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1.
Eye Vis (Lond) ; 11(1): 11, 2024 Mar 18.
Article in English | MEDLINE | ID: mdl-38494521

ABSTRACT

BACKGROUND: To describe the diagnostic performance of a deep learning (DL) algorithm in detecting Fuchs endothelial corneal dystrophy (FECD) based on specular microscopy (SM) and to reliably detect widefield peripheral SM images with an endothelial cell density (ECD) > 1000 cells/mm2. METHODS: Five hundred and forty-seven subjects had SM imaging performed for the central cornea endothelium. One hundred and seventy-three images had FECD, while 602 images had other diagnoses. Using fivefold cross-validation on the dataset containing 775 central SM images combined with ECD, coefficient of variation (CV) and hexagonal endothelial cell ratio (HEX), the first DL model was trained to discriminate FECD from other images and was further tested on an external set of 180 images. In eyes with FECD, a separate DL model was trained with 753 central/paracentral SM images to detect SM with ECD > 1000 cells/mm2 and tested on 557 peripheral SM images. Area under curve (AUC), sensitivity and specificity were evaluated. RESULTS: The first model achieved an AUC of 0.96 with 0.91 sensitivity and 0.91 specificity in detecting FECD from other images. With an external validation set, the model achieved an AUC of 0.77, with a sensitivity of 0.69 and specificity of 0.68 in differentiating FECD from other diagnoses. The second model achieved an AUC of 0.88 with 0.79 sensitivity and 0.78 specificity in detecting peripheral SM images with ECD > 1000 cells/mm2. CONCLUSIONS: Our pilot study developed a DL model that could reliably detect FECD from other SM images and identify widefield SM images with ECD > 1000 cells/mm2 in eyes with FECD. This could be the foundation for future DL models to track progression of eyes with FECD and identify candidates suitable for therapies such as Descemet stripping only.

2.
Front Med (Lausanne) ; 9: 875242, 2022.
Article in English | MEDLINE | ID: mdl-36314006

ABSTRACT

Background: Many artificial intelligence (AI) studies have focused on development of AI models, novel techniques, and reporting guidelines. However, little is understood about clinicians' perspectives of AI applications in medical fields including ophthalmology, particularly in light of recent regulatory guidelines. The aim for this study was to evaluate the perspectives of ophthalmologists regarding AI in 4 major eye conditions: diabetic retinopathy (DR), glaucoma, age-related macular degeneration (AMD) and cataract. Methods: This was a multi-national survey of ophthalmologists between March 1st, 2020 to February 29th, 2021 disseminated via the major global ophthalmology societies. The survey was designed based on microsystem, mesosystem and macrosystem questions, and the software as a medical device (SaMD) regulatory framework chaired by the Food and Drug Administration (FDA). Factors associated with AI adoption for ophthalmology analyzed with multivariable logistic regression random forest machine learning. Results: One thousand one hundred seventy-six ophthalmologists from 70 countries participated with a response rate ranging from 78.8 to 85.8% per question. Ophthalmologists were more willing to use AI as clinical assistive tools (88.1%, n = 890/1,010) especially those with over 20 years' experience (OR 3.70, 95% CI: 1.10-12.5, p = 0.035), as compared to clinical decision support tools (78.8%, n = 796/1,010) or diagnostic tools (64.5%, n = 651). A majority of Ophthalmologists felt that AI is most relevant to DR (78.2%), followed by glaucoma (70.7%), AMD (66.8%), and cataract (51.4%) detection. Many participants were confident their roles will not be replaced (68.2%, n = 632/927), and felt COVID-19 catalyzed willingness to adopt AI (80.9%, n = 750/927). Common barriers to implementation include medical liability from errors (72.5%, n = 672/927) whereas enablers include improving access (94.5%, n = 876/927). Machine learning modeling predicted acceptance from participant demographics with moderate to high accuracy, and area under the receiver operating curves of 0.63-0.83. Conclusion: Ophthalmologists are receptive to adopting AI as assistive tools for DR, glaucoma, and AMD. Furthermore, ML is a useful method that can be applied to evaluate predictive factors on clinical qualitative questionnaires. This study outlines actionable insights for future research and facilitation interventions to drive adoption and operationalization of AI tools for Ophthalmology.

3.
Front Immunol ; 13: 845417, 2022.
Article in English | MEDLINE | ID: mdl-35493516

ABSTRACT

P-cadherin is a cell-cell adhesion molecule that is overexpressed in several solid tumors. PF-06671008 is a T-cell-redirecting bispecific antibody that engages both P-cadherin on tumors and CD3ϵ on T cells and induces antitumor activity in preclinical models. We conducted a phase 1, open-label, first-in-human, dose-escalation study to characterize the safety and tolerability of PF-06671008, towards determining the recommended phase 2 dose. Adult patients with treatment-refractory solid tumors received PF-06671008 (1.5-400 ng/kg) as a weekly intravenous (IV) infusion on a 21-day/3-week cycle. Parallel cohorts evaluated dosing via subcutaneous injection (SC) or an IV-prime dose. Of the 27 patients enrolled in the study, 24 received PF-06671008 IV in escalating doses, two received SC, and one IV-prime. A dose-limiting toxicity of cytokine release syndrome (CRS) occurred in the 400-ng/kg IV group, prompting evaluation of SC and IV-prime schedules. In all, 25/27 patients who received PF-06671008 reported at least one treatment-related adverse event (TRAE); the most common were CRS (21/27), decreased lymphocyte count (9/27), and hypophosphatemia (8/27). Seven patients permanently discontinued treatment due to adverse events and no treatment-related deaths occurred. Cytokine peak concentrations and CRS grade appeared to positively correlate with Cmax. Although the study was terminated due to limited antitumor activity, it provides important insights into understanding and managing immune-related adverse events resulting from this class of molecules. Clinical Trial Registration: URL: https://clinicaltrials.gov/ct2/show/NCT02659631, ClinicalTrials.gov Identifier: NCT02659631.


Subject(s)
Antibodies, Bispecific , Neoplasms , Adult , Antibodies, Bispecific/adverse effects , Cadherins , Humans , Neoplasms/drug therapy , Neoplasms/pathology , Treatment Outcome
4.
Expert Rev Anticancer Ther ; 21(10): 1105-1124, 2021 10.
Article in English | MEDLINE | ID: mdl-34176404

ABSTRACT

Introduction: The cell cycle cyclin-dependent kinases (CDKs) play a critical role in controlling the transition between cell cycle phases, as well as cellular transcription. Aberrant CDK activation is common in cancer, and deregulation of the cell cycle a key hallmark of cancer. Although CDK4/6 inhibitors are now a standard-of-care option for first- and second-line HR+/HER2- metastatic breast cancer, resistance inevitably limits their clinical benefit.Areas covered: Early pan-CDK inhibitors targeted the cell cycle and RNA polymerase II phosphorylation, but were complicated by toxicity, providing a rationale and need for the development of selective CDK inhibitors. In this review, we highlight selected recent literature to provide a narrative review summarizing the current CDK inhibitor therapeutic landscape. We detail the challenges associated with targeting CDKs for the treatment of breast and other cancers and review emerging biomarkers that may aid response prediction. We also discuss the risk-benefit ratio for CDK therapy and explore promising combination approaches.Expert opinion: Although CDK inhibitors may stem the proliferation of cancer cells, resistance remains an issue, and currently there are limited biomarkers to predict response to therapy. Ongoing research investigating CDK inhibitors in cancer is of paramount importance to define appropriate and effective treatment regimens.


Subject(s)
Breast Neoplasms , Cyclin-Dependent Kinases , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Cell Cycle , Cyclin-Dependent Kinase 4 , Cyclin-Dependent Kinase 6 , Female , Humans , Protein Kinase Inhibitors/adverse effects
5.
AAPS J ; 22(2): 23, 2020 01 03.
Article in English | MEDLINE | ID: mdl-31900603

ABSTRACT

IL-7 receptor-α (IL-7Rα) blockade has been shown to reverse autoimmune diabetes in the non-obese diabetic mouse by promoting inhibition of effector T cells and consequently altering the balance of regulatory T (Treg) and effector memory (TEM) cells. PF-06342674 is a humanized monoclonal antibody that binds to and inhibits the function of IL-7Rα. In the current phase 1b study, subjects with type 1 diabetes (T1D) received subcutaneous doses of either placebo or PF-06342674 (1, 3, 8 mg/kg/q2w or 6 mg/kg/q1w) for 10 weeks and were followed up to 18 weeks. Nonlinear mixed effects models were developed to characterize the pharmacokinetics (PK), target engagement biomarkers, and immunomodulatory activity. PF-06342674 was estimated to have 20-fold more potent inhibitory effect on TEM cells relative to Treg cells resulting in a non-monotonic dose-response relationship for the Treg:TEM ratio, reaching maximum at ~ 3 mg/kg/q2w dose. Target-mediated elimination led to nonlinear PK with accelerated clearance at lower doses due to high affinity binding and rapid clearance of the drug-target complex. Doses ≥ 3 mg/kg q2w result in sustained PF-06342674 concentrations higher than the concentration of cellular IL-7 receptor and, in turn, maintain near maximal receptor occupancy over the dosing interval. The results provide important insight into the mechanism of IL-7Rα blockade and immunomodulatory activity of PF-06342674 and establish a rational framework for dose selection for subsequent clinical trials of PF-06342674. Furthermore, this analysis serves as an example of mechanistic modeling to support dose selection of a drug candidate in the early phases of development.


Subject(s)
Antibodies, Monoclonal, Humanized/pharmacokinetics , Diabetes Mellitus, Type 1/drug therapy , Hypoglycemic Agents/pharmacokinetics , Insulin-Secreting Cells/drug effects , Models, Biological , Receptors, Interleukin-17/antagonists & inhibitors , T-Lymphocytes, Regulatory/drug effects , Antibodies, Monoclonal, Humanized/administration & dosage , Diabetes Mellitus, Type 1/diagnosis , Diabetes Mellitus, Type 1/immunology , Dose-Response Relationship, Drug , Humans , Hypoglycemic Agents/administration & dosage , Injections, Subcutaneous , Insulin-Secreting Cells/immunology , Insulin-Secreting Cells/pathology , Nonlinear Dynamics , Receptors, Interleukin-17/immunology , T-Lymphocytes, Regulatory/immunology , Treatment Outcome
6.
Cancers (Basel) ; 11(5)2019 Apr 30.
Article in English | MEDLINE | ID: mdl-31052266

ABSTRACT

Failure to cure ovarian cancer relates to the persistence of dormant, drug-resistant cancer cells following surgery and chemotherapy. "Second look" surgery can detect small, poorly vascularized nodules of persistent ovarian cancer in ~50% of patients, where >80% are undergoing autophagy and express DIRAS3. Autophagy is one mechanism by which dormant cancer cells survive in nutrient poor environments. DIRAS3 is a tumor suppressor gene downregulated in >60% of primary ovarian cancers by genetic, epigenetic, transcriptional and post-transcriptional mechanisms, that upon re-expression can induce autophagy and dormancy in a xenograft model of ovarian cancer. We examined the expression of DIRAS3 and autophagy in ovarian cancer cells following nutrient deprivation and the mechanism by which they are upregulated. We have found that DIRAS3 mediates autophagy induced by amino acid starvation, where nutrient sensing by mTOR plays a central role. Withdrawal of amino acids downregulates mTOR, decreases binding of E2F1/4 to the DIRAS3 promoter, upregulates DIRAS3 and induces autophagy. By contrast, acute amino acid deprivation did not affect epigenetic regulation of DIRAS3 or expression of miRNAs that regulate DIRAS3. Under nutrient poor conditions DIRAS3 can be transcriptionally upregulated, inducing autophagy that could sustain dormant ovarian cancer cells.

7.
Cancer Treat Rev ; 76: 33-40, 2019 Jun.
Article in English | MEDLINE | ID: mdl-31108240

ABSTRACT

Attribution of adverse events (AEs) is critical to oncology drug development and the regulatory process. However, processes for determining the causality of AEs are often sub-optimal, unreliable, and inefficient. Thus, we conducted a toxicity-attribution workshop in Silver Springs MD to develop guidance for improving attribution of AEs in oncology clinical trials. Attribution stakeholder experts from regulatory agencies, sponsors and contract research organizations, clinical trial principal investigators, pre-clinical translational scientists, and research staff involved in capturing attribution information participated. We also included patients treated in oncology clinical trials and academic researchers with expertise in attribution. We identified numerous challenges with AE attribution, including the non-informative nature of and burdens associated with the 5-tier system of attribution, increased complexity of trial logistics, costs and time associated with AE attribution data collection, lack of training in attribution for early-career investigators, insufficient baseline assessments, and lack of consistency in the reporting of treatment-related and treatment-emergent AEs in publications and clinical scientific reports. We developed recommendations to improve attribution: we propose transitioning from the present 5-tier system to a 2-3 tier system for attribution, more complete baseline information on patients' clinical status at trial entry, and mechanisms for more rapid sharing of AE information during trials. Oncology societies should develop recommendations and training in attribution of toxicities. We call for further harmonization and synchronization of recommendations regarding causality safety reporting between FDA, EMA and other regulatory agencies. Finally, we suggest that journals maintain or develop standardized requirements for reporting attribution in oncology clinical trials.


Subject(s)
Adverse Drug Reaction Reporting Systems , Antineoplastic Agents/adverse effects , Clinical Trials, Phase III as Topic/methods , Drug Development/methods , Humans , Randomized Controlled Trials as Topic/methods
8.
Cancers (Basel) ; 11(4)2019 Apr 18.
Article in English | MEDLINE | ID: mdl-31003488

ABSTRACT

Autophagy can protect cancer cells from acute starvation and enhance resistance to chemotherapy. Previously, we reported that autophagy plays a critical role in the survival of dormant, drug resistant ovarian cancer cells using human xenograft models and correlated the up-regulation of autophagy and DIRAS3 expression in clinical samples obtained during "second look" operations. DIRAS3 is an imprinted tumor suppressor gene that encodes a 26 kD GTPase with homology to RAS that inhibits cancer cell proliferation and motility. Re-expression of DIRAS3 in ovarian cancer xenografts also induces dormancy and autophagy. DIRAS3 can bind to Beclin1 forming the Autophagy Initiation Complex that triggers autophagosome formation. Both the N-terminus of DIRAS3 (residues 15-33) and the switch II region of DIRAS3 (residues 93-107) interact directly with BECN1. We have identified an autophagy-inhibiting peptide based on the switch II region of DIRAS3 linked to Tat peptide that is taken up by ovarian cancer cells, binds Beclin1 and inhibits starvation-induced DIRAS3-mediated autophagy.

9.
Invest New Drugs ; 36(5): 836-847, 2018 10.
Article in English | MEDLINE | ID: mdl-29333575

ABSTRACT

Purpose and Methods Trop-2 is a glycoprotein over-expressed in many solid tumors but at low levels in normal human tissue, providing a potential therapeutic target. We conducted a phase 1 dose-finding study of PF-06664178, an antibody-drug conjugate that targets Trop-2 for the selective delivery of the cytotoxic payload Aur0101. The primary objective was to determine the maximum tolerated dose and recommended phase 2 dose. Secondary objectives included further characterization of the safety profile, pharmacokinetics and antitumor activity. Eligible patients were enrolled and received multiple escalating doses of PF-06664178 in an open-label and unblinded manner based on a modified continual reassessment method. Results Thirty-one patients with advanced or metastatic solid tumors were treated with escalating doses of PF-06664178 given intravenously every 21 days. Doses explored ranged from 0.15 mg/kg to 4.8 mg/kg. Seven patients experienced at least one dose limiting toxicity (DLT), either neutropenia or rash. Doses of 3.60 mg/kg, 4.2 mg/kg and 4.8 mg/kg were considered intolerable due to DLTs in skin rash, mucosa and neutropenia. Best overall response was stable disease in 11 patients (37.9%). None of the patients had a partial or complete response. Systemic exposure of PF-06664178 increased in a dose-related manner. Serum concentrations of free Aur0101 were substantially lower than those of PF-06664178 and total antibody. No correlation of Trop-2 expression and objective response was observed, although Trop-2 overexpression was not required for study entry. The intermediate dose of 2.4 mg/kg appeared to be the highest tolerated dose, but this was not fully explored as the study was terminated early due to excess toxicity. Conclusion PF-06664178 showed toxicity at high dose levels with modest antitumor activity. Neutropenia, skin rash and mucosal inflammation were dose limiting toxicities. Findings from this study may potentially aid in future antibody drug conjugate design and trials.


Subject(s)
Aminobenzoates/therapeutic use , Antineoplastic Agents/therapeutic use , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Cell Adhesion Molecules/antagonists & inhibitors , Immunoconjugates/therapeutic use , Neoplasms/drug therapy , Oligopeptides/therapeutic use , Aminobenzoates/pharmacokinetics , Antigens, Neoplasm/metabolism , Antineoplastic Agents/pharmacokinetics , Antineoplastic Combined Chemotherapy Protocols/pharmacokinetics , Cell Adhesion Molecules/metabolism , Exanthema/chemically induced , Female , Humans , Immunoconjugates/pharmacokinetics , Male , Maximum Tolerated Dose , Middle Aged , Neoplasms/metabolism , Neutropenia/chemically induced , Oligopeptides/pharmacokinetics , Treatment Outcome
10.
Autophagy ; 14(4): 637-653, 2018.
Article in English | MEDLINE | ID: mdl-29368982

ABSTRACT

Among the 3 GTPases in the DIRAS family, DIRAS3/ARHI is the best characterized. DIRAS3 is an imprinted tumor suppressor gene that encodes a 26-kDa GTPase that shares 60% homology to RAS and RAP. DIRAS3 is downregulated in many tumor types, including ovarian cancer, where re-expression inhibits cancer cell growth, reduces motility, promotes tumor dormancy and induces macroautophagy/autophagy. Previously, we demonstrated that DIRAS3 is required for autophagy in human cells. Diras3 has been lost from the mouse genome during evolutionary re-arrangement, but murine cells can still undergo autophagy. We have tested whether DIRAS1 and DIRAS2, which are homologs found in both human and murine cells, could serve as surrogates to DIRAS3 in the murine genome affecting autophagy and cancer cell growth. Similar to DIRAS3, these 2 GTPases share 40-50% homology to RAS and RAP, but differ from DIRAS3 primarily in the lengths of their N-terminal extensions. We found that DIRAS1 and DIRAS2 are downregulated in ovarian cancer and are associated with decreased disease-free and overall survival. Re-expression of these genes suppressed growth of human and murine ovarian cancer cells by inducing autophagy-mediated cell death. Mechanistically, DIRAS1 and DIRAS2 induce and regulate autophagy by inhibition of the AKT1-MTOR and RAS-MAPK signaling pathways and modulating nuclear localization of the autophagy-related transcription factors FOXO3/FOXO3A and TFEB. Taken together, these data suggest that DIRAS1 and DIRAS2 likely serve as surrogates in the murine genome for DIRAS3, and may function as a backup system to fine-tune autophagy in humans.


Subject(s)
Autophagy/physiology , Carcinoma, Ovarian Epithelial/metabolism , Monomeric GTP-Binding Proteins/metabolism , Ovarian Neoplasms/metabolism , Animals , Cell Line, Tumor , Female , GTP Phosphohydrolases/metabolism , Ovarian Neoplasms/pathology , Ovary/metabolism , Tumor Suppressor Proteins/metabolism
11.
J Environ Manage ; 198(Pt 1): 16-23, 2017 Aug 01.
Article in English | MEDLINE | ID: mdl-28441553

ABSTRACT

The aim of this study was to determine the critical operational conditions leading to the generation of sulfide in a domestic wastewater treated by a sulfur-utilizing denitrification process. The influence of various important parameters on the reduction of the sulfates present in denitrified domestic wastewaters to sulfide was studied. Experiments were carried out in batch mode with denitrified domestic wastewaters containing various amounts of both organic matter and sulfates. Preliminary results showed that aqueous sulfide was generated for DOC and sulfate contents higher than 56 mg/L and 371 mg/L, respectively, while DOC and sulfate contents of 77 mg/L and 412 mg/L, respectively, were required to allow the release of gaseous H2S. Good correlations were also observed between gaseous sulfide production and the values of ORP and DOC, while the amounts of dissolved sulfide produced seemed to be correlated with the ORP values and the concentration of sulfates. Additional experiments were conducted using a Box-Behnken methodology to determine if the production of aqueous or gaseous sulfide can be predicted depending on the DOC (from 50 to 90 mg/L) and sulfate contents (from 160 to 380 mg/L) at various temperatures ranging from 5 to 25 °C. The highest sulfide generation (H2S(g) = 84.8 ppm and H2S(aq) = 2.42 mg/L) occurred at 25 °C with DOC and sulfate concentrations starting from 90 mg/L and 270 mg/L, respectively, indicating that the production of sulfides from denitrified domestic wastewaters required conditions not likely to occur at the effluent of a sulfur-based denitrification unit following secondary treatment.


Subject(s)
Denitrification , Wastewater , Bioreactors , Sulfates , Sulfides , Sulfur
12.
Environ Sci Pollut Res Int ; 23(19): 19071-83, 2016 Oct.
Article in English | MEDLINE | ID: mdl-27343077

ABSTRACT

This study aimed to determine the potential of sulfide generation during infiltration through soil of domestic wastewater treated by a sulfur-utilizing denitrification process. Three types of soil with different permeability rates (K s = 0.028, 0.0013, and 0.00015 cm/s) were investigated to evaluate the potential risk of sulfur generation during the infiltration of domestic wastewater treated by a sulfur-utilizing denitrification system. These soils were thoroughly characterized and tested to assess their capacity to be used as drainages for wastewaters. Experiments were conducted under two operating modes (saturated and unsaturated). Sulfate, sulfide, and chemical oxygen demand (COD) levels were determined over a period of 100 days. Despite the high concentration of sulfates (200 mg/L) under anaerobic conditions (ORP = -297 mV), no significant amount of sulfide was generated in the aqueous (<0.2 mg/L) or gaseous (<0.15 ppm) phases. Furthermore, the soil permeability did not have a noticeable effect on the infiltration of domestic wastewater treated by a sulfur-utilizing denitrification system due to low contents of organic matter (i.e., dissolved organic carbon, DOC). The autotrophic denitrification process used to treat the domestic wastewater allowed the reduction of the concentration of biochemical oxygen demand (BOD5) below 5 mg/L, of DOC below 7 mg/L, and of COD below 100 mg/L.


Subject(s)
Denitrification , Soil/chemistry , Sulfides/analysis , Sulfur/chemistry , Wastewater/chemistry , Autotrophic Processes , Biological Oxygen Demand Analysis , Bioreactors , Risk Assessment , Sulfates/analysis , Sulfates/chemistry , Sulfides/chemistry
13.
Mol Cell ; 61(4): 520-534, 2016 Feb 18.
Article in English | MEDLINE | ID: mdl-26853146

ABSTRACT

Altered energy metabolism is a cancer hallmark as malignant cells tailor their metabolic pathways to meet their energy requirements. Glucose and glutamine are the major nutrients that fuel cellular metabolism, and the pathways utilizing these nutrients are often altered in cancer. Here, we show that the long ncRNA CCAT2, located at the 8q24 amplicon on cancer risk-associated rs6983267 SNP, regulates cancer metabolism in vitro and in vivo in an allele-specific manner by binding the Cleavage Factor I (CFIm) complex with distinct affinities for the two subunits (CFIm25 and CFIm68). The CCAT2 interaction with the CFIm complex fine-tunes the alternative splicing of Glutaminase (GLS) by selecting the poly(A) site in intron 14 of the precursor mRNA. These findings uncover a complex, allele-specific regulatory mechanism of cancer metabolism orchestrated by the two alleles of a long ncRNA.


Subject(s)
Glutaminase/genetics , Neoplasms/metabolism , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , mRNA Cleavage and Polyadenylation Factors/metabolism , Alleles , Alternative Splicing , Energy Metabolism , HCT116 Cells , Humans , Neoplasms/genetics , RNA Precursors/chemistry , RNA Precursors/metabolism , RNA, Messenger/metabolism
14.
J Biol Chem ; 291(11): 5623-5633, 2016 Mar 11.
Article in English | MEDLINE | ID: mdl-26769964

ABSTRACT

Membrane-bound cGMP-dependent protein kinase (PKG) II is a key regulator of bone growth, renin secretion, and memory formation. Despite its crucial physiological roles, little is known about its cyclic nucleotide selectivity mechanism due to a lack of structural information. Here, we find that the C-terminal cyclic nucleotide binding (CNB-B) domain of PKG II binds cGMP with higher affinity and selectivity when compared with its N-terminal CNB (CNB-A) domain. To understand the structural basis of cGMP selectivity, we solved co-crystal structures of the CNB domains with cyclic nucleotides. Our structures combined with mutagenesis demonstrate that the guanine-specific contacts at Asp-412 and Arg-415 of the αC-helix of CNB-B are crucial for cGMP selectivity and activation of PKG II. Structural comparison with the cGMP selective CNB domains of human PKG I and Plasmodium falciparum PKG (PfPKG) shows different contacts with the guanine moiety, revealing a unique cGMP selectivity mechanism for PKG II.


Subject(s)
Cyclic GMP-Dependent Protein Kinase Type II/chemistry , Cyclic GMP-Dependent Protein Kinase Type II/metabolism , Cyclic GMP/metabolism , Allosteric Regulation , Animals , COS Cells , Chlorocebus aethiops , Crystallography, X-Ray , Cyclic AMP/metabolism , HEK293 Cells , Humans , Models, Molecular , Protein Structure, Tertiary , Substrate Specificity
16.
Biochemistry ; 53(43): 6725-7, 2014 Nov 04.
Article in English | MEDLINE | ID: mdl-25271401

ABSTRACT

High selectivity of cyclic-nucleotide binding (CNB) domains for cAMP and cGMP are required for segregating signaling pathways; however, the mechanism of selectivity remains unclear. To investigate the mechanism of high selectivity in cGMP-dependent protein kinase (PKG), we determined a room-temperature joint X-ray/neutron (XN) structure of PKG Iß CNB-B, a domain 200-fold selective for cGMP over cAMP, bound to cGMP (2.2 Å), and a low-temperature X-ray structure of CNB-B with cAMP (1.3 Å). The XN structure directly describes the hydrogen bonding interactions that modulate high selectivity for cGMP, while the structure with cAMP reveals that all these contacts are disrupted, explaining its low affinity for cAMP.


Subject(s)
Cyclic GMP-Dependent Protein Kinase Type I/chemistry , Enzyme Activators/chemistry , Neutrons , Scattering, Radiation , Animals , Cyclic AMP/chemistry , Cyclic GMP/chemistry , Drug Design , Enzyme Activation , Humans , Hydrogen Bonding
17.
Structure ; 22(1): 116-24, 2014 Jan 07.
Article in English | MEDLINE | ID: mdl-24239458

ABSTRACT

Cyclic guanosine monophosphate (cGMP) and cyclic AMP (cAMP)-dependent protein kinases (PKG and PKA) are closely related homologs, and the cyclic nucleotide specificity of each kinase is crucial for keeping the two signaling pathways segregated, but the molecular mechanism of cyclic nucleotide selectivity is unknown. Here, we report that the PKG Iß C-terminal cyclic nucleotide binding domain (CNB-B) is highly selective for cGMP binding, and we have solved crystal structures of CNB-B with and without bound cGMP. These structures, combined with a comprehensive mutagenic analysis, allowed us to identify Leu296 and Arg297 as key residues that mediate cGMP selectivity. In addition, by comparing the cGMP bound and unbound structures, we observed large conformational changes in the C-terminal helices in response to cGMP binding, which were stabilized by recruitment of Tyr351 as a "capping residue" for cGMP. The observed rearrangements of the C-terminal helices provide a mechanical insight into release of the catalytic domain and kinase activation.


Subject(s)
Arginine/chemistry , Cyclic AMP/chemistry , Cyclic GMP-Dependent Protein Kinase Type I/chemistry , Cyclic GMP/chemistry , Leucine/chemistry , Amino Acid Sequence , Arginine/genetics , Binding Sites , Catalytic Domain , Crystallography, X-Ray , Cyclic AMP/metabolism , Cyclic GMP/metabolism , Cyclic GMP-Dependent Protein Kinase Type I/genetics , Cyclic GMP-Dependent Protein Kinase Type I/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , HEK293 Cells , Humans , Kinetics , Leucine/genetics , Models, Molecular , Molecular Sequence Data , Mutagenesis, Site-Directed , Protein Binding , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sequence Alignment , Thermodynamics
18.
J Appl Microbiol ; 116(1): 208-21, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24112699

ABSTRACT

AIMS: Bacterial community structure and composition of a drinking water network were assessed to better understand this ecosystem in relation to haloacetic acid (HAA) degradation and to identify new bacterial species having HAA degradation capacities. METHODS AND RESULTS: Biofilm samples were collected from a model system, simulating the end of the drinking water distribution network and supplied with different concentrations of dichloroacetic and trichloroacetic acids at different periods over the course of a year. The samples were analysed by culturing, denaturing gradient gel electrophoresis (DGGE) and sequencing. Pipe diameter and HAA ratios did not impact the bacterial community profiles, but the season had a clear influence. Based on DGGE profiles, it appeared that a particular biomass has developed during the summer compared with the other seasons. Among the bacteria isolated in this study, those from genus Cupriavidus were able to degrade dichloroacetic acid. Moreover, these bacteria degrade dichloroacetic acid at 18°C but not at 10°C. CONCLUSIONS: The microbial diversity evolved throughout the experiment, but the bacterial community was distinct during the summer. Results obtained on the capacity of Cupriavidus to degrade DCAA only at 18°C but not at 10°C indicate that water temperature is a major element affecting DCAA degradation and confirming observations made regarding season influence on HAA degradation in the drinking water distribution network. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first demonstration of the HAA biodegradation capacity of the genus Cupriavidus.

19.
Clin Pharmacokinet ; 52(2): 125-37, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23212610

ABSTRACT

BACKGROUND: Peripherally acting opioids, particularly peripheral κ-opioid agonists, may be effective for treating visceral pain by activating receptors expressed on afferent nerves within the gut. OBJECTIVE: The objective of this study was to investigate the pharmacokinetic/pharmacodynamic profile of a novel peripherally selective κ-opioid agonist, CR665 (JNJ-38488502), and compare it to that of oxycodone, a non-selective brain-penetrant opioid. METHODS: In a randomized, placebo-controlled, double-blind, three-way crossover study, healthy male volunteers were administered CR665 (0.36 mg/kg, intravenous), oxycodone (15 mg, oral) or placebo (intravenous and oral), followed by assessment of visceral pain tolerance thresholds (VPTT) measured as volume of water (mL) in the bag placed on an oesophageal probe. Plasma drug concentration data were used to generate pharmacokinetic models, which were then used to fit the VPTT data using NONMEM(®) VI to generate population pharmacokinetic/pharmacodynamic models. RESULTS: CR665 kinetics were optimally fitted with a two-compartment model, while oxycodone kinetics were best described by a one-compartment model with transit compartment absorption feeding directly into the central compartment. For both drugs, the plasma concentration effects on VPTT were best fit by a direct linear model, i.e. without the concentration-analgesia delay characteristic of brain-penetrant opioids. The slope of oxycodone (0.089 mL per ng/mL) was steeper than that of CR665 (0.0035 mL per ng/mL) for the plasma drug concentration acting on the VPTT. CONCLUSION: The results are consistent with the peripheral selectivity of CR665, as well as the possibility that peripheral actions of oxycodone contribute to its visceral analgesic efficacy.


Subject(s)
Analgesics/pharmacology , Opioid Peptides/pharmacology , Oxycodone/pharmacology , Receptors, Opioid, kappa/agonists , Adult , Analgesics/blood , Cross-Over Studies , Double-Blind Method , Humans , Male , Models, Biological , Opioid Peptides/blood , Oxycodone/blood , Pain Measurement , Pain Threshold/drug effects , Young Adult
20.
J Appl Microbiol ; 108(2): 437-49, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19614850

ABSTRACT

AIMS: Hypersensitivity pneumonitis of machinists associated with metalworking fluids (MWF) was recently linked to Mycobacterium immunogenum. In addition to Mycobacterium, impacts of continuous and massive contact to other micro-organisms, such as Pseudomonas, were little studied. This report intended to quantify and characterize the microbial load of 44 in-use MWF. METHODS AND RESULTS: The main biodiversity of MWF was assessed using cultural methods, quantitative PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE). Total bacteria concentrations ranged from undetectable to 10(9) 16S rRNA gene copies per millilitre. Concentrations obtained by qPCR were up to five orders of magnitude higher than by culture, suggesting that MWF contamination is generally underestimated. Two samples showed high concentrations of Myco. immunogenum (1.55 x 10(7) and 3.49 x 10(5) 16S rRNA gene copies per millilitre). The overall biodiversity was low, as observed by culture and DGGE, and was comparable to data found in the literature. Pseudomonas pseudoalcaligenes was by far the main bacteria found in MWF samples (33 out of 44), followed by Ochrobactrum anthropi (32 out of 44). There was no significant relationship between the biodiversity profiles and the kind of MWF or equipment used, making it difficult to predict which micro-organisms will colonize each particular MWF. CONCLUSIONS: Very high concentrations of bacteria were found in most MWF studied and limited biodiversities were observed. Many species of micro-organisms were retrieved from MWF samples, but they were mostly colonized by Pseudomonas pseudoalcaligenes and Ochrobactrum anthropi. SIGNIFICANCE AND IMPACT OF THE STUDY: The major micro-organisms observed or recovered in this study from in-use MWF were present in very high concentrations, and thus further studies are needed to confirm their role in workers' respiratory disorders or health-related problems.


Subject(s)
Equipment Contamination , Metallurgy , Mycobacterium/isolation & purification , Ochrobactrum anthropi/isolation & purification , Pseudomonas pseudoalcaligenes/isolation & purification , Biodiversity , Mycobacterium/genetics , Ochrobactrum anthropi/genetics , Polymerase Chain Reaction , Pseudomonas pseudoalcaligenes/genetics , RNA, Bacterial/isolation & purification , RNA, Ribosomal, 16S/isolation & purification
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