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Piehowski PD, Petyuk VA, Sandoval JD, Burnum KE, Kiebel GR, Monroe ME, Anderson GA, Camp DG, Smith RD. STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results. Proteomics 2013; 13:766-70. [PMID: 23303698 DOI: 10.1002/pmic.201200096] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 10/11/2012] [Accepted: 11/20/2012] [Indexed: 11/11/2022]
Abstract
For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifications are demonstrated using datasets derived from immunoaffinity-depleted blood serum and a bacterial cell lysate, two common proteomics sample types.
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Affiliation(s)
- Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA99352, USA
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2
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Wiedner SD, Burnum KE, Pederson LM, Anderson LN, Fortuin S, Chauvigné-Hines LM, Shukla AK, Ansong C, Panisko EA, Smith RD, Wright AT. Multiplexed activity-based protein profiling of the human pathogen Aspergillus fumigatus reveals large functional changes upon exposure to human serum. J Biol Chem 2012; 287:33447-59. [PMID: 22865858 PMCID: PMC3460446 DOI: 10.1074/jbc.m112.394106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/27/2012] [Indexed: 11/06/2022] Open
Abstract
Environmental adaptability is critical for survival of the fungal human pathogen Aspergillus fumigatus in the immunocompromised host lung. We hypothesized that exposure of the fungal pathogen to human serum would lead to significant alterations to the organism's physiology, including metabolic activity and stress response. Shifts in functional pathway and corresponding enzyme reactivity of A. fumigatus upon exposure to the human host may represent much needed prognostic indicators of fungal infection. To address this, we employed a multiplexed activity-based protein profiling (ABPP) approach coupled to quantitative mass spectrometry-based proteomics to measure broad enzyme reactivity of the fungus cultured with and without human serum. ABPP showed a shift from aerobic respiration to ethanol fermentation and utilization over time in the presence of human serum, which was not observed in serum-free culture. Our approach provides direct insight into this pathogen's ability to survive, adapt, and proliferate. Additionally, our multiplexed ABPP approach captured a broad swath of enzyme reactivity and functional pathways and provides a method for rapid assessment of the A. fumigatus response to external stimuli.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ellen A. Panisko
- the Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, Washington 99352
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3
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Burnum KE, Hirota Y, Baker ES, Yoshie M, Ibrahim YM, Monroe ME, Anderson GA, Smith RD, Daikoku T, Dey SK. Uterine deletion of Trp53 compromises antioxidant responses in the mouse decidua. Endocrinology 2012; 153:4568-79. [PMID: 22759378 PMCID: PMC3423619 DOI: 10.1210/en.2012-1335] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Preterm birth is a global health issue impacting millions of mothers and babies. However, the etiology of preterm birth is not clearly understood. Our recent finding that premature decidual senescence with terminal differentiation is a cause of preterm birth in mice with uterine Trp53 deletion, encoding p53 protein, led us to explore other potential factors that are related to preterm birth. Using proteomics approaches, here, we show that 183 candidate proteins show significant changes in deciduae with Trp53 deletion as compared with normal deciduae. Functional categorization of these proteins unveiled new pathways that are influenced by p53. In particular, down-regulation of a cluster of antioxidant enzymes in p53-deficient deciduae suggests that increased oxidative stress could be one cause of preterm birth in mice harboring uterine deletion of Trp53.
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Affiliation(s)
- Kristin E Burnum
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352-9104, USA
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4
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Diamond DL, Krasnoselsky AL, Burnum KE, Monroe ME, Webb-Robertson BJ, McDermott JE, Yeh MM, Dzib JFG, Susnow N, Strom S, Proll SC, Belisle SE, Purdy DE, Rasmussen AL, Walters KA, Jacobs JM, Gritsenko MA, Camp DG, Bhattacharya R, Perkins JD, Carithers RL, Liou IW, Larson AM, Benecke A, Waters KM, Smith RD, Katze MG. Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation. Hepatology 2012; 56:28-38. [PMID: 22331615 PMCID: PMC3387320 DOI: 10.1002/hep.25649] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/25/2012] [Indexed: 12/23/2022]
Abstract
UNLABELLED Liver transplant tissues offer the unique opportunity to model the longitudinal protein abundance changes occurring during hepatitis C virus (HCV)-associated liver disease progression in vivo. In this study, our goal was to identify molecular signatures, and potential key regulatory proteins, representative of the processes influencing early progression to fibrosis. We performed global protein profiling analyses on 24 liver biopsy specimens obtained from 15 HCV(+) liver transplant recipients at 6 and/or 12 months posttransplantation. Differentially regulated proteins associated with early progression to fibrosis were identified by analysis of the area under the receiver operating characteristic curve. Analysis of serum metabolites was performed on samples obtained from an independent cohort of 60 HCV(+) liver transplant patients. Computational modeling approaches were applied to identify potential key regulatory proteins of liver fibrogenesis. Among 4,324 proteins identified, 250 exhibited significant differential regulation in patients with rapidly progressive fibrosis. Patients with rapid fibrosis progression exhibited enrichment in differentially regulated proteins associated with various immune, hepatoprotective, and fibrogenic processes. The observed increase in proinflammatory activity and impairment in antioxidant defenses suggests that patients who develop significant liver injury experience elevated oxidative stresses. This was supported by an independent study demonstrating the altered abundance of oxidative stress-associated serum metabolites in patients who develop severe liver injury. Computational modeling approaches further highlight a potentially important link between HCV-associated oxidative stress and epigenetic regulatory mechanisms impacting on liver fibrogenesis. CONCLUSION Our proteome and metabolome analyses provide new insights into the role for increased oxidative stress in the rapid fibrosis progression observed in HCV(+) liver transplant recipients. These findings may prove useful in prognostic applications for predicting early progression to fibrosis.
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Affiliation(s)
- Deborah L. Diamond
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | | | - Kristin E. Burnum
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | | | - Jason E. McDermott
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA
| | - Matthew M. Yeh
- Dept. of Pathology, University of Washington School of Medicine, Seattle, WA
| | | | - Nathan Susnow
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Susan Strom
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Sean C. Proll
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Sarah E. Belisle
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - David E. Purdy
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Angela L. Rasmussen
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Kathie-Anne Walters
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Marina A. Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Renuka Bhattacharya
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - James D. Perkins
- Dept. of Surgery, University of Washington School of Medicine, Seattle, WA
| | - Robert L. Carithers
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Iris W. Liou
- Institut des Hautes Etudes Scientifiques, CNRS, Bures-sur-Yvette, France
| | - Anne M. Larson
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Arndt Benecke
- Institut des Hautes Etudes Scientifiques, CNRS, Bures-sur-Yvette, France
| | - Katrina M. Waters
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Michael G. Katze
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA,Washington National Primate Research Center, University of Washington, Seattle, WA
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Abstract
Progesterone (P(4)) signaling is critical for pregnancy. We previously showed that immunopilin FK506 binding protein (FKBP)52 serves as a cochaperone to optimize progesterone receptor (PR) function in the uterus, and its deficiency leads to P(4) resistance in a pregnancy stage-specific and genetic background-dependent manner in mice. In particular, sc placement of SILASTIC implants carrying P(4) rescued implantation failure in CD1 Fkbp52(-/-) mice, but the resorption rate was substantially high at midgestation due to reduced P(4) responsiveness. Because downstream targets of P(4)-FKBP52-PR signaling in the uterus to support pregnancy are not clearly understood, we performed proteomic analysis using Fkbp52(-/-), PR-deficient (Pgr(-/-)), and wild-type (WT) uteri. We found that the expression of galectin-1 (Gal1), an evolutionarily conserved glycan-binding protein, was significantly down-regulated in both Fkbp52(-/-) and Pgr(-/-) uteri compared with WT uteri. During early gestation, Lgals1, which encodes Gal1, was distinctly expressed in stromal and decidual cells. Lgals1 expression was much lower in d 4 Fkbp52(-/-) uteri compared with WT uteri, and this reduction was reversed by P(4) supplementation. More interestingly, concomitant supplementation of recombinant Gal1 significantly suppressed the high resorption rate and leukocyte infiltration at implantation sites in CD1 Fkbp52(-/-) females carrying P(4) SILASTIC implants. These findings suggest that uterine Gal1 is an important downstream target of P(4)-FKBP52-PR signaling in the uterus to support P(4) responsiveness during pregnancy.
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Affiliation(s)
- Yasushi Hirota
- Department of Obstetrics and Gynecology, University of Tokyo, Tokyo 113-8655, Japan
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Zhang H, Burnum KE, Luna ML, Petritis BO, Kim JS, Qian WJ, Moore RJ, Heredia-Langner A, Webb-Robertson BJM, Thrall BD, Camp DG, Smith RD, Pounds JG, Liu T. Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size. Proteomics 2011; 11:4569-77. [PMID: 21956884 DOI: 10.1002/pmic.201100037] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 06/10/2011] [Accepted: 09/13/2011] [Indexed: 12/21/2022]
Abstract
Nanoparticle biological activity, biocompatibility and fate can be directly affected by layers of readily adsorbed host proteins in biofluids. Here, we report a study on the interactions between human blood plasma proteins and nanoparticles with a controlled systematic variation of properties using (18)O-labeling and LC-MS-based quantitative proteomics. We developed a novel protocol to both simplify isolation of nanoparticle bound proteins and improve reproducibility. LC-MS analysis identified and quantified 88 human plasma proteins associated with polystyrene nanoparticles consisting of three different surface chemistries and two sizes, as well as, for four different exposure times (for a total of 24 different samples). Quantitative comparison of relative protein abundances was achieved by spiking an (18)O-labeled "universal" reference into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantification across the entire sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive patterns that classified the nanoparticles based on their surface properties and size. In addition, temporal data indicated that the formation of the stable protein corona was at equilibrium within 5 min. The comprehensive quantitative proteomics results obtained in this study provide rich data for computational modeling and have potential implications towards predicting nanoparticle biocompatibility.
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Affiliation(s)
- Haizhen Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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7
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Lennen RM, Kruziki MA, Kumar K, Zinkel RA, Burnum KE, Lipton MS, Hoover SW, Ranatunga DR, Wittkopp TM, Marner WD, Pfleger BF. Membrane stresses induced by overproduction of free fatty acids in Escherichia coli. Appl Environ Microbiol 2011; 77:8114-28. [PMID: 21948837 PMCID: PMC3208990 DOI: 10.1128/aem.05421-11] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [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: 05/09/2011] [Accepted: 09/15/2011] [Indexed: 02/05/2023] Open
Abstract
Microbially produced fatty acids are potential precursors to high-energy-density biofuels, including alkanes and alkyl ethyl esters, by either catalytic conversion of free fatty acids (FFAs) or enzymatic conversion of acyl-acyl carrier protein or acyl-coenzyme A intermediates. Metabolic engineering efforts aimed at overproducing FFAs in Escherichia coli have achieved less than 30% of the maximum theoretical yield on the supplied carbon source. In this work, the viability, morphology, transcript levels, and protein levels of a strain of E. coli that overproduces medium-chain-length FFAs was compared to an engineered control strain. By early stationary phase, an 85% reduction in viable cell counts and exacerbated loss of inner membrane integrity were observed in the FFA-overproducing strain. These effects were enhanced in strains endogenously producing FFAs compared to strains exposed to exogenously fed FFAs. Under two sets of cultivation conditions, long-chain unsaturated fatty acid content greatly increased, and the expression of genes and proteins required for unsaturated fatty acid biosynthesis were significantly decreased. Membrane stresses were further implicated by increased expression of genes and proteins of the phage shock response, the MarA/Rob/SoxS regulon, and the nuo and cyo operons of aerobic respiration. Gene deletion studies confirmed the importance of the phage shock proteins and Rob for maintaining cell viability; however, little to no change in FFA titer was observed after 24 h of cultivation. The results of this study serve as a baseline for future targeted attempts to improve FFA yields and titers in E. coli.
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Affiliation(s)
- Rebecca M. Lennen
- Department of Chemical and Biological Engineering; University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
| | - Max A. Kruziki
- Department of Chemical and Biological Engineering; University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706
| | - Kritika Kumar
- Department of Chemical and Biological Engineering; University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706
| | - Robert A. Zinkel
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
- University of Wisconsin Biotechnology Center, 425 Henry Mall, Madison, Wisconsin 53706
| | - Kristin E. Burnum
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99353
| | - Mary S. Lipton
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99353
| | - Spencer W. Hoover
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
| | - Don R. Ranatunga
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
| | - Tyler M. Wittkopp
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
| | - Wesley D. Marner
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
| | - Brian F. Pfleger
- Department of Chemical and Biological Engineering; University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706
- U.S. Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, 1550 Linden Drive, Madison, Wisconsin 53706
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8
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Hirota Y, Acar N, Tranguch S, Burnum KE, Xie H, Kodama A, Osuga Y, Ustunel I, Friedman DB, Caprioli RM, Daikoku T, Dey SK. Uterine FK506-binding protein 52 (FKBP52)-peroxiredoxin-6 (PRDX6) signaling protects pregnancy from overt oxidative stress. Proc Natl Acad Sci U S A 2010; 107:15577-82. [PMID: 20713718 PMCID: PMC2932576 DOI: 10.1073/pnas.1009324107] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [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: 11/18/2022] Open
Abstract
Immunophilin FK506-binding protein 52 (FKBP52) is a cochaperone that binds to the progesterone receptor (PR) to optimize progesterone (P(4))-PR signaling. We recently showed that Fkbp52-deficient (Fkbp52(-/-)) mice have reduced uterine PR responsiveness and implantation failure which is rescued by excess P(4) supplementation in a genetic background-dependent manner. This finding led us to hypothesize that FKBP52 has functions in addition to optimizing PR activity. Using proteomics analysis, we found that uterine levels of peroxiredoxin-6 (PRDX6), a unique antioxidant, are significantly lower in Fkbp52(-/-) mice than in WT and PR-null (Pgr(-/-)) mice. We also found that Fkbp52(-/-) mice with reduced uterine PRDX6 levels are susceptible to paraquat-induced oxidative stress (OS), leading to implantation failure even with P(4) supplementation. The same dose of paraquat did not interfere with implantation in WT mice. Moreover, treatment with antioxidants alpha-tocopherol and N-acetylcysteine (NAC) attenuated paraquat-induced implantation failure in P(4)-treated Fkbp52(-/-) mice. Functional analyses using mouse embryonic fibroblasts show that Fkbp52 deficiency associated with reduced PRDX6 levels promotes H(2)O(2)-induced cell death, which is reversed by the addition of NAC or by forced expression of PRDX6, suggesting that Fkbp52 deficiency diminishes the threshold against OS by reducing PRDX6 levels. These findings provide evidence that heightened uterine OS in Fkbp52(-/-) females with reduced PRDX6 levels induces implantation failure even in the presence of excess P(4). This study shows that FKBP52-PRDX6 signaling protects pregnancy from overt OS.
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Affiliation(s)
- Yasushi Hirota
- Division of Reproductive Sciences, The Perinatal Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- Department of Obstetrics and Gynecology, University of Tokyo, Tokyo 113-8655, Japan
| | - Nuray Acar
- Division of Reproductive Sciences, The Perinatal Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Antalya 07070, Turkey; and
| | - Susanne Tranguch
- Division of Reproductive Sciences, The Perinatal Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Kristin E. Burnum
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Huirong Xie
- Division of Reproductive Sciences, The Perinatal Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Ako Kodama
- Department of Obstetrics and Gynecology, University of Tokyo, Tokyo 113-8655, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, University of Tokyo, Tokyo 113-8655, Japan
| | - Ismail Ustunel
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Antalya 07070, Turkey; and
| | - David B. Friedman
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Takiko Daikoku
- Division of Reproductive Sciences, The Perinatal Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Sudhansu K. Dey
- Division of Reproductive Sciences, The Perinatal Institute, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
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9
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Burnum KE, Cornett DS, Puolitaival SM, Milne SB, Myers DS, Tranguch S, Brown HA, Dey SK, Caprioli RM. Spatial and temporal alterations of phospholipids determined by mass spectrometry during mouse embryo implantation. J Lipid Res 2009; 50:2290-8. [PMID: 19429885 DOI: 10.1194/jlr.m900100-jlr200] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular events involved in successful embryo implantation are not well understood. In this study, we used MALDI imaging mass spectrometry (IMS) technologies to characterize the spatial and temporal distribution of phospholipid species associated with mouse embryo implantation. Molecular images showing phospholipid distribution within implantation sites changed markedly between distinct cellular areas during days 4-8 of pregnancy. For example, by day 8, linoleate- and docosahexaenoate-containing phospholipids localized to regions destined to undergo cell death, whereas oleate-containing phospholipids localized to angiogenic regions. Arachidonate-containing phospholipids showed different segregation patterns depending on the lipid class, revealing a strong correlation of phosphatidylethanolamines and phosphatidylinositols with cytosolic phospholipase A(2alpha) and cyclooxygenase-2 during embryo implantation. LC-ESI-MS/MS was used to validate MALDI IMS phospholipid distribution patterns. Overall, molecular images revealed the dynamic complexity of lipid distributions in early pregnancy, signifying the importance of complex interplay of lipid molecules in uterine biology and implantation.
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Affiliation(s)
- Kristin E Burnum
- Departments of Biochemistry, Mass Spectrometry Research Center, Nashville, TN 37232, USA
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10
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Abstract
A reciprocal interaction between the implantation-competent blastocyst and receptive uterus is an absolute requirement for implantation, a process crucial for pregnancy success. A comprehensive understanding of this interaction has yet to be realized. One major difficulty in clearly defining this discourse is the complexity of the implantation process involving heterogeneous cell types of both the uterus and blastocyst, each endowed with unique molecular signatures that show dynamic changes during the course of pregnancy. Whereas gene expression studies by in situ hybridization or immunohistochemistry have shown differential expression patterns of specific genes during implantation, there is no report how numerous signaling proteins are spatially displayed at specific times and stages of implantation in the context of blastocyst-uterine juxtaposition. Using in situ imaging (matrix assisted laser desorption/ionization) mass spectrometry directly on uterine sections, here we provide molecular composition, relative abundance, and spatial distribution of a large number of proteins during the periimplantation period. This approach has allowed us for the first time to generate in situ proteome profiles of implantation and interimplantation sites in mice in a region- and stage-specific manner with the progression of implantation. This application is reliable because patterns of expression of several proteins displayed by in situ imaging mass spectrometry correlate well with in situ hybridization results. More interestingly, the use of this approach has provided new insights regarding uterine biology of cytosolic phospholipase A(2alpha) null females that show implantation defects.
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Affiliation(s)
- Kristin E Burnum
- Department of Chemistry and Biochemistry, Mass Spectrometry Research Center, Vanderbilt University Medical Center, MCN D4100, 1161 21st Avenue South, Nashville, TN 37232, USA
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11
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Puolitaival SM, Burnum KE, Cornett DS, Caprioli RM. Solvent-free matrix dry-coating for MALDI imaging of phospholipids. J Am Soc Mass Spectrom 2008; 19:882-6. [PMID: 18378160 PMCID: PMC2696184 DOI: 10.1016/j.jasms.2008.02.013] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 02/11/2008] [Accepted: 02/12/2008] [Indexed: 05/08/2023]
Abstract
A fast and simple, solvent-free matrix deposition protocol was developed for positive ionization mode phospholipid analysis in tissues. Finely ground 2,5-dihydroxybenzoic acid was deposited onto sagittal mouse brain sections using a dry-coating technique, in which solid matrix particles were filtered directly onto the tissue through a 20-microm stainless steel sieve. Phospholipid signals were obtained directly off these sections, allowing acquisition of high-resolution MS images. These images were compared to those from serial sections that were spray-coated with a thin-layer chromatography (TLC) reagent sprayer. Signals obtained from the dry matrix deposition method were comparable to those from spray-coated sections, producing identical localization patterns with a simpler and faster sample preparation with virtually no analyte delocalization. This approach was found to yield highly reproducible results, eliminating much of the variance caused by operator differences, and making it an attractive alternative to the currently used matrix application methods.
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Affiliation(s)
- Satu M. Puolitaival
- Department of Chemistry, Vanderbilt University, MRB 3 465 21 Ave S, Nashville, TN 37235
| | - Kristin E. Burnum
- Department of Biochemistry, Vanderbilt University, MRB 3 465 21 Ave S, Nashville, TN 37235
| | - D. Shannon Cornett
- Medical Center Mass Spectrometry Research Center, MRB 3 465 21 Ave S, Nashville, TN 37235
| | - Richard M. Caprioli
- Department of Chemistry, Vanderbilt University, MRB 3 465 21 Ave S, Nashville, TN 37235
- Department of Biochemistry, Vanderbilt University, MRB 3 465 21 Ave S, Nashville, TN 37235
- Medical Center Mass Spectrometry Research Center, MRB 3 465 21 Ave S, Nashville, TN 37235
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12
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Burnum KE, Frappier SL, Caprioli RM. Matrix-assisted laser desorption/ionization imaging mass spectrometry for the investigation of proteins and peptides. Annu Rev Anal Chem (Palo Alto Calif) 2008; 1:689-705. [PMID: 20636094 DOI: 10.1146/annurev.anchem.1.031207.112841] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Mass spectrometry (MS) is an excellent technology for molecular imaging because of its high data dimensionality. MS can monitor thousands of individual molecular data channels measured as mass-to-charge (m/z). We describe the use of matrix-assisted laser desorption/ionization (MALDI) MS for the image analysis of proteins, peptides, lipids, drugs, and metabolites in tissues. We discuss the basic instrumentation and sample preparation methods needed to produce high-resolution images and high image reproducibility. Matrix-addition protocols are briefly discussed along with normal operating procedures, and selected biological and medical applications of MALDI imaging MS are described. We give examples of both two- and three-dimensional imaging, including normal mouse embryo implantation, sperm maturation in mouse epididymis, protein distributions in brain sections, protein alterations as a result of drug administration, and protein changes in brain due to neurodegeneration and tumor formation. Advantages of this technology and future challenges for its improvement are discussed.
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Affiliation(s)
- Kristin E Burnum
- Mass Spectrometry Research Center, Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37221, USA.
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