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Article ; Online: The role of apolipoprotein E in neurodegeneration and cardiovascular disease.

Lopez, Mary F / Krastins, Bryan / Ning, MingMing

2014 Volume 11, Issue 3, Page(s) 371–381

Abstract: Apolipoprotein E (ApoE) is an abundant plasma protein that interacts with low density lipoprotein receptors and other proteins, participating in the transport of cholesterol and lipids. Research has revealed many other roles for this multifunctional ... ...

Abstract	Apolipoprotein E (ApoE) is an abundant plasma protein that interacts with low density lipoprotein receptors and other proteins, participating in the transport of cholesterol and lipids. Research has revealed many other roles for this multifunctional protein. ApoE is polymorphic and exists in three major isoforms: ApoE2, ApoE3 (the most common isoform) and ApoE4, which differ by only one amino acid, at positions 112 and 158. The altered binding to lipids and receptors by ApoE isoforms E2 and E4 results in an elevated risk for neurological, cerebrovascular and cardiovascular pathologies. Most notably, ApoE4 is associated with an elevated risk (relative to E3) for Alzheimer's disease. The application of mass spectrometry for genotyping and also direct measurement of ApoE protein isoforms is a recent development and is well suited to high-throughput applications. The precise quantification of protein isoforms will allow better characterization of effects resulting from heterozygous APOE genotypes.
MeSH term(s)	Alzheimer Disease/metabolism ; Apolipoproteins E/genetics ; Apolipoproteins E/metabolism ; Cardiovascular Diseases/metabolism ; Humans ; Neurodegenerative Diseases/metabolism ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Proteomics
Chemical Substances	Apolipoproteins E ; Protein Isoforms
Language	English
Publishing date	2014-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2299100-1
ISSN	1744-8387 ; 1478-9450
ISSN (online)	1744-8387
ISSN	1478-9450
DOI	10.1586/14789450.2014.901892
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Article ; Online: Mass spectrometric immunoassay raises doubt for the existence of parathyroid hormone fragment 7-84.

Singh, Ravinder J / Hines, Jolaine M / Lopez, Mary F / Krastins, Bryan / Hoofnagle, Andrew N

Clinical chemistry

2015 Volume 61, Issue 3, Page(s) 558–560

MeSH term(s)	Amino Acid Sequence ; Humans ; Immunoassay/methods ; Parathyroid Hormone/blood ; Parathyroid Hormone/chemistry ; Parathyroid Hormone/isolation & purification ; Peptide Fragments/blood ; Peptide Fragments/chemistry ; Peptide Fragments/isolation & purification ; Tandem Mass Spectrometry/methods
Chemical Substances	Parathyroid Hormone ; Peptide Fragments ; parathyroid hormone (7-84)
Language	English
Publishing date	2015-01-16
Publishing country	England
Document type	Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80102-1
ISSN	1530-8561 ; 0009-9147
ISSN (online)	1530-8561
ISSN	0009-9147
DOI	10.1373/clinchem.2014.235440
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Article ; Online: LC-MS candidate reference methods for the harmonisation of parathyroid hormone (PTH) measurement: a review of recent developments and future considerations.

Couchman, Lewis / Taylor, David R / Krastins, Bryan / Lopez, Mary F / Moniz, Cajetan F

Clinical chemistry and laboratory medicine

2014 Volume 52, Issue 9, Page(s) 1251–1263

Abstract: The analysis of intact parathyroid hormone (PTH) (PTH1-84) is useful in the diagnosis of hyper- and hypocalcaemia, hyperparathyroidism, and in the prevention of bone mineral disorders in renal patients. The analysis is complicated by the presence of PTH ... ...

Abstract	The analysis of intact parathyroid hormone (PTH) (PTH1-84) is useful in the diagnosis of hyper- and hypocalcaemia, hyperparathyroidism, and in the prevention of bone mineral disorders in renal patients. The analysis is complicated by the presence of PTH fragments, which may accumulate in renal failure and cross-react in immunoassays, including the most recent third-generation immunoassays. Large variability exists between different commercially available assays. This article reviews the current literature on PTH testing, with emphasis on the use of mass spectrometry-based methods, and considers the important sources of variation which still need to be addressed prior to the development of much needed candidate reference methods for PTH analysis. Recently, mass spectrometric methods have been developed for the quantitation of PTH1-84 using surrogate tryptic peptides, but even these methods are subject to significant interferences due to the presence of newly observed modified PTH species, such as oxidised and phosphorylated PTH variants, which can accumulate in patient samples. Further work, including: 1) the use of high-resolution mass spectrometry; and 2) the analysis of PTH without prior protease digestion, is required before these approaches can be considered as reference methods against which other methods should be harmonised.
MeSH term(s)	Blood Chemical Analysis/methods ; Blood Chemical Analysis/trends ; Chromatography, Liquid/methods ; Genetic Variation ; Humans ; Immunoassay/methods ; Mass Spectrometry/methods ; Oxidation-Reduction ; Parathyroid Hormone/blood ; Parathyroid Hormone/chemistry ; Parathyroid Hormone/genetics ; Peptide Fragments/blood ; Peptide Fragments/chemistry ; Peptide Fragments/genetics ; Phosphorylation ; Proteolysis ; Reference Values
Chemical Substances	PTH protein, human ; Parathyroid Hormone ; Peptide Fragments
Language	English
Publishing date	2014-09
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	1418007-8
ISSN	1437-4331 ; 1434-6621 ; 1437-8523
ISSN (online)	1437-4331
ISSN	1434-6621 ; 1437-8523
DOI	10.1515/cclm-2014-0150
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Article: Analytical Differences in Intraoperative Parathyroid Hormone Assays.

Leung, Edward K Y / Lee, Christine C / Angelos, Peter / Kaplan, Edwin L / Grogan, Raymon H / Sarracino, David A / Krastins, Bryan / Lopez, Mary F / Karrison, Theodore / Yeo, Kiang-Teck J

The journal of applied laboratory medicine

2019 Volume 3, Issue 5, Page(s) 788–798

Abstract: Background: We compared the rates of intraoperative parathyroid hormone (PTH) decline using the Siemens Immulite: Methods: Serial blood samples from 95 patients undergoing parathyroidectomy were collected and measured using the 2 immunoassays. ... ...

Abstract	Background: We compared the rates of intraoperative parathyroid hormone (PTH) decline using the Siemens Immulite Methods: Serial blood samples from 95 patients undergoing parathyroidectomy were collected and measured using the 2 immunoassays. Specimens from the first 15 patients were measured simultaneously in the OR and CCL and used for the TAT study. In addition to 2 baseline samples, specimens were collected at 5, 10, and 15 min (for some patients, >15 min) after parathyroidectomy. Results: In the TAT study, a significant difference was observed (OR median 20 min vs CCL median 27 min; Conclusions: There was a slightly longer TAT in the CCL compared with running the assay directly within the OR (median difference of approximately 7 min). For a majority of the patients, both methods showed equivalent rates of PTH decline; however, for approximately 20% of the patients, there was a slower rate of PTH decline using the Roche assay.
MeSH term(s)	Clinical Chemistry Tests/methods ; Female ; Humans ; Hyperparathyroidism, Primary/blood ; Hyperparathyroidism, Primary/surgery ; Immunoassay/methods ; Intraoperative Period ; Male ; Middle Aged ; Parathyroid Hormone/blood ; Parathyroidectomy/methods
Chemical Substances	Parathyroid Hormone
Language	English
Publishing date	2019-02-01
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2576-9456
ISSN	2576-9456
DOI	10.1373/jalm.2018.026815
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Article ; Online: The EBNA3 family of Epstein-Barr virus nuclear proteins associates with the USP46/USP12 deubiquitination complexes to regulate lymphoblastoid cell line growth.

Ohashi, Makoto / Holthaus, Amy M / Calderwood, Michael A / Lai, Chiou-Yan / Krastins, Bryan / Sarracino, David / Johannsen, Eric

PLoS pathogens

2015 Volume 11, Issue 4, Page(s) e1004822

Abstract: The Epstein-Barr virus (EBV) nuclear proteins EBNA3A, EBNA3B, and EBNA3C interact with the cell DNA binding protein RBPJ and regulate cell and viral genes. Repression of the CDKN2A tumor suppressor gene products p16(INK4A) and p14(ARF) by EBNA3A and ... ...

Abstract	The Epstein-Barr virus (EBV) nuclear proteins EBNA3A, EBNA3B, and EBNA3C interact with the cell DNA binding protein RBPJ and regulate cell and viral genes. Repression of the CDKN2A tumor suppressor gene products p16(INK4A) and p14(ARF) by EBNA3A and EBNA3C is critical for EBV mediated transformation of resting B lymphocytes into immortalized lymphoblastoid cell lines (LCLs). To define the composition of endogenous EBNA3 protein complexes, we generated lymphoblastoid cell lines (LCLs) expressing flag-HA tagged EBNA3A, EBNA3B, or EBNA3C and used tandem affinity purification to isolate each EBNA3 complex. Our results demonstrated that each EBNA3 protein forms a distinct complex with RBPJ. Mass-spectrometry revealed that the EBNA3A and EBNA3B complexes also contained the deubquitylation complex consisting of WDR48, WDR20, and USP46 (or its paralog USP12) and that EBNA3C complexes contained WDR48. Immunoprecipitation confirmed that EBNA3A, EBNA3B, and EBNA3C association with the USP46 complex. Using chromatin immunoprecipitation, we demonstrate that WDR48 and USP46 are recruited to the p14(ARF) promoter in an EBNA3C dependent manner. Mapping studies were consistent with WDR48 being the primary mediator of EBNA3 association with the DUB complex. By ChIP assay, WDR48 was recruited to the p14(ARF) promoter in an EBNA3C dependent manner. Importantly, WDR48 associated with EBNA3A and EBNA3C domains that are critical for LCL growth, suggesting a role for USP46/USP12 in EBV induced growth transformation.
MeSH term(s)	Blotting, Western ; Cell Line ; Cell Proliferation ; Cell Transformation, Viral/genetics ; Chromatin Immunoprecipitation ; Endopeptidases/genetics ; Endopeptidases/metabolism ; Epstein-Barr Virus Nuclear Antigens/metabolism ; Gene Expression Regulation, Viral/genetics ; Herpesvirus 4, Human/genetics ; Herpesvirus 4, Human/metabolism ; Humans ; Immunoprecipitation ; Mass Spectrometry ; Ubiquitin Thiolesterase/genetics ; Ubiquitin Thiolesterase/metabolism
Chemical Substances	EBNA-3A antigen ; EBNA-3B antigen ; EBNA-3C, epstein-barr virus ; Epstein-Barr Virus Nuclear Antigens ; USP12 protein, human ; Endopeptidases (EC 3.4.-) ; ubiquitin-specific peptidase 46, human (EC 3.4.-) ; Ubiquitin Thiolesterase (EC 3.4.19.12)
Language	English
Publishing date	2015-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7366
ISSN (online)	1553-7374
ISSN	1553-7366
DOI	10.1371/journal.ppat.1004822
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Article ; Online: Proteins other than the locus of enterocyte effacement-encoded proteins contribute to Escherichia coli O157:H7 adherence to bovine rectoanal junction stratified squamous epithelial cells.

Kudva, Indira T / Griffin, Robert W / Krastins, Bryan / Sarracino, David A / Calderwood, Stephen B / John, Manohar

BMC microbiology

2012 Volume 12, Page(s) 103

Abstract: Background: In this study, we present evidence that proteins encoded by the Locus of Enterocyte Effacement (LEE), considered critical for Escherichia coli O157 (O157) adherence to follicle-associated epithelial (FAE) cells at the bovine recto-anal ... ...

Abstract	Background: In this study, we present evidence that proteins encoded by the Locus of Enterocyte Effacement (LEE), considered critical for Escherichia coli O157 (O157) adherence to follicle-associated epithelial (FAE) cells at the bovine recto-anal junction (RAJ), do not appear to contribute to O157 adherence to squamous epithelial (RSE) cells also constituting this primary site of O157 colonization in cattle. Results: Antisera targeting intimin-γ, the primary O157 adhesin, and other essential LEE proteins failed to block O157 adherence to RSE cells, when this pathogen was grown in DMEM, a culture medium that enhances expression of LEE proteins. In addition, RSE adherence of a DMEM-grown-O157 mutant lacking the intimin protein was comparable to that seen with its wild-type parent O157 strain grown in the same media. These adherence patterns were in complete contrast to that observed with HEp-2 cells (the adherence to which is mediated by intimin-γ), assayed under same conditions. This suggested that proteins other than intimin-γ that contribute to adherence to RSE cells are expressed by this pathogen during growth in DMEM. To identify such proteins, we defined the proteome of DMEM-grown-O157 (DMEM-proteome). GeLC-MS/MS revealed that the O157 DMEM-proteome comprised 684 proteins including several components of the cattle and human O157 immunome, orthologs of adhesins, hypothetical secreted and outer membrane proteins, in addition to the known virulence and LEE proteins. Bioinformatics-based analysis of the components of the O157 DMEM proteome revealed several new O157-specific proteins with adhesin potential. Conclusion: Proteins other than LEE and intimin-γ proteins are involved in O157 adherence to RSE cells at the bovine RAJ. Such proteins, with adhesin potential, are expressed by this human pathogen during growth in DMEM. Ongoing experiments to evaluate their role in RSE adherence should provide both valuable insights into the O157-RSE interactions and new targets for more efficacious anti-adhesion O157 vaccines.
MeSH term(s)	Adhesins, Bacterial/isolation & purification ; Adhesins, Bacterial/metabolism ; Animals ; Bacterial Adhesion ; Cattle ; Cell Line ; Electrophoresis ; Epithelial Cells/microbiology ; Escherichia coli O157/chemistry ; Escherichia coli O157/pathogenicity ; Escherichia coli Proteins/isolation & purification ; Escherichia coli Proteins/metabolism ; Humans ; Proteome/analysis ; Tandem Mass Spectrometry
Chemical Substances	Adhesins, Bacterial ; Escherichia coli Proteins ; Proteome
Language	English
Publishing date	2012-06-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1471-2180
ISSN (online)	1471-2180
DOI	10.1186/1471-2180-12-103
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Article ; Online: Global profiling and relative quantifiction of histones, histone PTMs and histone-modifying enzymes in mesenchymal stem cells using LC-MS/MS and a novel PerfectPair mass difference algorithm.

Lopez, Mary F / Sarracino, David / Athanas, Michael / Krastins, Bryan / Prakash, Amol / Garces, Alejandra

Cell cycle (Georgetown, Tex.)

2011 Volume 10, Issue 24, Page(s) 4181–4183

MeSH term(s)	Aging/physiology ; Algorithms ; Chromatography, Liquid/methods ; Computational Biology/methods ; DNA Methylation/genetics ; Enzymes/genetics ; Epigenesis, Genetic ; Histones/genetics ; Humans ; Mesenchymal Stem Cells/chemistry ; Protein Processing, Post-Translational/genetics ; Tandem Mass Spectrometry/methods
Chemical Substances	Enzymes ; H2AX protein, human ; Histones
Language	English
Publishing date	2011-12-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2146183-1
ISSN	1551-4005 ; 1538-4101 ; 1554-8627
ISSN (online)	1551-4005
ISSN	1538-4101 ; 1554-8627
DOI	10.4161/cc.10.24.18836
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Article: Opposing activities of oncogenic MIR17HG and tumor suppressive MIR100HG clusters and their gene targets regulate replicative senescence in human adult stem cells.

Lopez, Mary F / Niu, Ping / Wang, Lu / Vogelsang, Maryann / Gaur, Meenakshi / Krastins, Bryan / Zhao, Yueqiang / Smagul, Aibek / Nussupbekova, Aliya / Akanov, Aikan A / Jordan, I King / Lunyak, Victoria V

NPJ aging and mechanisms of disease

2017 Volume 3, Page(s) 7

Abstract: Growing evidence suggests that many diseases of aging, including diseases associated with robust changes and adipose deports, may be caused by resident adult stem cell exhaustion due to the process called cellular senescence. Understanding how microRNA ... ...

Abstract	Growing evidence suggests that many diseases of aging, including diseases associated with robust changes and adipose deports, may be caused by resident adult stem cell exhaustion due to the process called cellular senescence. Understanding how microRNA pathways can regulate cellular senescence is crucial for the development of novel diagnostic and therapeutic strategies to combat these pathologies. Herein, using integrated transcriptomic and semi-quantitative proteomic analysis, we provide a system level view of the regulation of human adipose-derived stem cell senescence by a subset of mature microRNAs (termed senescence-associated-microRNAs) produced by biogenesis of oncogenic
Language	English
Publishing date	2017-04-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2836493-4
ISSN	2056-3973
ISSN	2056-3973
DOI	10.1038/s41514-017-0006-y
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Article ; Online: Delineating monoclonal antibody specificity by mass spectrometry.

Korbakis, Dimitrios / Prassas, Ioannis / Brinc, Davor / Batruch, Ihor / Krastins, Bryan / Lopez, Mary F / Diamandis, Eleftherios P

Journal of proteomics

2014 Volume 114, Page(s) 115–124

Abstract: Generation of monoclonal antibody (mAb) libraries against antigens in complex matrices can prove a valuable analytical tool. However, delineating the specificity of newly generated antibodies is the limiting step of the procedure. Here, we propose a ... ...

Abstract	Generation of monoclonal antibody (mAb) libraries against antigens in complex matrices can prove a valuable analytical tool. However, delineating the specificity of newly generated antibodies is the limiting step of the procedure. Here, we propose a strategy for mAb production by injecting mice with complex biological fluid and mAb characterization by coupling immunoaffinity techniques with Mass spectrometry (immuno-MS). Mice were immunized against fractionated seminal plasma and mAbs were produced. Different immuno-MS protocols based on four types of solid support (i.e. polystyrene microtiter plates, NHS-activated agarose beads, tosyl-activated magnetic beads and MSIA™ pipette tips) were established. A well-characterized mouse monoclonal anti-KLK3 (PSA) Ab was used as a model to evaluate each protocol's robustness and reproducibility and to establish a set of criteria which would allow antigen characterization of newly developed Abs. Three of the newly generated Abs were analyzed using our optimized protocols. Analysis revealed that all assay configurations used were capable of antibody characterization. Furthermore, low-abundance antigens (e.g. ribonuclease T2) could be identified as efficiently as the high-abundance ones. Our data suggest that complex biological samples can be used for the production of mAbs, which will facilitate the analysis of their proteome, while the established immuno-MS protocols can offer efficient mAb characterization. Biological significance: The inoculation of animals with complex biological samples is aiming at the discovery of novel disease biomarkers, present in the biological specimens, as well as the production of rare reagents that will facilitate the ultra-sensitive analysis of the biomolecules' native form. In the present study, we initially propose a general workflow concerning the handling of biological samples, as well as the monoclonal antibody production. Furthermore, we established protocols for the reliable and reproducible identification of antibody specificity using various immuno-affinity purification techniques coupled to mass spectrometry. Our data suggest that processed biological fluids can be used for the production of mAbs targeting proteins of varying abundance, and that various immuno-MS protocols can offer great capabilities for the mAb characterization procedure.
MeSH term(s)	Adipokines ; Animals ; Antibodies, Monoclonal/chemistry ; Antibodies, Monoclonal/immunology ; Antibody Specificity ; Carrier Proteins/chemistry ; Carrier Proteins/immunology ; Chromatography, Liquid ; Epitopes/immunology ; Female ; Glycoproteins/chemistry ; Glycoproteins/immunology ; Male ; Mass Spectrometry/methods ; Mice ; Mice, Inbred BALB C ; Prostate-Specific Antigen/immunology ; Tandem Mass Spectrometry
Chemical Substances	AZGP1 protein, human ; Adipokines ; Antibodies, Monoclonal ; Carrier Proteins ; Epitopes ; Glycoproteins ; Prostate-Specific Antigen (EC 3.4.21.77)
Language	English
Publishing date	2014-11-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2014.11.004
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Article ; Online: Hybrid data acquisition and processing strategies with increased throughput and selectivity: pSMART analysis for global qualitative and quantitative analysis.

Prakash, Amol / Peterman, Scott / Ahmad, Shadab / Sarracino, David / Frewen, Barbara / Vogelsang, Maryann / Byram, Gregory / Krastins, Bryan / Vadali, Gouri / Lopez, Mary

Journal of proteome research

2014 Volume 13, Issue 12, Page(s) 5415–5430

Abstract: Data-dependent acquisition (DDA) and data-independent acquisition strategies (DIA) have both resulted in improved understanding of proteomics samples. Both strategies have advantages and disadvantages that are well-published, where DDA is typically ... ...

Abstract	Data-dependent acquisition (DDA) and data-independent acquisition strategies (DIA) have both resulted in improved understanding of proteomics samples. Both strategies have advantages and disadvantages that are well-published, where DDA is typically applied for deep discovery and DIA may be used to create sample records. In this paper, we present a hybrid data acquisition and processing strategy (pSMART) that combines the strengths of both techniques and provides significant benefits for qualitative and quantitative peptide analysis. The performance of pSMART is compared to published DIA strategies in an experiment that allows the objective assessment of DIA performance with respect to interrogation of previously acquired MS data. The results of this experiment demonstrate that pSMART creates fewer decoy hits than a standard DIA strategy. Moreover, we show that pSMART is more selective, sensitive, and reproducible than either standard DIA or DDA strategies alone.
MeSH term(s)	Amino Acid Sequence ; Automatic Data Processing/methods ; Chromatography, Liquid/methods ; Mass Spectrometry/methods ; Molecular Sequence Data ; Peptides/analysis ; Peptides/metabolism ; Proteome/analysis ; Proteome/metabolism ; Proteomics/methods ; Reproducibility of Results ; Software
Chemical Substances	Peptides ; Proteome
Language	English
Publishing date	2014-12-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/pr5003017
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