Other search tools

About this data

The publication data currently available has been vetted by Vanderbilt faculty, staff, administrators and trainees. The data itself is retrieved directly from NCBI's PubMed and is automatically updated on a weekly basis to ensure accuracy and completeness.

If you have any questions or comments, please contact us.

Results: 1 to 10 of 37

Publication Record


The Response of Acinetobacter baumannii to Zinc Starvation.
Nairn BL, Lonergan ZR, Wang J, Braymer JJ, Zhang Y, Calcutt MW, Lisher JP, Gilston BA, Chazin WJ, de Crécy-Lagard V, Giedroc DP, Skaar EP
(2016) Cell Host Microbe 19: 826-36
MeSH Terms: Acinetobacter Infections, Acinetobacter baumannii, Animals, Bacterial Proteins, Chlorides, GTP Phosphohydrolases, Gene Expression Regulation, Bacterial, Genes, Bacterial, Histidine, Histidine Ammonia-Lyase, Metallochaperones, Mice, Mice, Inbred C57BL, Mutation, Zinc, Zinc Compounds
Show Abstract · Added April 8, 2017
Zinc (Zn) is an essential metal that vertebrates sequester from pathogens to protect against infection. Investigating the opportunistic pathogen Acinetobacter baumannii's response to Zn starvation, we identified a putative Zn metallochaperone, ZigA, which binds Zn and is required for bacterial growth under Zn-limiting conditions and for disseminated infection in mice. ZigA is encoded adjacent to the histidine (His) utilization (Hut) system. The His ammonia-lyase HutH binds Zn very tightly only in the presence of high His and makes Zn bioavailable through His catabolism. The released Zn enables A. baumannii to combat host-imposed Zn starvation. These results demonstrate that A. baumannii employs several mechanisms to ensure bioavailability of Zn during infection, with ZigA functioning predominately during Zn starvation, but HutH operating in both Zn-deplete and -replete conditions to mobilize a labile His-Zn pool.
Copyright © 2016 Elsevier Inc. All rights reserved.
0 Communities
2 Members
0 Resources
16 MeSH Terms
Impact of NRAS mutations for patients with advanced melanoma treated with immune therapies.
Johnson DB, Lovly CM, Flavin M, Panageas KS, Ayers GD, Zhao Z, Iams WT, Colgan M, DeNoble S, Terry CR, Berry EG, Iafrate AJ, Sullivan RJ, Carvajal RD, Sosman JA
(2015) Cancer Immunol Res 3: 288-295
MeSH Terms: Antibodies, Monoclonal, Female, GTP Phosphohydrolases, Humans, Immunotherapy, Interleukin-2, Ipilimumab, Male, Melanoma, Membrane Proteins, Middle Aged, Mutation, Prognosis, Retrospective Studies
Show Abstract · Added September 10, 2020
Activating NRAS mutations are found in 15% to 20% of melanomas. Immune therapies have become a mainstay in advanced melanoma treatment. We sought to evaluate whether tumor genotype (e.g., NRAS mutations) correlates with benefit from immune therapy in melanoma. We identified 229 patients with melanoma treated with immune therapies [IL2, ipilimumab, or anti-programmed cell death-1/ligand-1 (PD-1/PD-L1)] at three centers and compared clinical outcomes following immune therapy for patients with or without NRAS mutations. Of the 229 patients with melanoma, 60 had NRAS mutation, 53 had BRAF mutation, and 116 had NRAS/BRAF wild type. The NRAS-mutant cohort had superior or a trend to superior outcomes compared with the other cohorts in terms of response to first-line immune therapy (28% vs. 16%, P = 0.04), response to any line of immune therapy (32% vs. 20%, P = 0.07), clinical benefit (response + stable disease lasting ≥ 24 weeks; 50% vs. 31%, P < 0.01), and progression-free survival (median, 4.1 vs. 2.9 months, P = 0.09). Benefit from anti-PD-1/PD-L1 was particularly marked in the NRAS cohort (clinical benefit rate 73% vs. 35%). In an independent group of patient samples, NRAS-mutant melanoma had higher PD-L1 expression (although not statistically significant) compared with other genotypes (8/12 vs. 9/20 samples with ≥ 1% expression; 6/12 vs. 6/20 samples with ≥ 5% expression), suggesting a potential mechanism for the clinical results. This retrospective study suggests that NRAS mutations in advanced melanoma correlate with increased benefit from immune-based therapies compared with other genetic subtypes. If confirmed by prospective studies, this may be explained in part by high rates of PD-L1 expression.
©2015 American Association for Cancer Research.
0 Communities
1 Members
0 Resources
MeSH Terms
Clinically relevant genes and regulatory pathways associated with NRASQ61 mutations in melanoma through an integrative genomics approach.
Jiang W, Jia P, Hutchinson KE, Johnson DB, Sosman JA, Zhao Z
(2015) Oncotarget 6: 2496-508
MeSH Terms: CpG Islands, DNA Methylation, GTP Phosphohydrolases, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Genomics, Humans, Melanoma, Membrane Proteins, MicroRNAs, Models, Genetic, Mutation, Signal Transduction, Skin Neoplasms
Show Abstract · Added February 13, 2015
Therapies such as BRAF inhibitors have become standard treatment for melanoma patients whose tumors harbor activating BRAFV600 mutations. However, analogous therapies for inhibiting NRAS mutant signaling have not yet been well established. In this study, we performed an integrative analysis of DNA methylation, gene expression, and microRNA expression data to identify potential regulatory pathways associated with the most common driver mutations in NRAS (Q61K/L/R) through comparison of NRASQ61-mutated melanomas with pan-negative melanomas. Surprisingly, we found dominant hypomethylation (98.03%) in NRASQ61-mutated melanomas. We identified 1,150 and 49 differentially expressed genes and microRNAs, respectively. Integrated functional analyses of alterations in all three data types revealed important signaling pathways associated with NRASQ61 mutations, such as the MAPK pathway, as well as other novel cellular processes, such as axon guidance. Further analysis of the relationship between DNA methylation and gene expression changes revealed 9 hypermethylated and down-regulated genes and 112 hypomethylated and up-regulated genes in NRASQ61 melanomas. Finally, we identified 52 downstream regulatory cascades of three hypomethylated and up-regulated genes (PDGFD, ZEB1, and THRB). Collectively, our observation of predominant gene hypomethylation in NRASQ61 melanomas and the identification of NRASQ61-linked pathways will be useful for the development of targeted therapies against melanomas harboring NRASQ61 mutations.
0 Communities
1 Members
0 Resources
15 MeSH Terms
Molecular pathways: targeting NRAS in melanoma and acute myelogenous leukemia.
Johnson DB, Smalley KS, Sosman JA
(2014) Clin Cancer Res 20: 4186-92
MeSH Terms: Antineoplastic Agents, GTP Phosphohydrolases, Humans, Leukemia, Myeloid, Acute, Melanoma, Membrane Proteins, Molecular Targeted Therapy, Prognosis, Signal Transduction
Show Abstract · Added June 27, 2014
Successful targeting of specific oncogenic "driver" mutations with small-molecule inhibitors has represented a major advance in cancer therapeutics over the past 10 to 15 years. The most common activating oncogene in human malignancy, RAS (rat sarcoma), has proved to be an elusive target. Activating mutations in RAS induce mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase-AKT pathway signaling and drive malignant progression in up to 30% of cancers. Oncogenic NRAS mutations occur in several cancer types, notably melanoma, acute myelogenous leukemia (AML), and less commonly, colon adenocarcinoma, thyroid carcinoma, and other hematologic malignancies. Although NRAS-mutant tumors have been recalcitrant to targeted therapeutic strategies historically, newer agents targeting MAP/ERK kinase 1 (MEK1)/2 have recently shown signs of clinical efficacy as monotherapy. Combination strategies of MEK inhibitors with other targeted agents have strong preclinical support and are being evaluated in clinical trials. This review discusses the recent preclinical and clinical studies about the role of NRAS in cancer, with a focus on melanoma and AML.
©2014 American Association for Cancer Research.
0 Communities
1 Members
0 Resources
9 MeSH Terms
An efficient, nonlinear stability analysis for detecting pattern formation in reaction diffusion systems.
Holmes WR
(2014) Bull Math Biol 76: 157-83
MeSH Terms: Chemotaxis, Computer Simulation, Diffusion, GTP Phosphohydrolases, Kinetics, Linear Models, Mathematical Concepts, Models, Biological, Nonlinear Dynamics, Pattern Recognition, Automated, Phosphatidylinositols, Systems Biology
Show Abstract · Added February 26, 2016
Reaction diffusion systems are often used to study pattern formation in biological systems. However, most methods for understanding their behavior are challenging and can rarely be applied to complex systems common in biological applications. I present a relatively simple and efficient, nonlinear stability technique that greatly aids such analysis when rates of diffusion are substantially different. This technique reduces a system of reaction diffusion equations to a system of ordinary differential equations tracking the evolution of a large amplitude, spatially localized perturbation of a homogeneous steady state. Stability properties of this system, determined using standard bifurcation techniques and software, describe both linear and nonlinear patterning regimes of the reaction diffusion system. I describe the class of systems this method can be applied to and demonstrate its application. Analysis of Schnakenberg and substrate inhibition models is performed to demonstrate the methods capabilities in simplified settings and show that even these simple models have nonlinear patterning regimes not previously detected. The real power of this technique, however, is its simplicity and applicability to larger complex systems where other nonlinear methods become intractable. This is demonstrated through analysis of a chemotaxis regulatory network comprised of interacting proteins and phospholipids. In each case, predictions of this method are verified against results of numerical simulation, linear stability, asymptotic, and/or full PDE bifurcation analyses.
0 Communities
1 Members
0 Resources
12 MeSH Terms
Structural and functional characterization of the N terminus of Schizosaccharomyces pombe Cwf10.
Livesay SB, Collier SE, Bitton DA, Bähler J, Ohi MD
(2013) Eukaryot Cell 12: 1472-89
MeSH Terms: Amino Acid Motifs, Amino Acid Sequence, Binding Sites, GTP Phosphohydrolases, Molecular Sequence Data, Mutation, Protein Binding, Protein Structure, Tertiary, RNA Splicing, Ribonucleoprotein, U5 Small Nuclear, Schizosaccharomyces, Schizosaccharomyces pombe Proteins, Spliceosomes
Show Abstract · Added March 7, 2014
The spliceosome is a dynamic macromolecular machine that catalyzes the removal of introns from pre-mRNA, yielding mature message. Schizosaccharomyces pombe Cwf10 (homolog of Saccharomyces cerevisiae Snu114 and human U5-116K), an integral member of the U5 snRNP, is a GTPase that has multiple roles within the splicing cycle. Cwf10/Snu114 family members are highly homologous to eukaryotic translation elongation factor EF2, and they contain a conserved N-terminal extension (NTE) to the EF2-like portion, predicted to be an intrinsically unfolded domain. Using S. pombe as a model system, we show that the NTE is not essential, but cells lacking this domain are defective in pre-mRNA splicing. Genetic interactions between cwf10-ΔNTE and other pre-mRNA splicing mutants are consistent with a role for the NTE in spliceosome activation and second-step catalysis. Characterization of Cwf10-NTE by various biophysical techniques shows that in solution the NTE contains regions of both structure and disorder. The first 23 highly conserved amino acids of the NTE are essential for its role in splicing but when overexpressed are not sufficient to restore pre-mRNA splicing to wild-type levels in cwf10-ΔNTE cells. When the entire NTE is overexpressed in the cwf10-ΔNTE background, it can complement the truncated Cwf10 protein in trans, and it immunoprecipitates a complex similar in composition to the late-stage U5.U2/U6 spliceosome. These data show that the structurally flexible NTE is capable of independently incorporating into the spliceosome and improving splicing function, possibly indicating a role for the NTE in stabilizing conformational rearrangements during a splice cycle.
0 Communities
2 Members
0 Resources
13 MeSH Terms
Pharmacodynamic effects and mechanisms of resistance to vemurafenib in patients with metastatic melanoma.
Trunzer K, Pavlick AC, Schuchter L, Gonzalez R, McArthur GA, Hutson TE, Moschos SJ, Flaherty KT, Kim KB, Weber JS, Hersey P, Long GV, Lawrence D, Ott PA, Amaravadi RK, Lewis KD, Puzanov I, Lo RS, Koehler A, Kockx M, Spleiss O, Schell-Steven A, Gilbert HN, Cockey L, Bollag G, Lee RJ, Joe AK, Sosman JA, Ribas A
(2013) J Clin Oncol 31: 1767-74
MeSH Terms: Administration, Oral, Adolescent, Adult, Aged, Aged, 80 and over, Antineoplastic Agents, Apoptosis, Cell Cycle, Cell Proliferation, Disease Progression, Drug Resistance, Neoplasm, Female, GTP Phosphohydrolases, Humans, Immunohistochemistry, Indoles, MAP Kinase Kinase 1, MAP Kinase Signaling System, Male, Melanoma, Membrane Proteins, Middle Aged, Mitogen-Activated Protein Kinase Kinases, Point Mutation, Proto-Oncogene Proteins B-raf, Skin Neoplasms, Sulfonamides, Tumor Cells, Cultured, Vemurafenib
Show Abstract · Added March 5, 2014
PURPOSE To assess pharmacodynamic effects and intrinsic and acquired resistance mechanisms of the BRAF inhibitor vemurafenib in BRAF(V600)-mutant melanoma, leading to an understanding of the mechanism of action of vemurafenib and ultimately to optimization of metastatic melanoma therapy. METHODS In the phase II clinical study NP22657 (BRIM-2), patients received oral doses of vemurafenib (960 mg twice per day). Serial biopsies were collected to study changes in mitogen-activated protein kinase (MAPK) signaling, cell-cycle progression, and factors causing intrinsic or acquired resistance by immunohistochemistry, DNA sequencing, or somatic mutation profiling. Results Vemurafenib inhibited MAPK signaling and cell-cycle progression. An association between the decrease in extracellular signal-related kinase (ERK) phosphorylation and objective response was observed in paired biopsies (n = 22; P = .013). Low expression of phosphatase and tensin homolog showed a modest association with lower response. Baseline mutations in MEK1(P124) coexisting with BRAF(V600) were noted in seven of 92 samples; their presence did not preclude objective tumor responses. Acquired resistance to vemurafenib associated with reactivation of MAPK signaling as observed by elevated ERK1/2 phosphorylation levels in progressive lesions and the appearance of secondary NRAS(Q61) mutations or MEK1(Q56P) or MEK1(E203K) mutations. These two activating MEK1 mutations had not previously been observed in vivo in biopsies of progressive melanoma tumors. CONCLUSION Vemurafenib inhibits tumor proliferation and oncogenic BRAF signaling through the MAPK pathway. Acquired resistance results primarily from MAPK reactivation driven by the appearance of secondary mutations in NRAS and MEK1 in subsets of patients. The data suggest that inhibition downstream of BRAF should help to overcome acquired resistance.
0 Communities
2 Members
0 Resources
29 MeSH Terms
Characteristics of lung cancers harboring NRAS mutations.
Ohashi K, Sequist LV, Arcila ME, Lovly CM, Chen X, Rudin CM, Moran T, Camidge DR, Vnencak-Jones CL, Berry L, Pan Y, Sasaki H, Engelman JA, Garon EB, Dubinett SM, Franklin WA, Riely GJ, Sos ML, Kris MG, Dias-Santagata D, Ladanyi M, Bunn PA, Pao W
(2013) Clin Cancer Res 19: 2584-91
MeSH Terms: Adenocarcinoma, Adult, Aged, Aged, 80 and over, Antineoplastic Agents, Benzimidazoles, Cell Line, Tumor, DNA Mutational Analysis, Female, GTP Phosphohydrolases, Gene Frequency, Genetic Association Studies, Humans, Inhibitory Concentration 50, Lung Neoplasms, Male, Membrane Proteins, Middle Aged, Mutation, Missense, Protein Kinase Inhibitors, Proto-Oncogene Proteins, Proto-Oncogene Proteins p21(ras), Pyridones, Pyrimidinones, ras Proteins
Show Abstract · Added September 3, 2013
PURPOSE - We sought to determine the frequency and clinical characteristics of patients with lung cancer harboring NRAS mutations. We used preclinical models to identify targeted therapies likely to be of benefit against NRAS-mutant lung cancer cells.
EXPERIMENTAL DESIGN - We reviewed clinical data from patients whose lung cancers were identified at six institutions or reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) to harbor NRAS mutations. Six NRAS-mutant cell lines were screened for sensitivity against inhibitors of multiple kinases (i.e., EGFR, ALK, MET, IGF-1R, BRAF, PI3K, and MEK).
RESULTS - Among 4,562 patients with lung cancers tested, NRAS mutations were present in 30 (0.7%; 95% confidence interval, 0.45%-0.94%); 28 of these had no other driver mutations. 83% had adenocarcinoma histology with no significant differences in gender. While 95% of patients were former or current smokers, smoking-related G:C>T:A transversions were significantly less frequent in NRAS-mutated lung tumors than KRAS-mutant non-small cell lung cancer [NSCLC; NRAS: 13% (4/30), KRAS: 66% (1772/2733), P < 0.00000001]. Five of 6 NRAS-mutant cell lines were sensitive to the MEK inhibitors, selumetinib and trametinib, but not to other inhibitors tested.
CONCLUSION - NRAS mutations define a distinct subset of lung cancers (∼1%) with potential sensitivity to MEK inhibitors. Although NRAS mutations are more common in current/former smokers, the types of mutations are not those classically associated with smoking.
©2013 AACR.
0 Communities
4 Members
0 Resources
25 MeSH Terms
The RhoG/ELMO1/Dock180 signaling module is required for spine morphogenesis in hippocampal neurons.
Kim JY, Oh MH, Bernard LP, Macara IG, Zhang H
(2011) J Biol Chem 286: 37615-24
MeSH Terms: Adaptor Proteins, Signal Transducing, Animals, Cell Movement, GTP Phosphohydrolases, Hippocampus, Morphogenesis, Nerve Tissue Proteins, Neurons, RNA Interference, Rats, Signal Transduction, Spine, rac GTP-Binding Proteins
Show Abstract · Added March 5, 2014
Dendritic spines are actin-rich structures, the formation and plasticity of which are regulated by the Rho GTPases in response to synaptic input. Although several guanine nucleotide exchange factors (GEFs) have been implicated in spine development and plasticity in hippocampal neurons, it is not known how many different Rho GEFs contribute to spine morphogenesis or how they coordinate the initiation, establishment, and maintenance of spines. In this study, we screened 70 rat Rho GEFs in cultured hippocampal neurons by RNA interference and identified a number of candidates that affected spine morphogenesis. Of these, Dock180, which plays a pivotal role in a variety of cellular processes including cell migration and phagocytosis, was further investigated. We show that depletion of Dock180 inhibits spine morphogenesis, whereas overexpression of Dock180 promotes spine morphogenesis. ELMO1, a protein necessary for in vivo functions of Dock180, functions in a complex with Dock180 in spine morphogenesis through activating the Rac GTPase. Moreover, RhoG, which functions upstream of the ELMO1/Dock180 complex, is also important for spine formation. Together, our findings uncover a role for the RhoG/ELMO1/Dock180 signaling module in spine morphogenesis in hippocampal neurons.
0 Communities
1 Members
0 Resources
13 MeSH Terms
Fragmented mitochondria are sensitized to Bax insertion and activation during apoptosis.
Brooks C, Cho SG, Wang CY, Yang T, Dong Z
(2011) Am J Physiol Cell Physiol 300: C447-55
MeSH Terms: Animals, Apoptosis, Apoptosis Regulatory Proteins, Cell Line, Cells, Cultured, Dynamins, Enzyme Activation, GTP Phosphohydrolases, Gene Knockdown Techniques, HeLa Cells, Humans, Membrane Fusion, Membrane Transport Proteins, Mice, Mice, Knockout, Microtubule-Associated Proteins, Mitochondria, Mitochondrial Diseases, Mitochondrial Membrane Transport Proteins, Mitochondrial Proteins, RNA Interference, Rats, Stress, Physiological, bcl-2-Associated X Protein
Show Abstract · Added September 12, 2016
Recent studies have shown mitochondrial fragmentation during cell stress and have suggested a role for the morphological change in mitochondrial injury and ensuing apoptosis. However, the underlying mechanism remains elusive. Here we demonstrate that mitochondrial fragmentation facilitates Bax insertion and activation in mitochondria, resulting in the release of apoptogenic factors. In HeLa cells, overexpression of mitofusins attenuated mitochondrial fragmentation during cisplatin- and azide-induced cell injury, which was accompanied by less apoptosis and less cytochrome c release from mitochondria. Similar effects were shown by inhibiting the mitochondrial fission protein Drp1 with a dominant negative mutant (dn-Drp1). Mitofusins and dn-Drp1 did not seem to significantly affect Bax translocation/accumulation to mitochondria; however, they blocked Bax insertion and activation in mitochondrial membrane. Consistently, in rat kidney proximal tubular cells, small interfering RNA knockdown of Drp1 prevented mitochondrial fragmentation during azide-induced ATP depletion, which was accompanied by less Bax activation, insertion, and oligomerization in mitochondria. These cells released less cytochrome c and AIF from mitochondria and showed significantly lower apoptosis. Finally, mitofusin-null mouse embryonic fibroblasts (MEF) had fragmented mitochondria. These MEFs were more sensitive to cisplatin-induced Bax activation, release of cytochrome c, and apoptosis. Together, this study provides further support for a role of mitochondrial fragmentation in mitochondrial injury and apoptosis. Mechanistically, mitochondrial fragmentation may sensitize the cells to Bax insertion and activation in mitochondria, facilitating the release of apoptogenic factors and consequent apoptosis.
0 Communities
1 Members
0 Resources
24 MeSH Terms