understood. However, it is becoming increasingly accepted that the hepatic ECM proteome (i.e., matrisome) responds dynamically to stress well before fibrosis. The term "transitional tissue remodeling" describes qualitative and quantitative ECM changes in response to injury that do not alter the overall architecture of the organ; these changes in ECM may contribute to early disease initiation and/or progression. The nature and magnitude of these changes to the ECM in liver injury are poorly understood. The goals of this work were to validate analysis of the ECM proteome and compare the impact of 6 weeks of ethanol diet and/or acute lipopolysaccharide (LPS). Liver sections were processed in a series of increasingly rigorous extraction buffers to separate proteins by solubility. Extracted proteins were identified using liquid chromatography/tandem mass spectrometry (LC-MS/MS). Both ethanol and LPS dramatically increased the number of matrisome proteins ∼25%. The enhancement of LPS-induced liver damage by ethanol preexposure was associated with unique protein changes. CONCLUSION An extraction method to enrich the hepatic ECM was characterized. The results demonstrate that the hepatic matrisome responds dynamically to both acute (LPS) and chronic (ethanol) stresses, long before more-dramatic fibrotic changes to the liver occur. The changes to the mastrisome may contribute, at least in part, to the pathological responses to these stresses. It is also interesting that several ECM proteins responded similarly to both stresses, suggesting a common mechanism in both models. Nevertheless, there were responses that were unique to the individual and combined exposures. (Hepatology 2017;65:969-982).
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Affiliation(s)
- Veronica L. Massey
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Christine E. Dolin
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Lauren G. Poole
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Shanice V. Hudson
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Deanna L. Siow
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
| | - Guy N. Brock
- Department of Bioinformatics and Biostatistics, University of Louisville Health Sciences Center, Louisville, KY
| | - Michael L. Merchant
- University of Louisville Alcohol Research Center, Louisville, KY,Department of Medicine, University of Louisville Health Sciences Center, Louisville, KY
| | - Daniel W. Wilkey
- University of Louisville Alcohol Research Center, Louisville, KY,Department of Medicine, University of Louisville Health Sciences Center, Louisville, KY
| | - Gavin E. Arteel
- Department of Pharmacology and Toxicology, University of Louisville Health Sciences Center, Louisville, KY,University of Louisville Alcohol Research Center, Louisville, KY
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27
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Villafuerte BC, Barati MT, Rane MJ, Isaacs S, Li M, Wilkey DW, Merchant ML. Over-expression of insulin-response element binding protein-1 (IRE-BP1) in mouse pancreatic islets increases expression of RACK1 and TCTP: Beta cell markers of high glucose sensitivity. Biochim Biophys Acta Proteins Proteom 2016; 1865:186-194. [PMID: 27816562 DOI: 10.1016/j.bbapap.2016.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/16/2016] [Accepted: 10/31/2016] [Indexed: 12/29/2022]
Abstract
BACKGROUND A targeted analysis of the 50kDa C-terminal fragment of insulin-response element binding protein-1 (IRE-BP1) activation of target genes through the insulin receptor substrate receptor/PI-3 kinase/Akt pathway has been demonstrated for the insulin growth factor-1 receptor. The broader effects of 50kDa C-terminal IRE-BP1 fragment over-expression on protein abundance in pancreatic islet beta cells have not been determined. RESULTS Liquid-chromatography coupled to tandem mass spectrometry (LC-MS/MS) analyses of replicate lysates of pancreatic islets isolated from background strain animals and transgenic animals, overexpressing IRE-BP1 in pancreatic islet beta cells, demonstrated statistically significant increases in the expression of proteins involved in protein synthesis, endoplasmic reticulum (ER) stress and scaffolding proteins important for protein kinase C signaling; some of which were confirmed by immunoblot analyses. Bioinformatic analysis of protein expression network patterns suggested IRE-BP1 over-expression leads to protein expression patterns indicative of activation of functional protein networks utilized for protein post-translational modification, protein folding, and protein synthesis. Co-immunoprecipitation experiments demonstrate a novel interaction between two differentially regulated proteins receptor for activated protein kinase C (RACK1) and translationally controlled tumor protein (TCTP). CONCLUSIONS Proteomic analysis of IRE-BP1 over-expression in pancreatic islet beta cells suggest IRE-BP1 (a) directly or indirectly through establishing hyperglycemia results in increased expression of ribosomal proteins and markers of ER stress and (b) leads to the enhanced and previously un-described interaction of RACK1 and TCTP. SIGNIFICANCE This study identified C-terminal 50kDa domain of IRE-BP1 over-expression results in increased markers of ER-stress and a novel interaction between the scaffolding proteins RACK1 and TCTP.
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Affiliation(s)
- Betty C Villafuerte
- Department of Medicine, University of Louisville, Louisville, KY, United States
| | - Michelle T Barati
- Department of Medicine, University of Louisville, Louisville, KY, United States
| | - Madhavi J Rane
- Department of Medicine, University of Louisville, Louisville, KY, United States
| | - Susan Isaacs
- Department of Medicine, University of Louisville, Louisville, KY, United States; Core Proteomics Laboratory, University of Louisville, Louisville, KY, United States
| | - Ming Li
- Department of Medicine, University of Louisville, Louisville, KY, United States; Core Proteomics Laboratory, University of Louisville, Louisville, KY, United States
| | - Daniel W Wilkey
- Department of Medicine, University of Louisville, Louisville, KY, United States; Core Proteomics Laboratory, University of Louisville, Louisville, KY, United States
| | - Michael L Merchant
- Department of Medicine, University of Louisville, Louisville, KY, United States; Core Proteomics Laboratory, University of Louisville, Louisville, KY, United States.
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28
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Barnoud T, Wilkey DW, Merchant ML, Clark JA, Donninger H. Proteomics Analysis Reveals Novel RASSF2 Interaction Partners. Cancers (Basel) 2016; 8:cancers8030037. [PMID: 26999212 PMCID: PMC4810121 DOI: 10.3390/cancers8030037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 02/18/2016] [Accepted: 03/09/2016] [Indexed: 12/30/2022] Open
Abstract
RASSF2 is a tumor suppressor that shares homology with other Ras-association domain (RASSF) family members. It is a powerful pro-apoptotic K-Ras effector that is frequently inactivated in many human tumors. The exact mechanism by which RASSF2 functions is not clearly defined, but it likely acts as a scaffolding protein, modulating the activity of other pro-apoptotic effectors, thereby regulating and integrating tumor suppressor pathways. However, only a limited number of RASSF2 interacting partners have been identified to date. We used a proteomics based approach to identify additional RASSF2 interactions, and thereby gain a better insight into the mechanism of action of RASSF2. We identified several proteins, including C1QBP, Vimentin, Protein phosphatase 1G and Ribonuclease inhibitor that function in diverse biological processes, including protein post-translational modifications, epithelial-mesenchymal transition, cell migration and redox homeostasis, which have not previously been reported to interact with RASSF2. We independently validated two of these novel interactions, C1QBP and Vimentin and found that the interaction with C1QBP was enhanced by K-Ras whereas, interestingly, the Vimentin interaction was reduced by K-Ras. Additionally, RASSF2/K-Ras regulated the acetylation of Vimentin. Our data thus reveal novel mechanisms by which RASSF2 may exert its functions, several of which may be Ras-regulated.
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Affiliation(s)
- Thibaut Barnoud
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA.
| | - Daniel W Wilkey
- Department of Medicine, James Graham Brown Cancer Center, Molecular Targets Program, University of Louisville, Louisville, KY 40202, USA.
| | - Michael L Merchant
- Department of Medicine, James Graham Brown Cancer Center, Molecular Targets Program, University of Louisville, Louisville, KY 40202, USA.
| | - Jennifer A Clark
- Department of Medicine, James Graham Brown Cancer Center, Molecular Targets Program, University of Louisville, Louisville, KY 40202, USA.
| | - Howard Donninger
- Department of Medicine, James Graham Brown Cancer Center, Molecular Targets Program, University of Louisville, Louisville, KY 40202, USA.
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29
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Barati MT, Gould JC, Salyer SA, Isaacs S, Wilkey DW, Merchant ML. Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells. J Diabetes Res 2016; 2016:3537863. [PMID: 26839892 PMCID: PMC4709621 DOI: 10.1155/2016/3537863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 11/22/2015] [Accepted: 11/30/2015] [Indexed: 01/30/2023] Open
Abstract
The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG) growth conditions as compared to isoosmotic/normal glucose control (NG(⁎)) conditions. Unique protein expression changes at 2 h HG treatment were measured for 51 protein spots. These proteins could be broadly grouped into two categories: (1) proteins involved in cell survival/cell signaling and (2) proteins involved in stress response. Immunoblot experiments for a protein belonging to both categories, prohibitin (PHB), supported a trend for increased total expression as well as significant increases in an acidic PHB isoform. Additional studies confirmed the regulation of proteasomal subunit alpha-type 2 and the endoplasmic reticulum chaperone and oxidoreductase PDI (protein disulfide isomerase), suggesting altered ER protein folding capacity and proteasomal function in response to acute HG. We conclude that short term high glucose induces subtle changes in protein abundances suggesting posttranslational modifications and regulation of pathways involved in proteostasis.
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Affiliation(s)
- Michelle T. Barati
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - James C. Gould
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sarah A. Salyer
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- Tuskegee University School of Veterinary Medicine, Tuskegee, AL 36088, USA
| | - Susan Isaacs
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Daniel W. Wilkey
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Michael L. Merchant
- Kidney Disease Program, Department of Medicine, University of Louisville, Louisville, KY 40202, USA
- *Michael L. Merchant:
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30
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Rood IM, Merchant ML, Wilkey DW, Zhang T, Zabrouskov V, van der Vlag J, Dijkman HB, Willemsen BK, Wetzels JF, Klein JB, Deegens JK. Increased expression of lysosome membrane protein 2 in glomeruli of patients with idiopathic membranous nephropathy. Proteomics 2015; 15:3722-30. [PMID: 26304790 DOI: 10.1002/pmic.201500127] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/13/2015] [Accepted: 08/18/2015] [Indexed: 11/10/2022]
Abstract
Urinary microvesicles constitute a rich source of membrane-bound and intracellular proteins that may provide important clues of pathophysiological mechanisms in renal disease. In the current study, we analyzed and compared the proteome of urinary microvesicles from patients with idiopathic membranous nephropathy (iMN), idiopathic focal segmental glomerulosclerosis (iFSGS), and normal controls using an approach that combined both proteomics and pathology analysis. Lysosome membrane protein-2 (LIMP-2) was increased greater than twofold in urinary microvesicles obtained from patients with iMN compared to microvesicles of patients with iFSGS and normal controls. Immunofluorescence analysis of renal biopsies confirmed our proteomics findings that LIMP-2 was upregulated in glomeruli from patients with iMN but not in glomeruli of diseased patients (iFSGS, minimal change nephropathy, IgA nephropathy, membranoproliferative glomerulonephritis) and normal controls. Confocal laser microscopy showed co-localization of LIMP-2 with IgG along the glomerular basement membrane. Serum antibodies against LIMP-2 could not be detected. In conclusion, our data show the value of urinary microvesicles in biomarker discovery and provide evidence for de novo expression of LIMP-2 in glomeruli of patients with iMN.
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Affiliation(s)
- Ilse M Rood
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael L Merchant
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville, Louisville, KY, USA
| | - Daniel W Wilkey
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville, Louisville, KY, USA
| | | | | | - Johan van der Vlag
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Henry B Dijkman
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brigith K Willemsen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jack F Wetzels
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jon B Klein
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville, Louisville, KY, USA
- Veterans Administration Medical Center, Louisville, KY, USA
| | - Jeroen K Deegens
- Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
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31
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Caster DJ, Korte EA, Merchant ML, Klein JB, Wilkey DW, Rovin BH, Birmingham DJ, Harley JB, Cobb BL, Namjou B, McLeish KR, Powell DW. Autoantibodies targeting glomerular annexin A2 identify patients with proliferative lupus nephritis. Proteomics Clin Appl 2015; 9:1012-20. [PMID: 25824007 DOI: 10.1002/prca.201400175] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/10/2015] [Accepted: 03/26/2015] [Indexed: 11/09/2022]
Abstract
PURPOSE Patients with systemic lupus erythematosus (SLE) frequently develop lupus nephritis (LN), a complication frequently leading to end stage kidney disease. Immune complex deposition in the glomerulus is central to the development of LN. Using a targeted proteomic approach, we tested the hypothesis that autoantibodies targeting glomerular antigens contribute to the development of LN. EXPERIMENTAL DESIGN Human podocyte and glomerular proteins were separated by SDS-PAGE and immunoblotted with sera from SLE patients with and without LN. The regions of those gels corresponding to reactive bands observed with sera from LN patients were analyzed using LC-MS/MS. RESULTS LN reactive bands were seen at approximately 50 kDa in podocyte extracts and between 36 and 50 kDa in glomerular extracts. Those bands were analyzed by LC-MS/MS and 102 overlapping proteins were identified. Bioinformatic analysis determined that 36 of those proteins were membrane associated, including a protein previously suggested to contribute to glomerulonephritis and LN, annexin A2. By ELISA, patients with proliferative LN demonstrated significantly increased antibodies against annexin A2. CONCLUSION AND CLINICAL RELEVANCE Proteomic approaches identified multiple candidate antigens for autoantibodies in patients with LN. Serum antibodies against annexin A2 were significantly elevated in subjects with proliferative LN, validating those antibodies as potential biomarkers.
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Affiliation(s)
- Dawn J Caster
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA.,Robley Rex Veterans Affairs Medical Center, Louisville, KY, USA
| | - Erik A Korte
- Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, KY, USA
| | - Michael L Merchant
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Jon B Klein
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA.,Robley Rex Veterans Affairs Medical Center, Louisville, KY, USA
| | - Daniel W Wilkey
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Brad H Rovin
- Department of Medicine, the Ohio State University, Columbus, OH, USA
| | - Dan J Birmingham
- Department of Medicine, the Ohio State University, Columbus, OH, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and the University of Cincinnati, Cincinnati, OH, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Beth L Cobb
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and the University of Cincinnati, Cincinnati, OH, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and the University of Cincinnati, Cincinnati, OH, USA
| | - Kenneth R McLeish
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA.,Robley Rex Veterans Affairs Medical Center, Louisville, KY, USA
| | - David W Powell
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY, USA.,Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, KY, USA
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Merchant ML, Niewczas MA, Ficociello LH, Lukenbill JA, Wilkey DW, Li M, Khundmiri SJ, Warram JH, Krolewski AS, Klein JB. Plasma kininogen and kininogen fragments are biomarkers of progressive renal decline in type 1 diabetes. Kidney Int 2013; 83:1177-84. [PMID: 23466993 PMCID: PMC4241022 DOI: 10.1038/ki.2013.8] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The ability of microalbuminuria to predict early progressive renal function decline in type-1 diabetic patients has been questioned. To resolve this, we determined the plasma proteome differences between microalbuminuric patients with type-1 diabetes and stable renal function (controls) and patients at risk for early progressive renal function decline (cases) and asked whether these differences have value as surrogate biomarkers. Mass spectrometry was used to analyze small (less than 3 kDa) plasma peptides isolated from well-matched case and control plasma obtained at the beginning of an 8-12 year follow-up period. Spearman analysis of plasma peptide abundance and the rate of renal function decline during follow-up identified seven masses with a significant negative correlation with early progressive renal function decline. Tandem mass spectrometry identified three fragments of high molecular weight kininogen. Increased plasma high molecular weight kininogen in the cases was confirmed by immunoblot. One peptide, des-Arg9-BK(1-8), induced Erk1/2 phosphorylation when added apically to two proximal tubular cell lines grown on permeable inserts. Thus, we have identified plasma protein fragments, some of which have biological activity with moderate to strong correlation, with early progressive renal function decline in microalbuminuric patients with type-1 diabetes. Other peptides are candidates for validation as candidate biomarkers of diabetes-associated renal dysfunction.
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Affiliation(s)
- Michael L Merchant
- Kidney Disease Program, University of Louisville, Louisville, Kentucky, USA
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Merchant ML, Gaweda AE, Dailey AJ, Wilkey DW, Zhang X, Rovin BH, Klein JB, Brier ME. Oncostatin M receptor β and cysteine/histidine-rich 1 are biomarkers of the response to erythropoietin in hemodialysis patients. Kidney Int 2011; 79:546-554. [PMID: 21150872 PMCID: PMC4024449 DOI: 10.1038/ki.2010.468] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biomarkers that evaluate the response to erythropoietic-stimulating agents largely measure inflammation and iron availability. While these are important factors in modifying an individual's response to these agents, they do not address all aspects of a poor response. To clarify this, we isolated peptides in the serum of good and poor responders to erythropoietin in order to identify biomarkers of stimulating agent response. Ninety-one candidate biomarker targets were identified and characterized using mass spectrometry, of which tandem mass spectroscopy provided partial amino-acid sequence information of 17 different peptides for 16 peptide masses whose abundance significantly differed between poor and good responders. The analysis concluded that three peptides associated with a poor response were derived from oncostatin M receptor β (OSMRβ). The 13 serum peptides associated with a good response were derived from fibrinogen α and β, coagulation factor XIII, complement C3, and cysteine/histidine rich 1(CYHR1). Poor response was most strongly associated with the OSMRβ fragment with the largest molecular weight, while a good response was most strongly associated with CYHR1. Immunoblots found the abundance of intact OSMRβ and CYHR1 significantly differed between good and poor responders. Thus, two measurable biomarkers of the response to erythropoietic-stimulating agents are present in the serum of treated patients.
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Affiliation(s)
| | - Adam E. Gaweda
- Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Andrew J. Dailey
- Department of Medicine, University of Louisville, Louisville, Kentucky, USA
- The Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky, USA
| | - Daniel W. Wilkey
- Department of Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Xiaolan Zhang
- Department of Medicine, Ohio State University School of Medicine, Columbus, Ohio, USA
| | - Brad H. Rovin
- Department of Medicine, Ohio State University School of Medicine, Columbus, Ohio, USA
| | - Jon B. Klein
- Department of Medicine, University of Louisville, Louisville, Kentucky, USA
- The Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky, USA
| | - Michael E. Brier
- Department of Medicine, University of Louisville, Louisville, Kentucky, USA
- The Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky, USA
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Rood IM, Deegens JKJ, Merchant ML, Tamboer WPM, Wilkey DW, Wetzels JFM, Klein JB. Comparison of three methods for isolation of urinary microvesicles to identify biomarkers of nephrotic syndrome. Kidney Int 2010; 78:810-6. [PMID: 20686450 DOI: 10.1038/ki.2010.262] [Citation(s) in RCA: 194] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Urinary microvesicles, such as 40-100 nm exosomes and 100-1000 nm microparticles, contain many proteins that may serve as biomarkers of renal disease. Microvesicles have been isolated by ultracentrifugation or nanomembrane ultrafiltration from normal urine; however, little is known about the efficiency of these methods in isolating microvesicles from patients with nephrotic-range proteinuria. Here we compared three techniques to isolate microvesicles from nephrotic urine: nanomembrane ultrafiltration, ultracentrifugation, and ultracentrifugation followed by size-exclusion chromatography (UC-SEC). Highly abundant urinary proteins were still present in sufficient quantity after ultrafiltration or ultracentrifugation to blunt detection of less abundant microvesicular proteins by MALDI-TOF-TOF mass spectrometry. The microvesicular markers neprilysin, aquaporin-2, and podocalyxin were highly enriched following UC-SEC compared with preparations by ultrafiltration or ultracentrifugation alone. Electron microscopy of the UC-SEC fractions found microvesicles of varying size, compatible with the presence of both exosomes and microparticles. Thus, UC-SEC following ultracentrifugation to further enrich and purify microparticles facilitates the search for prognostic biomarkers that might be used to predict the clinical course of nephrotic syndrome.
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Affiliation(s)
- Ilse M Rood
- Department of Nephrology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
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Merchant ML, Powell DW, Wilkey DW, Cummins TD, Deegens JK, Rood IM, McAfee KJ, Fleischer C, Klein E, Klein JB. Microfiltration isolation of human urinary exosomes for characterization by MS. Proteomics Clin Appl 2009; 4:84-96. [PMID: 21137018 DOI: 10.1002/prca.200800093] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2008] [Revised: 09/14/2009] [Accepted: 09/28/2009] [Indexed: 12/12/2022]
Abstract
PURPOSE The purpose of this study was to address the hypothesis that small vesicular urinary particles known as exosomes could be selectively microfiltered using low protein-binding size exclusion filters, thereby simplifying their use in clinical biomarker discovery studies. EXPERIMENTAL DESIGN We characterized a microfiltration approach using a low protein binding, hydrophilized polyvinylidene difluoride membrane to easily and efficiently isolate urinary exosomes from fresh, room temperature or 4°C urine, with a simultaneous depletion of abundant urinary proteins. Using LC-MS, immunoblot analysis, and electron microscopy methods, we demonstrate this method to isolate intact exosomes and thereby enrich for a low abundant urinary proteome. RESULTS In comparison to other standard methods of exosome isolation including ultracentrifugation and nanofiltration, we demonstrate equivalent enrichment of the exosome proteome with reduced co-purification of abundant urinary proteins. CONCLUSION AND CLINICAL RELEVANCE In conclusion, we demonstrate a microfiltration isolation method that preserves the exosome structure, reduces contamination from higher abundant urinary proteins, and can be easily implemented into mass spectrometry analysis for biomarker discovery efforts or incorporation into routine clinical laboratory applications to yield higher sample throughput.
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Merchant ML, Perkins BA, Boratyn GM, Ficociello LH, Wilkey DW, Barati MT, Bertram CC, Page GP, Rovin BH, Warram JH, Krolewski AS, Klein JB. Urinary peptidome may predict renal function decline in type 1 diabetes and microalbuminuria. J Am Soc Nephrol 2009; 20:2065-74. [PMID: 19643930 DOI: 10.1681/asn.2008121233] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
One third of patients with type 1 diabetes and microalbuminuria experience an early, progressive decline in renal function that leads to advanced stages of chronic kidney disease and ESRD. We hypothesized that the urinary proteome may distinguish between stable renal function and early renal function decline among patients with type 1 diabetes and microalbuminuria. We followed patients with normal renal function and microalbuminuria for 10 to 12 yr and classified them into case patients (n = 21) with progressive early renal function decline and control subjects (n = 40) with stable renal function. Using liquid chromatography matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, we identified three peptides that decreased in the urine of patients with early renal function decline [fragments of alpha1(IV) and alpha1(V) collagens and tenascin-X] and three peptides that increased (fragments of inositol pentakisphosphate 2-kinase, zona occludens 3, and FAT tumor suppressor 2). In renal biopsies from patients with early nephropathy from type 1 diabetes, we observed increased expression of inositol pentakisphosphate 2-kinase, which was present in granule-like cytoplasmic structures, and zona occludens 3. These results indicate that urinary peptide fragments reflect changes in expression of intact protein in the kidney, suggesting new potential mediators of diabetic nephropathy and candidate biomarkers for progressive renal function decline.
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Merchant ML, Cummins TD, Wilkey DW, Salyer SA, Powell DW, Klein JB, Lederer ED. Proteomic analysis of renal calculi indicates an important role for inflammatory processes in calcium stone formation. Am J Physiol Renal Physiol 2008; 295:F1254-8. [PMID: 18701630 DOI: 10.1152/ajprenal.00134.2008] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Even though renal stones/calculi occur in approximately 10% of individuals, they are an enormous economic burden to the entire US health system. While the relative metabolic composition of renal calculi is generally known, there is no clear understanding of the genetics of renal stone formation, nor are there clear prognostic indicators of renal stone formation. The application of proteomics to the analysis of renal calculi axiomatically holds that insight into renal stone pathobiology can be gained by a more comprehensive understanding of renal calculus protein composition. We analyzed isolated renal stone matrix proteins with mass spectrometric and immunohistochemical methods identifying 158 proteins with high confidence, including 28 common proteins. The abundant proteins included those identified previously in stones and proteins identified here for the first time, such as myeloid lineage-specific, integral membrane and lipid regulatory proteins. Pathway analyses of all proteins identified suggested that a significant fraction of the most abundant matrix proteins participate in inflammatory processes. These proteomic results support the hypothesis that stone formation induces a cellular inflammatory response and the protein components of this response contribute to the abundant stone matrix proteome.
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Affiliation(s)
- Michael L Merchant
- Department of Medicine, James Graham Brown Cancer Center, University of Louiville, Rm. 102S, Donald Baxter Research Bldg., 570 S. Preston St., Louisville, KY 40202, USA.
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Canter MP, Graham CA, Heit MH, Blackwell LS, Wilkey DW, Klein JB, Merchant ML. Proteomic techniques identify urine proteins that differentiate patients with interstitial cystitis from asymptomatic control subjects. Am J Obstet Gynecol 2008; 198:553.e1-6. [PMID: 18455532 DOI: 10.1016/j.ajog.2008.01.052] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 11/20/2007] [Accepted: 01/24/2008] [Indexed: 11/19/2022]
Abstract
OBJECTIVE The purpose of this study was to identify differences in urine proteins between patients with interstitial cystitis (IC) and asymptomatic control (AC) subjects with the use of proteomic techniques. STUDY DESIGN Nine patients with IC and their age-, race-, and sex-matched AC subjects volunteered a urine specimen. Urine proteins were separated with the use of 2-dimensional polyacrylamide gels. Differing proteins underwent digestion and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Computer-assisted data analysis was used to identify the corresponding protein. Differences in urine protein responses between patients with IC and AC subjects were evaluated by the Mann-Whitney U test to account for the nonnormal frequency distribution of the parameter estimate or chi-square when data were bimodal. RESULTS Four proteins differed significantly between patients with IC and AC subjects. The AC subjects had a greater concentration of a uromodulin (P = .019) and two kininogens (P = .023, .046). The patients with IC had a greater concentration of inter-alpha-trypsin inhibitor heavy chain H4 (P = .019). CONCLUSION These urine protein isoforms may be biomarkers for IC.
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Affiliation(s)
- Maria P Canter
- Division of Urogynecology, Department of Obstetrics and Gynecology, Virginia Hospital Center, Arlington, VA 22205, USA.
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Colella R, Lu C, Hodges B, Wilkey DW, Roisen FJ. GM1 enhances the association of neuron-specific MAP2 with actin in MAP2-transfected 3T3 cells. Brain Res Dev Brain Res 2000; 121:1-9. [PMID: 10837887 DOI: 10.1016/s0165-3806(00)00018-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ganglioside GM1 is a glycosphingolipid which enhances process formation of several neuronal lines and potentiates some growth factor-mediated responses. Previously we have shown that 24 h exposure of Neuro 2a cells to GM1 mobilized the neuron-specific microtubule-associated protein, MAP2, away from microtubule-rich areas to areas of neurite sprouting where MAP2 was more closely associated with the subcortical actin network. To examine the role of GM1 in fostering the shift of the association of MAP2 from tubulin to actin, NIH 3T3 cells were co-transfected with pHook-1, which expresses a surface antigen, and a construct expressing MAP2. Transfected cells were selected with magnetic beads coated with a hapten that binds to the expressed surface antigen and treated with 150 microg/ml GM1 for 18-24 h. Actin and MAP2 or tubulin and MAP2 were immunolocalized and examined with confocal microscopy. MAP2 was found throughout the cytoplasm as well as associated with actin filaments. As observed previously with Neuro 2a, GM1 treatment of transfected fibroblasts redistributed the MAP2 away from direct association with microtubules to peripheral areas where the association of MAP2 with actin was enhanced. GM1 did not induce neurite-like processes in MAP2-transfected cells. Treatment with cytochalasin B, which is reported to result in process formation, also did not induce neurite-like processes. These studies suggest that GM1's ability to mobilize MAP2 and promote its association with actin is not restricted to neurons.
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Affiliation(s)
- R Colella
- Department of Anatomical Sciences and Neurobiology, University of Louisville School of Medicine, 500 S. Preston Street, Louisville, KY 40292, USA.
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