scholarly journals Yeast-Based Genetic Interaction Analysis of Human Kinome

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1156
Author(s):  
Jae-Hong Kim ◽  
Yeojin Seo ◽  
Myungjin Jo ◽  
Hyejin Jeon ◽  
Won-Ha Lee ◽  
...  
Keyword(s):  
Cell Death ◽  
Intracellular Signaling ◽  
Drug Targets ◽  
Large Scale ◽  
Genetic Interaction ◽  
Interaction Analysis ◽  
Inflammatory Diseases ◽  
Molecular Transport ◽  
Multiple Drug ◽  
Network Analyses

Kinases are critical intracellular signaling proteins. To better understand kinase-mediated signal transduction, a large-scale human–yeast genetic interaction screen was performed. Among 597 human kinase genes tested, 28 displayed strong toxicity in yeast when overexpressed. En masse transformation of these toxic kinase genes into 4653 homozygous diploid yeast deletion mutants followed by barcode sequencing identified yeast toxicity modifiers and thus their human orthologs. Subsequent network analyses and functional grouping revealed that the 28 kinases and their 676 interaction partners (corresponding to a total of 969 genetic interactions) are enriched in cell death and survival (34%), small-molecule biochemistry (18%) and molecular transport (11%), among others. In the subnetwork analyses, a few kinases were commonly associated with glioma, cell migration and cell death/survival. Our analysis enabled the creation of a first draft of the kinase genetic interactome network and identified multiple drug targets for inflammatory diseases and cancer, in which deregulated kinase signaling plays a pathogenic role.

scholarly journals Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways

2020 ◽  
Vol 295 (50) ◽  
pp. 16906-16919
Author(s):  
Jae-Hong Kim ◽  
Yeojin Seo ◽  
Myungjin Jo ◽  
Hyejin Jeon ◽  
Young-Seop Kim ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Cell Migration ◽  
Intracellular Signaling ◽  
Mammalian Cells ◽  
Drug Targets ◽  
Large Scale ◽  
Genetic Interaction ◽  
Genetic Interactions ◽  
Signal Transduction Pathways ◽  
Global View

Kinases are critical components of intracellular signaling pathways and have been extensively investigated with regard to their roles in cancer. p21-activated kinase-1 (PAK1) is a serine/threonine kinase that has been previously implicated in numerous biological processes, such as cell migration, cell cycle progression, cell motility, invasion, and angiogenesis, in glioma and other cancers. However, the signaling network linked to PAK1 is not fully defined. We previously reported a large-scale yeast genetic interaction screen using toxicity as a readout to identify candidate PAK1 genetic interactions. En masse transformation of the PAK1 gene into 4,653 homozygous diploid Saccharomyces cerevisiae yeast deletion mutants identified ∼400 candidates that suppressed yeast toxicity. Here we selected 19 candidate PAK1 genetic interactions that had human orthologs and were expressed in glioma for further examination in mammalian cells, brain slice cultures, and orthotopic glioma models. RNAi and pharmacological inhibition of potential PAK1 interactors confirmed that DPP4, KIF11, mTOR, PKM2, SGPP1, TTK, and YWHAE regulate PAK1-induced cell migration and revealed the importance of genes related to the mitotic spindle, proteolysis, autophagy, and metabolism in PAK1-mediated glioma cell migration, drug resistance, and proliferation. AKT1 was further identified as a downstream mediator of the PAK1-TTK genetic interaction. Taken together, these data provide a global view of PAK1-mediated signal transduction pathways and point to potential new drug targets for glioma therapy.

scholarly journals Phosphoproteomic analysis sheds light on intracellular signaling cascades triggered by Formyl-Peptide Receptor 2

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Fabio Cattaneo ◽  
Rosita Russo ◽  
Martina Castaldo ◽  
Angela Chambery ◽  
Cristiana Zollo ◽  
...  
Keyword(s):  
Intracellular Signaling ◽  
Drug Targets ◽  
Large Scale ◽  
Cellular Proliferation ◽  
Biological Effects ◽  
Formyl Peptide Receptor ◽  
Ros Generation ◽  
Systematic Analysis ◽  
Phosphorylated Proteins ◽  
Formyl Peptide

AbstractFormyl peptide receptors (FPRs) belong to the family of seven transmembrane Gi-protein coupled receptors (GPCR). FPR2 is considered the most promiscuous member of this family since it recognizes a wide variety of ligands. It plays a crucial role in several physio-pathological processes and different studies highlighted the correlation between its expression and the higher propensity to invasion and metastasis of some cancers. FPR2 stimulation by its synthetic agonist WKYMVm triggers multiple phosphorylations of intracellular signaling molecules, such as ERKs, PKC, PKB, p38MAPK, PI3K, PLC, and of non-signaling proteins, such as p47phox and p67phox which are involved in NADPH oxidase-dependent ROS generation. Biological effects of FPR2 stimulation include intracellular Ca2+ mobilization, cellular proliferation and migration, and wound healing. A systematic analysis of the phosphoproteome in FPR2-stimulated cells has not been yet reported. Herein, we describe a large-scale phosphoproteomic study in WKYMVm-stimulated CaLu-6 cells. By using high resolution MS/MS we identified 290 differentially phosphorylated proteins and 53 unique phosphopeptides mapping on 40 proteins. Phosphorylations on five selected phospho-proteins were further validated by western blotting, confirming their dependence on FPR2 stimulation. Interconnection between some of the signalling readout identified was also evaluated. Furthermore, we show that FPR2 stimulation with two anti-inflammatory agonists induces the phosphorylation of selected differentially phosphorylated proteins, suggesting their role in the resolution of inflammation. These data provide a promising resource for further studies on new signaling networks triggered by FPR2 and on novel molecular drug targets for human diseases.

p38 Pathway Kinases as Anti-inflammatory Drug Targets

2007 ◽  
Vol 86 (9) ◽  
pp. 800-811 ◽  
Author(s):  
J.F. Schindler ◽  
J.B. Monahan ◽  
W.G. Smith
Keyword(s):  
Protein Kinase ◽  
Nuclear Export ◽  
Intracellular Signaling ◽  
Drug Targets ◽  
Inflammatory Diseases ◽  
Direct Proof ◽  
P38 Map Kinase ◽  
Mitogen Activated Protein Kinase ◽  
Selective Inhibitors ◽  
Mitogen Activated Protein

Mitogen-activated protein kinases (MAPK) are intracellular signaling molecules involved in cytokine synthesis. Several classes of mammalian MAPK have been identified, including extracellular signal-regulated kinase, c-jun N-terminal kinase, and p38 MAP kinase. p38α is a key MAPK involved in tumor necrosis factor α and other cytokine production, as well as enzyme induction (cyclooxygenase-2, inducible nitric oxide synthase, and matrix metalloproteinases) and adhesion molecule expression. An understanding of the broad biologic and pathophysiological roles of p38 MAPK family members has grown significantly over the past decade, as has the complexity of the signaling network leading to their activation. Downstream substrates of MAPK include other kinases ( e.g., mitogen-activated protein-kinase-activated protein kinase 2) and factors that regulate transcription, nuclear export, and mRNA stability and translation. The high-resolution crystal structure of p38α has led to the design of selective inhibitors that have good pharmacological activity. Despite the strong rationale for MAPK inhibitors in human disease, direct proof of concept in the clinic has yet to be demonstrated, with most compounds demonstrating dose-limiting adverse effects. The role of MAPK in inflammation makes them attractive targets for new therapies, and efforts are continuing to identify newer, more selective inhibitors for inflammatory diseases.

scholarly journals Expanding the drug discovery space with predicted metabolite–target interactions

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Andrea Nuzzo ◽  
Somdutta Saha ◽  
Ellen Berg ◽  
Channa Jayawickreme ◽  
Joel Tocker ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Drug Targets ◽  
Large Scale ◽  
Association Studies ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Host Protein ◽  
Multiple Drug ◽  
Genome Wide Association Studies

AbstractMetabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite–host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potential metabolite–target interactions using the Inflammatory Bowel Disease (IBD) cohort dataset of the Human Microbiome Project 2 (HMP2). Using a consensus of multiple machine learning methods, we ranked metabolites based on importance to IBD, followed by virtual ligand-based screening to identify possible human targets and adding evidence from compound assay, differential gene expression, pathway enrichment, and genome-wide association studies. We confirmed known metabolite–target pairs such as nicotinic acid–GPR109a or linoleoyl ethanolamide–GPR119 and inferred interactions of interest including oleanolic acid–GABRG2 and alpha-CEHC–THRB. Eleven metabolites were tested for bioactivity in vitro using human primary cell-types. By expanding the universe of possible microbial metabolite–host protein interactions, we provide multiple drug targets for potential immune-therapies.

Soil/Tire Interaction Analysis Using FEM and FVM

2005 ◽  
Vol 33 (1) ◽  
pp. 38-62 ◽  
Author(s):  
S. Oida ◽  
E. Seta ◽  
H. Heguri ◽  
K. Kato
Keyword(s):  
Large Scale ◽  
Interaction Analysis ◽  
Yield Criterion ◽  
Surrounding Medium ◽  
Flow Analysis ◽  
Measurement Data ◽  
Traction Force ◽  
Elastoplastic Material ◽  
The Road ◽  
Soil Flow

Abstract Vehicles, such as an agricultural tractor, construction vehicle, mobile machinery, and 4-wheel drive vehicle, are often operated on unpaved ground. In many cases, the ground is deformable; therefore, the deformation should be taken into consideration in order to assess the off-the-road performance of a tire. Recent progress in computational mechanics enabled us to simulate the large scale coupling problem, in which the deformation of tire structure and of surrounding medium can be interactively considered. Using this technology, hydroplaning phenomena and tire traction on snow have been predicted. In this paper, the simulation methodology of tire/soil coupling problems is developed for pneumatic tires of arbitrary tread patterns. The Finite Element Method (FEM) and the Finite Volume Method (FVM) are used for structural and for soil-flow analysis, respectively. The soil is modeled as an elastoplastic material with a specified yield criterion and a nonlinear elasticity. The material constants are referred to measurement data, so that the cone penetration resistance and the shear resistance are represented. Finally, the traction force of the tire in a cultivated field is predicted, and a good correlation with experiments is obtained.

scholarly journals Actin-Related Protein 6 (Arp6) Influences Double-Strand Break Repair in Yeast

2021 ◽  
Vol 1 (2) ◽  
pp. 225-238
Author(s):  
Mohsen Hooshyar ◽  
Daniel Burnside ◽  
Maryam Hajikarimlou ◽  
Katayoun Omidi ◽  
Alexander Jesso ◽  
...  
Keyword(s):  
Dna Damage ◽  
Chromatin Remodeling ◽  
Genetic Interaction ◽  
Interaction Analysis ◽  
Strand Break ◽  
Dna Double Strand Breaks ◽  
Dsb Repair ◽  
Dna Damaging Agents ◽  
Repair Efficiency ◽  
Chromosomal Breaks

DNA double-strand breaks (DSBs) are the most deleterious form of DNA damage and are repaired through non-homologous end-joining (NHEJ) or homologous recombination (HR). Repair initiation, regulation and communication with signaling pathways require several histone-modifying and chromatin-remodeling complexes. In budding yeast, this involves three primary complexes: INO80-C, which is primarily associated with HR, SWR1-C, which promotes NHEJ, and RSC-C, which is involved in both pathways as well as the general DNA damage response. Here we identify ARP6 as a factor involved in DSB repair through an RSC-C-related pathway. The loss of ARP6 significantly reduces the NHEJ repair efficiency of linearized plasmids with cohesive ends, impairs the repair of chromosomal breaks, and sensitizes cells to DNA-damaging agents. Genetic interaction analysis indicates that ARP6, MRE11 and RSC-C function within the same pathway, and the overexpression of ARP6 rescues rsc2∆ and mre11∆ sensitivity to DNA-damaging agents. Double mutants of ARP6, and members of the INO80 and SWR1 complexes, cause a significant reduction in repair efficiency, suggesting that ARP6 functions independently of SWR1-C and INO80-C. These findings support a novel role for ARP6 in DSB repair that is independent of the SWR1 chromatin remodeling complex, through an apparent RSC-C and MRE11-associated DNA repair pathway.

Sign in / Sign up

Export Citation Format

Share Document