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Cleuren A, Molema G. Organotypic heterogeneity in microvascular endothelial cell responses in sepsis-a molecular treasure trove and pharmacological Gordian knot. Front Med (Lausanne) 2023; 10:1252021. [PMID: 38020105 PMCID: PMC10665520 DOI: 10.3389/fmed.2023.1252021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
In the last decades, it has become evident that endothelial cells (ECs) in the microvasculature play an important role in the pathophysiology of sepsis-associated multiple organ dysfunction syndrome (MODS). Studies on how ECs orchestrate leukocyte recruitment, control microvascular integrity and permeability, and regulate the haemostatic balance have provided a wealth of knowledge and potential molecular targets that could be considered for pharmacological intervention in sepsis. Yet, this information has not been translated into effective treatments. As MODS affects specific vascular beds, (organotypic) endothelial heterogeneity may be an important contributing factor to this lack of success. On the other hand, given the involvement of ECs in sepsis, this heterogeneity could also be leveraged for therapeutic gain to target specific sites of the vasculature given its full accessibility to drugs. In this review, we describe current knowledge that defines heterogeneity of organ-specific microvascular ECs at the molecular level and elaborate on studies that have reported EC responses across organ systems in sepsis patients and animal models of sepsis. We discuss hypothesis-driven, single-molecule studies that have formed the basis of our understanding of endothelial cell engagement in sepsis pathophysiology, and include recent studies employing high-throughput technologies. The latter deliver comprehensive data sets to describe molecular signatures for organotypic ECs that could lead to new hypotheses and form the foundation for rational pharmacological intervention and biomarker panel development. Particularly results from single cell RNA sequencing and spatial transcriptomics studies are eagerly awaited as they are expected to unveil the full spatiotemporal signature of EC responses to sepsis. With increasing awareness of the existence of distinct sepsis subphenotypes, and the need to develop new drug regimen and companion diagnostics, a better understanding of the molecular pathways exploited by ECs in sepsis pathophysiology will be a cornerstone to halt the detrimental processes that lead to MODS.
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Affiliation(s)
- Audrey Cleuren
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Grietje Molema
- Department Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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2
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Wang XY, Xu YM, Lau ATY. Proteogenomics in Cancer: Then and Now. J Proteome Res 2023; 22:3103-3122. [PMID: 37725793 DOI: 10.1021/acs.jproteome.3c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
For years, the paths of sequencing technologies and mass spectrometry have occurred in isolation, with each developing its own unique culture and expertise. These two technologies are crucial for inspecting complementary aspects of the molecular phenotype across the central dogma. Integrative multiomics strives to bridge the analysis gap among different fields to complete more comprehensive mechanisms of life events and diseases. Proteogenomics is one integrated multiomics field. Here in this review, we mainly summarize and discuss three aspects: workflow of proteogenomics, proteogenomics applications in cancer research, and the SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis of proteogenomics in cancer research. In conclusion, proteogenomics has a promising future as it clarifies the functional consequences of many unannotated genomic abnormalities or noncanonical variants and identifies driver genes and novel therapeutic targets across cancers, which would substantially accelerate the development of precision oncology.
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Affiliation(s)
- Xiu-Yun Wang
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
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3
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Jones AB, Schanel TL, Rigsby MR, Griguer CE, McFarland BC, Anderson JC, Willey CD, Hjelmeland AB. Tumor Treating Fields Alter the Kinomic Landscape in Glioblastoma Revealing Therapeutic Vulnerabilities. Cells 2023; 12:2171. [PMID: 37681903 PMCID: PMC10486683 DOI: 10.3390/cells12172171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
Treatment for the deadly brain tumor glioblastoma (GBM) has been improved through the non-invasive addition of alternating electric fields, called tumor treating fields (TTFields). Improving both progression-free and overall survival, TTFields are currently approved for treatment of recurrent GBMs as a monotherapy and in the adjuvant setting alongside TMZ for newly diagnosed GBMs. These TTFields are known to inhibit mitosis, but the full molecular impact of TTFields remains undetermined. Therefore, we sought to understand the ability of TTFields to disrupt the growth patterns of and induce kinomic landscape shifts in TMZ-sensitive and -resistant GBM cells. We determined that TTFields significantly decreased the growth of TMZ-sensitive and -resistant cells. Kinomic profiling predicted kinases that were induced or repressed by TTFields, suggesting possible therapy-specific vulnerabilities. Serving as a potential pro-survival mechanism for TTFields, kinomics predicted the increased activity of platelet-derived growth-factor receptor alpha (PDGFRα). We demonstrated that the addition of the PDGFR inhibitor, crenolanib, to TTFields further reduced cell growth in comparison to either treatment alone. Collectively, our data suggest the efficacy of TTFields in vitro and identify common signaling responses to TTFields in TMZ-sensitive and -resistant populations, which may support more personalized medicine approaches.
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Affiliation(s)
- Amber B. Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (A.B.J.); (M.R.R.); (B.C.M.)
| | - Taylor L. Schanel
- Department of Radiation Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (T.L.S.); (J.C.A.)
| | - Mikayla R. Rigsby
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (A.B.J.); (M.R.R.); (B.C.M.)
| | - Corinne E. Griguer
- Department of Radiation Oncology, University of Iowa, Iowa City, IA 52242, USA;
| | - Braden C. McFarland
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (A.B.J.); (M.R.R.); (B.C.M.)
| | - Joshua C. Anderson
- Department of Radiation Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (T.L.S.); (J.C.A.)
| | - Christopher D. Willey
- Department of Radiation Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (T.L.S.); (J.C.A.)
| | - Anita B. Hjelmeland
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA; (A.B.J.); (M.R.R.); (B.C.M.)
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4
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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
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5
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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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6
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DePasquale EAK, Alganem K, Bentea E, Nawreen N, McGuire JL, Tomar T, Naji F, Hilhorst R, Meller J, McCullumsmith RE. KRSA: An R package and R Shiny web application for an end-to-end upstream kinase analysis of kinome array data. PLoS One 2021; 16:e0260440. [PMID: 34919543 PMCID: PMC8682895 DOI: 10.1371/journal.pone.0260440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/09/2021] [Indexed: 12/22/2022] Open
Abstract
Phosphorylation by serine-threonine and tyrosine kinases is critical for determining protein function. Array-based platforms for measuring reporter peptide signal levels allow for differential phosphorylation analysis between conditions for distinct active kinases. Peptide array technologies like the PamStation12 from PamGene allow for generating high-throughput, multi-dimensional, and complex functional proteomics data. As the adoption rate of such technologies increases, there is an imperative need for software tools that streamline the process of analyzing such data. We present Kinome Random Sampling Analyzer (KRSA), an R package and R Shiny web-application for analyzing kinome array data to help users better understand the patterns of functional proteomics in complex biological systems. KRSA is an All-In-One tool that reads, formats, fits models, analyzes, and visualizes PamStation12 kinome data. While the underlying algorithm has been experimentally validated in previous publications, we demonstrate KRSA workflow on dorsolateral prefrontal cortex (DLPFC) in male (n = 3) and female (n = 3) subjects to identify differential phosphorylation signatures and upstream kinase activity. Kinase activity differences between males and females were compared to a previously published kinome dataset (11 female and 7 male subjects) which showed similar global phosphorylation signals patterns.
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Affiliation(s)
- Erica A. K. DePasquale
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Boston, Massachusetts, United States of America
| | - Khaled Alganem
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, Ohio, United States of America
- * E-mail:
| | - Eduard Bentea
- Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nawshaba Nawreen
- Department of Neuroscience, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Jennifer L. McGuire
- Department of Neurosurgery, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Tushar Tomar
- PamGene International B.V., s’-Hertogenbosch, The Netherlands
| | - Faris Naji
- Tercen Data Analytics Ltd, Co Waterford, Ireland
| | - Riet Hilhorst
- PamGene International B.V., s’-Hertogenbosch, The Netherlands
| | - Jaroslaw Meller
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computing Systems, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Department of Informatics, Nicolaus Copernicus University, Torun, Poland
| | - Robert E. McCullumsmith
- Department of Neurosciences, University of Toledo College of Medicine, Toledo, Ohio, United States of America
- Neurosciences institute, ProMedica, Toledo, Ohio, United States of America
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Denomy C, Lazarou C, Hogan D, Facciuolo A, Scruten E, Kusalik A, Napper S. PIIKA 2.5: Enhanced quality control of peptide microarrays for kinome analysis. PLoS One 2021; 16:e0257232. [PMID: 34506584 PMCID: PMC8432839 DOI: 10.1371/journal.pone.0257232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/27/2021] [Indexed: 11/19/2022] Open
Abstract
Peptide microarrays consisting of defined phosphorylation target sites are an effective approach for high throughput analysis of cellular kinase (kinome) activity. Kinome peptide arrays are highly customizable and do not require species-specific reagents to measure kinase activity, making them amenable for kinome analysis in any species. Our group developed software, Platform for Integrated, Intelligent Kinome Analysis (PIIKA), to enable more effective extraction of meaningful biological information from kinome peptide array data. A subsequent version, PIIKA2, unveiled new statistical tools and data visualization options. Here we introduce PIIKA 2.5 to provide two essential quality control metrics and a new background correction technique to increase the accuracy and consistency of kinome results. The first metric alerts users to improper spot size and informs them of the need to perform manual resizing to enhance the quality of the raw intensity data. The second metric uses inter-array comparisons to identify outlier arrays that sometimes emerge as a consequence of technical issues. In addition, a new background correction method, background scaling, can sharply reduce spatial biases within a single array in comparison to background subtraction alone. Collectively, the modifications of PIIKA 2.5 enable identification and correction of technical issues inherent to the technology and better facilitate the extraction of meaningful biological information. We show that these metrics demonstrably enhance kinome analysis by identifying low quality data and reducing batch effects, and ultimately improve clustering of treatment groups and enhance reproducibility. The web-based and stand-alone versions of PIIKA 2.5 are freely accessible at via http://saphire.usask.ca.
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Affiliation(s)
- Connor Denomy
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Conor Lazarou
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Daniel Hogan
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization (VIDO), Saskatoon, Canada
| | - Erin Scruten
- Vaccine and Infectious Disease Organization (VIDO), Saskatoon, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
- * E-mail: (AK); (SN)
| | - Scott Napper
- Vaccine and Infectious Disease Organization (VIDO), Saskatoon, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Canada
- * E-mail: (AK); (SN)
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8
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Preynat-Seauve O, Nguyen EBV, Westermaier Y, Héritier M, Tardy S, Cambet Y, Feyeux M, Caillon A, Scapozza L, Krause KH. Novel Mechanism for an Old Drug: Phenazopyridine is a Kinase Inhibitor Affecting Autophagy and Cellular Differentiation. Front Pharmacol 2021; 12:664608. [PMID: 34421588 PMCID: PMC8371461 DOI: 10.3389/fphar.2021.664608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Phenazopyridine is a widely used drug against urinary tract pain. The compound has also been shown to enhance neural differentiation of pluripotent stem cells. However, its mechanism of action is not understood. Based on its chemical structure, we hypothesized that phenazopyridine could be a kinase inhibitor. Phenazopyridine was investigated in the following experimental systems: 1) activity of kinases in pluripotent stem cells; 2) binding to recombinant kinases, and 3) functional impact on pluripotent stem cells. Upon addition to pluripotent stem cells, phenazopyridine induced changes in kinase activities, particularly involving Mitogen-Activated Protein Kinases, Cyclin-Dependent Kinases, and AKT pathway kinases. To identify the primary targets of phenazopyridine, we screened its interactions with 401 human kinases. Dose-inhibition curves showed that three of these kinases interacted with phenazopyridine with sub-micromolar binding affinities: cyclin-G-associated kinase, and the two phosphatidylinositol kinases PI4KB and PIP4K2C, the latter being known for participating in pain induction. Docking revealed that phenazopyridine forms strong H-bonds with the hinge region of the ATP-binding pocket of these kinases. As previous studies suggested increased autophagy upon inhibition of the phosphatidyl-inositol/AKT pathway, we also investigated the impact of phenazopyridine on this pathway and found an upregulation. In conclusion, our study demonstrates for the first time that phenazopyridine is a kinase inhibitor, impacting notably phosphatidylinositol kinases involved in nociception.
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Affiliation(s)
- Olivier Preynat-Seauve
- Laboratory of Therapy and Stem Cells, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Evelyne Bao-Vi Nguyen
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Yvonne Westermaier
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Margaux Héritier
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Sébastien Tardy
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Yves Cambet
- READS Unit, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Maxime Feyeux
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aurélie Caillon
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Leonardo Scapozza
- Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Karl-Heinz Krause
- Laboratory of Therapy and Stem Cells, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Bekkar A, Nasrallah A, Guex N, Fajas L, Xenarios I, Lopez-Mejia IC. PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling. Bioinformatics 2021; 36:5117-5119. [PMID: 31922550 PMCID: PMC7755406 DOI: 10.1093/bioinformatics/btz858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 10/09/2019] [Accepted: 01/06/2020] [Indexed: 11/20/2022] Open
Abstract
Protein phosphorylation––catalyzed by protein kinases–is the most common post-translational modification. It increases the functional diversity of the proteome and influences various aspects of normal physiology and can be altered in disease states. High throughput profiling of kinases is becoming an essential experimental approach to investigate their activity and this can be achieved using technologies such as PamChip® arrays provided by PamGene for kinase activity measurement. Here, we present ‘pamgeneAnalyzeR’, an R package developed as an alternative to the manual steps necessary to extract the data from PamChip® peptide microarrays images in a reproducible and robust manner. The extracted data can be directly used for downstream analysis. Availability and implementation PamgeneAnalyzeR is implemented in R and can be obtained from https://github.com/amelbek/pamgeneAnalyzeR.
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Affiliation(s)
- Amel Bekkar
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland
| | - Anita Nasrallah
- Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Nicolas Guex
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne CH-1015, Switzerland
| | - Lluis Fajas
- Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Isabel C Lopez-Mejia
- Center for Integrative Genomics, University of Lausanne, Lausanne CH-1015, Switzerland
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10
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Ibrahim AN, Yamashita D, Anderson JC, Abdelrashid M, Alwakeal A, Estevez-Ordonez D, Komarova S, Markert JM, Goidts V, Willey CD, Nakano I. Intratumoral spatial heterogeneity of BTK kinomic activity dictates distinct therapeutic response within a single glioblastoma tumor. J Neurosurg 2019; 133:1683-1694. [PMID: 31628288 PMCID: PMC7961807 DOI: 10.3171/2019.7.jns191376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Despite significant recent efforts applied toward the development of efficacious therapies for glioblastoma (GBM) through exploration of GBM's genome and transcriptome, curative therapeutic strategies remain highly elusive. As such, novel and effective therapeutics are urgently required. In this study, the authors sought to explore the kinomic landscape of GBM from a previously underutilized approach (i.e., spatial heterogeneity), followed by validation of Bruton's tyrosine kinase (BTK) targeting according to this stepwise kinomic-based novel approach. METHODS Twelve GBM tumor samples were obtained and characterized histopathologically from 2 patients with GBM. PamStation peptide-array analysis of these tissues was performed to measure the kinomic activity of each sample. The Ivy GBM database was then utilized to determine the intratumoral spatial localization of BTK activity by investigating the expression of BTK-related transcription factors (TFs) within tumors. Genetic inhibition of BTK family members through lentiviral short hairpin RNA (shRNA) knockdown was performed to determine their function in the core-like and edge-like GBM neurosphere models. Finally, the small-molecule inhibitor of BTK, ONO/GS-4059, which is currently under clinical investigation in nonbrain cancers, was applied for pharmacological inhibition of regionally specified newly established GBM edge and core neurosphere models. RESULTS Kinomic investigation identified two major subclusters of GBM tissues from both patients exhibiting distinct profiles of kinase activity. Comparatively, in these spatially defined subgroups, BTK was the centric kinase differentially expressed. According to the Ivy GBM database, BTK-related TFs were highly expressed in the tumor core, but not in edge counterparts. Short hairpin RNA-mediated gene silencing of BTK in previously established edge- and core-like GBM neurospheres demonstrated increased apoptotic activity with predominance of the sub-G1 phase of core-like neurospheres compared to edge-like neurospheres. Lastly, pharmacological inhibition of BTK by ONO/GS-4059 resulted in growth inhibition of regionally derived GBM core cells and, to a lesser extent, their edge counterparts. CONCLUSIONS This study identifies significant heterogeneity in kinase activity both within and across distinct GBM tumors. The study findings indicate that BTK activity is elevated in the classically therapy-resistant GBM tumor core. Given these findings, targeting GBM's resistant core through BTK may potentially provide therapeutic benefit for patients with GBM.
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Affiliation(s)
- Ahmed N. Ibrahim
- Department of Neurosurgery, University of Alabama at Birmingham, Alabama
| | - Daisuke Yamashita
- Department of Neurosurgery, University of Alabama at Birmingham, Alabama
| | - Joshua C. Anderson
- Department of Radiation Oncology, University of Alabama at Birmingham, Alabama
| | - Moaaz Abdelrashid
- Department of Neurosurgery, University of Alabama at Birmingham, Alabama
| | - Amr Alwakeal
- Department of Neurosurgery, University of Alabama at Birmingham, Alabama
| | | | - Svetlana Komarova
- Department of Neurosurgery, University of Alabama at Birmingham, Alabama
| | - James M. Markert
- Department of Neurosurgery, University of Alabama at Birmingham, Alabama
| | - Violaine Goidts
- Brain Tumor Translational Targets, German Cancer Research Center, Heidelberg, Germany
| | | | - Ichiro Nakano
- Department of Neurosurgery, University of Alabama at Birmingham, Alabama
- Comprehensive Cancer Center, University of Alabama at Birmingham, Alabama
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Willey CD, Anderson JC, Trummell HQ, Naji F, de Wijn R, Yang ES, Bredel M, Thudi NK, Bonner JA. Differential escape mechanisms in cetuximab-resistant head and neck cancer cells. Biochem Biophys Res Commun 2019; 517:36-42. [PMID: 31311651 DOI: 10.1016/j.bbrc.2019.06.159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/13/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023]
Abstract
Acquired cetuximab resistance is a challenge for oncologists treating advanced head and neck carcinoma (HNC). While intrinsic cetuximab resistance mechanism in colorectal cancer is known, resistance in HNC is unclear. We established two different cetuximab resistant HNC cell lines by culturing epidermal growth factor (EGFR) expressing UM-SCC-1 and UM-SCC-6 cell lines in the presence of 5 μg/ml cetuximab. We then explored potential mechanisms of resistance. We found that the 2 cell lines developed resistance by different mechanisms. Specifically, we found that UM-SCC-1 resistant cells (UM-SCC-1R) showed enhanced EGF-induced downstream signals while UM-SCC-6 resistant cells (UM-SCC-6R) demonstrated EGF-independent signaling. Global kinase activity (kinomic) profiling revealed unique signaling differences in the two resistant cell lines. However, both of the resistant lines demonstrated increased phospho-serine 727 and total STAT3 expression compared to the parental lines. STAT3 knockdown promoted increased cytotoxicity both in the presence and absence of cetuximab in the resistant lines suggesting that STAT3 may be a common target in cetuximab resistance.
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Affiliation(s)
- Christopher D Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - Joshua C Anderson
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - Hoa Q Trummell
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - Faris Naji
- PamGene International, 's-Hertogenbosch, the Netherlands
| | - Rik de Wijn
- PamGene International, 's-Hertogenbosch, the Netherlands
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - Markus Bredel
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - Nanda K Thudi
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA
| | - James A Bonner
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35249, USA.
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