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Kedia K, Harris R, Ekroos K, Moser KW, DeBord D, Tiberi P, Goracci L, Zhang NR, Wang W, Spellman DS, Bateman K. Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species. J Am Soc Mass Spectrom 2023; 34:2176-2186. [PMID: 37703523 DOI: 10.1021/jasms.3c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Lipids are structurally diverse molecules that play a pivotal role in a plethora of biological processes. However, deciphering the biological roles of the specific lipids is challenging due to the existence of numerous isomers. This high chemical complexity of the lipidome is one of the major challenges in lipidomics research, as the traditional liquid chromatography-mass spectrometry (LC-MS) based approaches are often not powerful enough to resolve these isomeric and isobaric nuances within complex samples. Thus, lipids are uniquely suited to the benefits provided by multidimensional liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) analysis. However, many forms of lipid isomerism, including double-bond positional isomers and regioisomers, are structurally similar such that their collision cross section (CCS) differences are unresolvable via conventional IM approaches. Here we evaluate the performance of a high resolution ion mobility (HRIM) system based on structures for lossless ion manipulation (SLIM) technology interfaced to a high resolution quadrupole time-of-flight (QTOF) analyzer to address the noted lipidomic isomerism challenge. SLIM implements the traveling wave ion mobility technique along an ∼13 m ion path, providing longer path lengths to enable improved separation of isomeric features. We demonstrate the power of HRIM-MS to dissect isomeric PC standards differing only in double bond (DB) and stereospecific number (SN) positions. The partial separation of protonated DB isomers is significantly enhanced when they are analyzed as metal adducts. For sodium adducts, we achieve close to baseline separation of three different PC 18:1/18:1 isomers with different cis-double bond locations. Similarly, PC 18:1/18:1 (cis-9) can be resolved from the corresponding PC 18:1/18:1 (trans-9) form. The separation capacity is further enhanced when using silver ion doping, enabling the baseline separation of regioisomers that cannot be resolved when measured as sodium adducts. The sensitivity and reproducibility of the approach were assessed, and the performance for more complex mixtures was benchmarked by identifying PC isomers in total brain and liver lipid extracts.
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Affiliation(s)
- Komal Kedia
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rachel Harris
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Kim Ekroos
- Lipidomics Consulting Ltd, Irisviksvägen 31D, 02230 Esbo, Finland
| | - Kelly W Moser
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Daniel DeBord
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Paolo Tiberi
- Molecular Discovery Ltd., Centennial Park, Borehamwood, Hertfordshire WD6 3FG United Kingdom
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | | | - Weixun Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Kevin Bateman
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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Argemi J, Kedia K, Gritsenko MA, Clemente-Sanchez A, Asghar A, Herranz JM, Liu ZX, Atkinson SR, Smith RD, Norden-Krichmar TM, Day LZ, Stolz A, Tayek JA, Bataller R, Morgan TR, Jacobs JM. Integrated Transcriptomic and Proteomic Analysis Identifies Plasma Biomarkers of Hepatocellular Failure in Alcohol-Associated Hepatitis. Am J Pathol 2022; 192:1658-1669. [PMID: 36243044 PMCID: PMC9765311 DOI: 10.1016/j.ajpath.2022.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/08/2022] [Accepted: 08/31/2022] [Indexed: 11/07/2022]
Abstract
Alcohol-associated hepatitis (AH) is a form of liver failure with high short-term mortality. Recent studies have shown that defective function of hepatocyte nuclear factor 4 alpha (HNF4a) and systemic inflammation are major disease drivers of AH. Plasma biomarkers of hepatocyte function could be useful for diagnostic and prognostic purposes. Herein, an integrative analysis of hepatic RNA sequencing and liquid chromatography-tandem mass spectrometry was performed to identify plasma protein signatures for patients with mild and severe AH. Alcohol-related liver disease cirrhosis, nonalcoholic fatty liver disease, and healthy subjects were used as comparator groups. Levels of identified proteins primarily involved in hepatocellular function were decreased in patients with AH, which included hepatokines, clotting factors, complement cascade components, and hepatocyte growth activators. A protein signature of AH disease severity was identified, including thrombin, hepatocyte growth factor α, clusterin, human serum factor H-related protein, and kallistatin, which exhibited large abundance shifts between severe and nonsevere AH. The combination of thrombin and hepatocyte growth factor α discriminated between severe and nonsevere AH with high sensitivity and specificity. These findings were correlated with the liver expression of genes encoding secreted proteins in a similar cohort, finding a highly consistent plasma protein signature reflecting HNF4A and HNF1A functions. This unbiased proteomic-transcriptome analysis identified plasma protein signatures and pathways associated with disease severity, reflecting HNF4A/1A activity useful for diagnostic assessment in AH.
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Affiliation(s)
- Josepmaria Argemi
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania; Hepatology Program, Centro de Investigación Médica Aplicada, Liver Unit, Clinica Universidad de Navarra, Instituto de Investigacion de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Komal Kedia
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co, Inc., West Point, Pennsylvania
| | - Marina A Gritsenko
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Ana Clemente-Sanchez
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania; Biomedical Research Networking Center in Hepatic and Digestive Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Aliya Asghar
- Gasteroenterology Service, VA Long Beach Healthcare System, Long Beach, California
| | - Jose M Herranz
- Hepatology Program, Centro de Investigación Médica Aplicada, Liver Unit, Clinica Universidad de Navarra, Instituto de Investigacion de Navarra, Universidad de Navarra, Pamplona, Spain
| | - Zhang-Xu Liu
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Stephen R Atkinson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Trina M Norden-Krichmar
- Department of Epidemiology, School of Medicine, University of California, Irvine, Irvine, California
| | - Le Z Day
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Andrew Stolz
- Division of Gastrointestinal and Liver Disease, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - John A Tayek
- Harbor-University of California, Los Angeles Medical Center, Torrance, California
| | - Ramon Bataller
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Timothy R Morgan
- Gasteroenterology Service, VA Long Beach Healthcare System, Long Beach, California.
| | - Jon M Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington.
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Jarsberg LG, Kedia K, Wendler J, Wright AT, Piehowski PD, Gritsenko MA, Shi T, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Keane J, Jacobs JM, Nahid P. Nutritional markers and proteome in patients undergoing treatment for pulmonary tuberculosis differ by geographic region. PLoS One 2021; 16:e0250586. [PMID: 33951066 PMCID: PMC8099102 DOI: 10.1371/journal.pone.0250586] [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] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/09/2021] [Indexed: 11/24/2022] Open
Abstract
Introduction Contemporary phase 2 TB disease treatment clinical trials have found that microbiologic treatment responses differ between African versus non-African regions, the reasons for which remain unclear. Understanding host and disease phenotypes that may vary by region is important for optimizing curative treatments. Methods We characterized clinical features and the serum proteome of phase 2 TB clinical trial participants undergoing treatment for smear positive, culture-confirmed TB, comparing host serum protein expression in clinical trial participants enrolled in African and Non-African regions. Serum samples were collected from 289 participants enrolled in the Centers for Disease Control and Prevention TBTC Study 29 (NCT00694629) at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Results After a peptide level proteome analysis utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS) and subsequent statistical analysis, a total of 183 core proteins demonstrated significant differences at both baseline and at week 8 timepoints between participants enrolled from African and non-African regions. The majority of the differentially expressed proteins were upregulated in participants from the African region, and included acute phase proteins, mediators of inflammation, as well as coagulation and complement pathways. Downregulated proteins in the African population were primarily linked to nutritional status and lipid metabolism pathways. Conclusions We have identified differentially expressed nutrition and lipid pathway proteins by geographic region in TB patients undergoing treatment for pulmonary tuberculosis, which appear to be associated with differential treatment responses. Future TB clinical trials should collect expanded measures of nutritional status and further evaluate the relationship between nutrition and microbiologic treatment response.
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Affiliation(s)
- Leah G. Jarsberg
- Division of Pulmonary and Critical Care Medicine and UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, California, United States of America
| | - Komal Kedia
- Department of Pharmacokinetics, Pharmacodynamics & Drug Metabolism (PPDM) Merck & Co., Inc., West Point, Pennsylvania, United States of America
| | - Jason Wendler
- Seattle Children’s Hospital, Seattle, Washington, United States of America
| | - Aaron T. Wright
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington, United States of America
| | - Paul D. Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Marina A. Gritsenko
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David M. Lewinsohn
- Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, Oregon, United States of America
| | - George B. Sigal
- Meso Scale Diagnostics, Rockville, Maryland, United States of America
| | - Marc H. Weiner
- University of Texas Health Science Center at San Antonio and the South Texas VAMC, San Antonio, Texas, United States of America
| | - Richard D. Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Joseph Keane
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, Dublin, Ireland
| | - Jon M. Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- * E-mail:
| | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine and UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, California, United States of America
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Nagarajan A, Zhou M, Nguyen AY, Liberton M, Kedia K, Shi T, Piehowski P, Shukla A, Fillmore TL, Nicora C, Smith RD, Koppenaal DW, Jacobs JM, Pakrasi HB. Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973. Biomolecules 2019; 9:biom9080374. [PMID: 31426316 PMCID: PMC6722726 DOI: 10.3390/biom9080374] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 11/16/2022] Open
Abstract
Phycobilisomes (PBSs) are large (3-5 megadalton) pigment-protein complexes in cyanobacteria that associate with thylakoid membranes and harvest light primarily for photosystem II. PBSs consist of highly ordered assemblies of pigmented phycobiliproteins (PBPs) and linker proteins that can account for up to half of the soluble protein in cells. Cyanobacteria adjust to changing environmental conditions by modulating PBS size and number. In response to nutrient depletion such as nitrogen (N) deprivation, PBSs are degraded in an extensive, tightly controlled, and reversible process. In Synechococcus elongatus UTEX 2973, a fast-growing cyanobacterium with a doubling time of two hours, the process of PBS degradation is very rapid, with 80% of PBSs per cell degraded in six hours under optimal light and CO2 conditions. Proteomic analysis during PBS degradation and re-synthesis revealed multiple proteoforms of PBPs with partially degraded phycocyanobilin (PCB) pigments. NblA, a small proteolysis adaptor essential for PBS degradation, was characterized and validated with targeted mass spectrometry. NblA levels rose from essentially 0 to 25,000 copies per cell within 30 min of N depletion, and correlated with the rate of decrease in phycocyanin (PC). Implications of this correlation on the overall mechanism of PBS degradation during N deprivation are discussed.
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Affiliation(s)
- Aparna Nagarajan
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Mowei Zhou
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Amelia Y Nguyen
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Michelle Liberton
- Department of Biology, Washington University, St. Louis, MO 63130, USA
| | - Komal Kedia
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Paul Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Anil Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Carrie Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David W Koppenaal
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
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Nagy G, Kedia K, Attah IK, Garimella SVB, Ibrahim YM, Petyuk VA, Smith RD. Separation of β-Amyloid Tryptic Peptide Species with Isomerized and Racemized l-Aspartic Residues with Ion Mobility in Structures for Lossless Ion Manipulations. Anal Chem 2019; 91:4374-4380. [PMID: 30816701 PMCID: PMC6596305 DOI: 10.1021/acs.analchem.8b04696] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Accumulation of β-amyloid (Aβ) is one of the hallmarks of Alzheimer's disease. The deposition of β-amyloid plaques is likely to start years in advance of manifestation of clinical symptoms, although the exact timing is unknown. Over the years, Aβ peptides undergo both post-translational modification and stereoisomerization. Analysis of the resulting stereoisomers is particularly challenging because of their identical elemental composition and similar physicochemical properties. Herein, we have utilized our recently developed structures for lossless ion manipulations ion mobility-mass spectrometry platform (SLIM IM-MS), in conjunction with serpentine ultralong path with extended routing (SUPER), to baseline resolve four distinct sets of Aβ17-28 tryptic peptide epimers on a rapid (∼1 s) time scale. We discovered that sodium adduct ions, [M + H + Na]2+, allowed baseline SLIM SUPER IM resolution for all Aβ epimer sets assessed, while such baseline separations were unachievable for their [M + 2H]2+ doubly protonated ions.
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Affiliation(s)
- Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Komal Kedia
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Isaac K. Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Sandilya V. B. Garimella
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vladislav A. Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Kedia K, Wendler JP, Baker ES, Burnum-Johnson KE, Jarsberg LG, Stratton KG, Wright AT, Piehowski PD, Gritsenko MA, Lewinsohn DM, Sigal GB, Weiner MH, Smith RD, Jacobs JM, Nahid P. Application of multiplexed ion mobility spectrometry towards the identification of host protein signatures of treatment effect in pulmonary tuberculosis. Tuberculosis (Edinb) 2018; 112:52-61. [PMID: 30205969 PMCID: PMC6181582 DOI: 10.1016/j.tube.2018.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 03/25/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 01/22/2023]
Abstract
Rationale: The monitoring of TB treatments in clinical practice and clinical trials relies on traditional sputum-based culture status indicators at specific time points. Accurate, predictive, blood-based protein markers would provide a simpler and more informative view of patient health and response to treatment. Objective: We utilized sensitive, high throughput multiplexed ion mobility-mass spectrometry (IM-MS) to characterize the serum proteome of TB patients at the start of and at 8 weeks of rifamycin-based treatment. We sought to identify treatment specific signatures within patients as well as correlate the proteome signatures to various clinical markers of treatment efficacy. Methods: Serum samples were collected from 289 subjects enrolled in CDC TB Trials Consortium Study 29 at time of enrollment and at the end of the intensive phase (after 40 doses of TB treatment). Serum proteins were immunoaffinity-depleted of high abundant components, digested to peptides and analyzed for data acquisition utilizing a unique liquid chromatography IM-MS platform (LC-IM-MS). Linear mixed models were utilized to identify serum protein changes in the host response to antibiotic treatment as well as correlations with culture status end points. Results: A total of 10,137 peptides corresponding to 872 proteins were identified, quantified, and used for statistical analysis across the longitudinal patient cohort. In response to TB treatment, 244 proteins were significantly altered. Pathway/network comparisons helped visualize the interconnected proteins, identifying up regulated (lipid transport, coagulation cascade, endopeptidase activity) and down regulated (acute phase) processes and pathways in addition to other cross regulated networks (inflammation, cell adhesion, extracellular matrix). Detection of possible lung injury serum proteins such as HPSE, significantly downregulated upon treatment. Analyses of microbiologic data over time identified a core set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2) which change in response to treatment and also strongly correlate with culture status. A similar set of proteins at baseline were found to be predictive of week 6 and 8 culture status. Conclusion: A comprehensive host serum protein dataset reflective of TB treatment effect is defined. A repeating set of serum proteins (TTHY, AFAM, CRP, RET4, SAA1, PGRP2, among others) were found to change significantly in response to treatment, to strongly correlate with culture status, and at baseline to be predictive of future culture conversion. If validated in cohorts with long term follow-up to capture failure and relapse of TB, these protein markers could be developed for monitoring of treatment in clinical trials and in patient care.
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Affiliation(s)
- Komal Kedia
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jason P Wendler
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Erin S Baker
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Leah G Jarsberg
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kelly G Stratton
- Computational and Statistical Analysis Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aaron T Wright
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David M Lewinsohn
- Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA
| | | | - Marc H Weiner
- University of Texas Health Science Center at San Antonio and the South Texas VAMC, San Antonio, TX, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jon M Jacobs
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Payam Nahid
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
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Kedia K, Smith SF, Wright AH, Barnes JM, Tolley HD, Esplin MS, Graves SW. Global "omics" evaluation of human placental responses to preeclamptic conditions. Am J Obstet Gynecol 2016; 215:238.e1-238.e20. [PMID: 26970495 DOI: 10.1016/j.ajog.2016.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/29/2016] [Accepted: 03/02/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Preeclampsia (PE) is a leading cause of maternal death. Its cause is still debated but there is general agreement that the placenta plays a central role. Perhaps the most commonly proposed contributors to PE include placental hypoxia, oxidative stress, and increased proinflammatory cytokines. How the placenta responds to these abnormalities has been considered but not as part of a comprehensive analysis of low-molecular-weight biomolecules and their responses to these accepted PE conditions. OBJECTIVE Using a peptidomic approach, we sought to identify a set of molecules exhibiting differential expression in consequence of provocative agents/chemical mediators of PE applied to healthy human placental tissue. STUDY DESIGN Known PE conditions were imposed on normal placental tissue from 13 uncomplicated pregnancies and changes in the low-molecular-weight peptidome were evaluated. A t test was used to identify potential markers for each imposed stress. These markers were then submitted to a least absolute shrinkage and selection operator multinomial logistic regression model to identify signatures specific to each stressor. Estimates of model performance on external data were obtained through internal validation. RESULTS A total of 146 markers were increased/decreased as a consequence of exposure to proposed mediators of PE. Of these 75 changed with hypoxia; 23 with hypoxia-reoxygenation/oxidative stress and 48 from exposure to tumor necrosis factor-α. These markers were chemically characterized using tandem mass spectrometry. Identification rates were: hypoxia, 34%; hypoxia-reoxygenation, 60%; and tumor necrosis factor-α, 50%. Least absolute shrinkage and selection operator modeling specified 16 markers that effectively distinguished all groups, ie, the 3 abnormal conditions and control. Bootstrap estimates of misclassification rates, multiclass area under the curve, and Brier score were 0.108, 0.944, and 0.160, respectively. CONCLUSION Using this approach we found previously unknown molecular changes in response to individual PE conditions that allowed development biomolecular signatures for exposure to each accepted pathogenic condition.
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Affiliation(s)
- C.D. Zippe
- Departments of Urology and Biostatistics, Andrology-Oncology Research Laboratory, Cleveland Clinic Foundation and Lutheran Hospital, Cleveland, Ohio
| | - A.W. Kedia
- Departments of Urology and Biostatistics, Andrology-Oncology Research Laboratory, Cleveland Clinic Foundation and Lutheran Hospital, Cleveland, Ohio
| | - K. Kedia
- Departments of Urology and Biostatistics, Andrology-Oncology Research Laboratory, Cleveland Clinic Foundation and Lutheran Hospital, Cleveland, Ohio
| | - D.R. Nelson
- Departments of Urology and Biostatistics, Andrology-Oncology Research Laboratory, Cleveland Clinic Foundation and Lutheran Hospital, Cleveland, Ohio
| | - A. Agarwal
- Departments of Urology and Biostatistics, Andrology-Oncology Research Laboratory, Cleveland Clinic Foundation and Lutheran Hospital, Cleveland, Ohio
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Abstract
OBJECTIVES To determine whether the response to the new oral medication, sildenafil citrate (Viagra), was influenced by the presence or absence of the neurovascular bundles, as recent reports on its success did not specify the efficacy of the drug in patients with erectile dysfunction after radical prostatectomy. METHODS Baseline and follow-up data from 28 healthy patients presenting with erectile dysfunction after radical prostatectomy were obtained. Patients receiving any neoadjuvant/adjuvant hormones or adjuvant radiation therapy were excluded. Patients reported what their erectile status was before surgery, before sildenafil therapy, and after using a minimum of four doses of sildenafil. Both the patients and their spouses were interviewed using the Cleveland Clinic post-prostatectomy questionnaire, which includes questions about response to therapy, duration of intercourse, spousal satisfaction, side effects, and related topics. The patients were compared on the basis of the type of surgical procedure they had undergone-nerve sparing or non-nerve sparing. A positive response to sildenafil was defined as erection sufficient for vaginal penetration. RESULTS Of the 15 patients who had bilateral nerve-sparing procedures, 12 (80%) had a positive response to sildenafil, with a mean duration of 6.92 minutes of vaginal intercourse. These 12 patients also reported a spousal satisfaction rate of 80%. All 12 of the responders had a positive response within the first three doses, and 10 of the 12 responded with the first or second dose. None of the 3 patients who had undergone a unilateral nerve-sparing procedure responded, nor did any of the 10 patients who had undergone a non-nerve-sparing procedure. The two most common side effects of the drug were transient headaches (39%) and abnormal color vision (11%). No patients discontinued the medication because of side effects. CONCLUSIONS Successful treatment of erectile dysfunction in a patient after prostatectomy with sildenafil citrate may depend on the presence of bilateral neurovascular bundles. No patient who had undergone a non-nerve-sparing procedure responded. Whether patients who undergo unilateral nerve-sparing procedures will respond to sildenafil is still unclear because of the small number of patients in our study. These findings should encourage urologists to continue to perform and perfect the nerve-sparing approach. The ability to restore potency with an oral medication after radical prostatectomy will impact our discussion with the patient on the surgical morbidity of radical prostatectomy.
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Affiliation(s)
- C D Zippe
- Department of Urology, The Cleveland Clinic Foundation, Ohio 44195, USA
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Chung-Park M, Ricanati E, Lankerani M, Kedia K. Acquired Renal Cysts and Multiple Renal Cell and Urothelial Tumors. J Urol 1983. [DOI: 10.1016/s0022-5347(17)51329-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M. Chung-Park
- Departments of Pathology, Medicine and Urology, Case Western Reserve University, Cleveland, Ohio
| | - E. Ricanati
- Departments of Pathology, Medicine and Urology, Case Western Reserve University, Cleveland, Ohio
| | - M. Lankerani
- Departments of Pathology, Medicine and Urology, Case Western Reserve University, Cleveland, Ohio
| | - K. Kedia
- Departments of Pathology, Medicine and Urology, Case Western Reserve University, Cleveland, Ohio
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Abstract
This paper reports two cases of acquired renal cysts and multiple renal cell tumors in end-stage kidneys with a discussion of the pathogenesis of these lesions. The first patient had been on maintenance dialysis for approximately three years when he was found to have multiple renal cysts and renal cell tumors. He subsequently developed multifocal urothelial carcinomas of the lower urinary tract. The second patient had progressive renal failure due to hypertensive vascular disease when he underwent left nephrectomy because of multiple renal cysts and renal cell carcinoma. He later developed terminal renal failure and was maintained on chronic dialysis. He expired three years later. At autopsy, the right kidney also demonstrated multiple cysts and renal cell tumors.
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Abstract
The courses of 6 patients with various forms or ureteral injury and disruption herein illustrate the value and worth of percutaneous nephrostomy drainage and study. The nature and degree of injury are ascertained, and sepsis and obstruction are managed without formal anesthesia or surgical intervention, leading to ultimate repair in a planned and orderly fashion.
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15
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Abstract
Infertility in a patient on pharmacological agents with sympatholoytic activity was found to be caused by ejaculatory failure owing to absent contraction of the seminal vesicle, ampulla and ductus deferens, rather than the previously accepted reason of retrograde ejaculation. These findings suggest that pharmacological agents producing alpha-adrenergic blockage may produce temporary interference with ejaculation, suggesting investigation of their use as reversible male contraceptives.
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16
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Abstract
A case of adult teratoma of the testis in a 19-year-old white man is presented, The tumor metastasized to the retroperitoneal lymph nodes and the metastases were also well differentiated, benign-appearing tissues. This case suggests that even the benign-appearing components of these tumors have malignant potential. Because these tumors are malignant, they should be treated by radical orchiectomy and radical retroperitoneal dissection.
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17
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Fraley EE, Markland C, Kedia K. Treatment of testicular tumors. Minn Med 1973; 56:593-6. [PMID: 4351874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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18
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Markland C, Kedia K, Fraley EE. Inadequate orchiectomy for patients with testicular tumors. JAMA 1973; 224:1025-6. [PMID: 4739918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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