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  1. Article ; Online: Exploratory study reveals far reaching systemic and cellular effects of verapamil treatment in subjects with type 1 diabetes

    Guanlan Xu / Tiffany D. Grimes / Truman B. Grayson / Junqin Chen / Lance A. Thielen / Hubert M. Tse / Peng Li / Matt Kanke / Tai-Tu Lin / Athena A. Schepmoes / Adam C. Swensen / Vladislav A. Petyuk / Fernando Ovalle / Praveen Sethupathy / Wei-Jun Qian / Anath Shalev

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Volume 9

    Abstract: Oral verapamil lowers inflammatory markers and daily insulin needs in subjects with type 1 diabetes and helps preserve pancreatic beta cell function for at least two years. In this context, serum chromogranin A provides a promising therapy marker. ...

    Abstract Oral verapamil lowers inflammatory markers and daily insulin needs in subjects with type 1 diabetes and helps preserve pancreatic beta cell function for at least two years. In this context, serum chromogranin A provides a promising therapy marker.
    Keywords Science ; Q
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer

    Adam C. Swensen / Jingtang He / Alexander C. Fang / Yinyin Ye / Carrie D. Nicora / Tujin Shi / Alvin Y. Liu / Tara K. Sigdel / Minnie M. Sarwal / Wei-Jun Qian

    Frontiers in Medicine, Vol

    2021  Volume 8

    Abstract: Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for ... ...

    Abstract Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.
    Keywords LC-MS/MS ; urine proteome ; proteomics ; urinary biomarkers ; prostate cancer ; kidney disease ; Medicine (General) ; R5-920
    Subject code 610
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Corrigendum

    Tara K. Sigdel / Paul D. Piehowski / Sudeshna Roy / Juliane Liberto / Joshua R. Hansen / Adam C. Swensen / Rui Zhao / Ying Zhu / Priyanka Rashmi / Andrew Schroeder / Izabella Damm / Swastika Sur / Jinghui Luo / Yingbao Yang / Wei-Jun Qian / Minnie M. Sarwal

    Frontiers in Medicine, Vol

    Near-Single-Cell Proteomics Profiling of the Proximal Tubular and Glomerulus of the Normal Human Kidney

    2021  Volume 7

    Keywords glomerulus ; mass spectrometry ; single cell analysis ; proteomics ; kidney ; Medicine (General) ; R5-920
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Insulin receptor-mediated signaling regulates pluripotency markers and lineage differentiation

    Manoj K. Gupta / Dario F. De Jesus / Sevim Kahraman / Ivan A. Valdez / Farnaz Shamsi / Lian Yi / Adam C. Swensen / Yu-Hua Tseng / Wei-Jun Qian / Rohit N. Kulkarni

    Molecular Metabolism, Vol 18, Iss , Pp 153-

    2018  Volume 163

    Abstract: Objectives: Insulin receptor (IR)-mediated signaling is involved in the regulation of pluripotent stem cells; however, its direct effects on regulating the maintenance of pluripotency and lineage development are not fully understood. The main objective ... ...

    Abstract Objectives: Insulin receptor (IR)-mediated signaling is involved in the regulation of pluripotent stem cells; however, its direct effects on regulating the maintenance of pluripotency and lineage development are not fully understood. The main objective of this study is to understand the role of IR signaling in pluripotency and lineage development. Methods: To explore the role of IR signaling, we generated IR knock-out (IRKO) mouse induced pluripotent stem cells (miPSCs) from E14.5 mouse embryonic fibroblasts (MEFs) of global IRKO mice using a cocktail of four reprogramming factors: Oct4, Sox2, Klf4, cMyc. We performed pluripotency characterization and directed the differentiation of control and IRKO iPSCs into neural progenitors (ectoderm), adipocyte progenitors (mesoderm), and pancreatic beta-like cells (endoderm). We mechanistically confirmed these findings via phosphoproteomics analyses of control and IRKO iPSCs. Results: Interestingly, expression of pluripotency markers including Klf4, Lin28a, Tbx3, and cMyc were upregulated, while abundance of Oct4 and Nanog were enhanced by 4-fold and 3-fold, respectively, in IRKO iPSCs. Analyses of signaling pathways demonstrated downregulation of phospho-STAT3, p-mTor and p-Erk and an increase in the total mTor and Erk proteins in IRKO iPSCs in the basal unstimulated state. Stimulation with leukemia inhibitory factor (LIF) showed a ∼33% decrease of phospho-ERK in IRKO iPSCs. On the contrary, Erk phosphorylation was increased during in vitro spontaneous differentiation of iPSCs lacking IRs. Lineage-specific directed differentiation of the iPSCs revealed that cells lacking IR showed enhanced expression of neuronal lineage markers (Pax6, Tubb3, Ascl1 and Oligo2) while exhibiting a decrease in adipocyte (Fas, Acc, Pparγ, Fabp4, C/ebpα, and Fsp27) and pancreatic beta cell markers (Ngn3, Isl1, and Sox9). Further molecular characterization by phosphoproteomics confirmed the novel IR-mediated regulation of the global pluripotency network including several key proteins involved ...
    Keywords Internal medicine ; RC31-1245
    Subject code 571
    Language English
    Publishing date 2018-12-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Near-Single-Cell Proteomics Profiling of the Proximal Tubular and Glomerulus of the Normal Human Kidney

    Tara K. Sigdel / Paul D. Piehowski / Sudeshna Roy / Juliane Liberto / Joshua R. Hansen / Adam C. Swensen / Rui Zhao / Ying Zhu / Priyanka Rashmi / Andrew Schroeder / Izabella Damm / Swastika Sur / Jinghui Luo / Yingbao Yang / Wei-Jun Qian / Minnie M. Sarwal / The Kidney Precision Medicine Project (KPMP) Consortium

    Frontiers in Medicine, Vol

    2020  Volume 7

    Abstract: Molecular assessments at the single cell level can accelerate biological research by providing detailed assessments of cellular organization and tissue heterogeneity in both disease and health. The human kidney has complex multi-cellular states with ... ...

    Abstract Molecular assessments at the single cell level can accelerate biological research by providing detailed assessments of cellular organization and tissue heterogeneity in both disease and health. The human kidney has complex multi-cellular states with varying functionality, much of which can now be completely harnessed with recent technological advances in tissue proteomics at a near single-cell level. We discuss the foundational steps in the first application of this mass spectrometry (MS) based proteomics method for analysis of sub-sections of the normal human kidney, as part of the Kidney Precision Medicine Project (KPMP). Using ~30–40 laser captured micro-dissected kidney cells, we identified more than 2,500 human proteins, with specificity to the proximal tubular (PT; n = 25 proteins) and glomerular (Glom; n = 67 proteins) regions of the kidney and their unique metabolic functions. This pilot study provides the roadmap for application of our near-single-cell proteomics workflow for analysis of other renal micro-compartments, on a larger scale, to unravel perturbations of renal sub-cellular function in the normal kidney as well as different etiologies of acute and chronic kidney disease.
    Keywords glomerulus ; mass spectrometry ; single cell analysis ; proteomics ; kidney ; Medicine (General) ; R5-920
    Subject code 616
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Multi-Site Observational Study to Assess Biomarkers for Susceptibility or Resilience to Chronic Pain

    Giovanni Berardi / Laura Frey-Law / Kathleen A. Sluka / Emine O. Bayman / Christopher S. Coffey / Dixie Ecklund / Carol G. T. Vance / Dana L. Dailey / John Burns / Asokumar Buvanendran / Robert J. McCarthy / Joshua Jacobs / Xiaohong Joe Zhou / Richard Wixson / Tessa Balach / Chad M. Brummett / Daniel Clauw / Douglas Colquhoun / Steven E. Harte /
    Richard E. Harris / David A. Williams / Andrew C. Chang / Jennifer Waljee / Kathleen M. Fisch / Kristen Jepsen / Louise C. Laurent / Michael Olivier / Carl D. Langefeld / Timothy D. Howard / Oliver Fiehn / Jon M. Jacobs / Panshak Dakup / Wei-Jun Qian / Adam C. Swensen / Anna Lokshin / Martin Lindquist / Brian S. Caffo / Ciprian Crainiceanu / Scott Zeger / Ari Kahn / Tor Wager / Margaret Taub / James Ford

    Frontiers in Medicine, Vol

    The Acute to Chronic Pain Signatures (A2CPS) Study Protocol

    2022  Volume 9

    Abstract: Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors ... ...

    Abstract Chronic pain has become a global health problem contributing to years lived with disability and reduced quality of life. Advances in the clinical management of chronic pain have been limited due to incomplete understanding of the multiple risk factors and molecular mechanisms that contribute to the development of chronic pain. The Acute to Chronic Pain Signatures (A2CPS) Program aims to characterize the predictive nature of biomarkers (brain imaging, high-throughput molecular screening techniques, or “omics,” quantitative sensory testing, patient-reported outcome assessments and functional assessments) to identify individuals who will develop chronic pain following surgical intervention. The A2CPS is a multisite observational study investigating biomarkers and collective biosignatures (a combination of several individual biomarkers) that predict susceptibility or resilience to the development of chronic pain following knee arthroplasty and thoracic surgery. This manuscript provides an overview of data collection methods and procedures designed to standardize data collection across multiple clinical sites and institutions. Pain-related biomarkers are evaluated before surgery and up to 3 months after surgery for use as predictors of patient reported outcomes 6 months after surgery. The dataset from this prospective observational study will be available for researchers internal and external to the A2CPS Consortium to advance understanding of the transition from acute to chronic postsurgical pain.
    Keywords postsurgical pain ; thoracic surgery ; pain ; biomarker ; risk factors ; protocol ; Medicine (General) ; R5-920
    Subject code 616
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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