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1.
J Am Chem Soc ; 144(3): 1205-1217, 2022 01 26.
Article in English | MEDLINE | ID: mdl-35020383

ABSTRACT

The design of molecular catalysts typically involves reconciling multiple conflicting property requirements, largely relying on human intuition and local structural searches. However, the vast number of potential catalysts requires pruning of the candidate space by efficient property prediction with quantitative structure-property relationships. Data-driven workflows embedded in a library of potential catalysts can be used to build predictive models for catalyst performance and serve as a blueprint for novel catalyst designs. Herein we introduce kraken, a discovery platform covering monodentate organophosphorus(III) ligands providing comprehensive physicochemical descriptors based on representative conformer ensembles. Using quantum-mechanical methods, we calculated descriptors for 1558 ligands, including commercially available examples, and trained machine learning models to predict properties of over 300000 new ligands. We demonstrate the application of kraken to systematically explore the property space of organophosphorus ligands and how existing data sets in catalysis can be used to accelerate ligand selection during reaction optimization.

2.
Acc Chem Res ; 54(4): 849-860, 2021 02 16.
Article in English | MEDLINE | ID: mdl-33528245

ABSTRACT

The ongoing revolution of the natural sciences by the advent of machine learning and artificial intelligence sparked significant interest in the material science community in recent years. The intrinsically high dimensionality of the space of realizable materials makes traditional approaches ineffective for large-scale explorations. Modern data science and machine learning tools developed for increasingly complicated problems are an attractive alternative. An imminent climate catastrophe calls for a clean energy transformation by overhauling current technologies within only several years of possible action available. Tackling this crisis requires the development of new materials at an unprecedented pace and scale. For example, organic photovoltaics have the potential to replace existing silicon-based materials to a large extent and open up new fields of application. In recent years, organic light-emitting diodes have emerged as state-of-the-art technology for digital screens and portable devices and are enabling new applications with flexible displays. Reticular frameworks allow the atom-precise synthesis of nanomaterials and promise to revolutionize the field by the potential to realize multifunctional nanoparticles with applications from gas storage, gas separation, and electrochemical energy storage to nanomedicine. In the recent decade, significant advances in all these fields have been facilitated by the comprehensive application of simulation and machine learning for property prediction, property optimization, and chemical space exploration enabled by considerable advances in computing power and algorithmic efficiency.In this Account, we review the most recent contributions of our group in this thriving field of machine learning for material science. We start with a summary of the most important material classes our group has been involved in, focusing on small molecules as organic electronic materials and crystalline materials. Specifically, we highlight the data-driven approaches we employed to speed up discovery and derive material design strategies. Subsequently, our focus lies on the data-driven methodologies our group has developed and employed, elaborating on high-throughput virtual screening, inverse molecular design, Bayesian optimization, and supervised learning. We discuss the general ideas, their working principles, and their use cases with examples of successful implementations in data-driven material discovery and design efforts. Furthermore, we elaborate on potential pitfalls and remaining challenges of these methods. Finally, we provide a brief outlook for the field as we foresee increasing adaptation and implementation of large scale data-driven approaches in material discovery and design campaigns.

3.
Acta Neurochir (Wien) ; 163(2): 423-440, 2021 02.
Article in English | MEDLINE | ID: mdl-33354733

ABSTRACT

BACKGROUND: Due to the lack of high-quality evidence which has hindered the development of evidence-based guidelines, there is a need to provide general guidance on cranioplasty (CP) following traumatic brain injury (TBI), as well as identify areas of ongoing uncertainty via a consensus-based approach. METHODS: The international consensus meeting on post-traumatic CP was held during the International Conference on Recent Advances in Neurotraumatology (ICRAN), in Naples, Italy, in June 2018. This meeting was endorsed by the Neurotrauma Committee of the World Federation of Neurosurgical Societies (WFNS), the NIHR Global Health Research Group on Neurotrauma, and several other neurotrauma organizations. Discussions and voting were organized around 5 pre-specified themes: (1) indications and technique, (2) materials, (3) timing, (4) hydrocephalus, and (5) paediatric CP. RESULTS: The participants discussed published evidence on each topic and proposed consensus statements, which were subject to ratification using anonymous real-time voting. Statements required an agreement threshold of more than 70% for inclusion in the final recommendations. CONCLUSIONS: This document is the first set of practical consensus-based clinical recommendations on post-traumatic CP, focusing on timing, materials, complications, and surgical procedures. Future research directions are also presented.


Subject(s)
Brain Injuries, Traumatic/surgery , Consensus Development Conferences as Topic , Craniotomy/standards , Plastic Surgery Procedures/standards , Humans , Hydrocephalus/surgery , Italy
4.
Nanomaterials (Basel) ; 12(1)2021 Dec 29.
Article in English | MEDLINE | ID: mdl-35010041

ABSTRACT

Ethylene oxide oligomers and polymers, free and tethered to gold nanoparticles, were dispersed in blue phase liquid crystals (BPLC). Gold nanospheres (AuNPs) and nanorods (AuNRs) were functionalized with thiolated ethylene oxide ligands with molecular weights ranging from 200 to 5000 g/mol. The BPLC mixture (ΔTBP ~6 °C) was based on the mesogenic acid heterodimers, n-hexylbenzoic acid (6BA) and n-trans-butylcyclohexylcarboxylic acid (4-BCHA) with the chiral dopant (R)-2-octyl 4-[4-(hexyloxy)benzoyloxy]benzoate. The lowest molecular weight oligomer lowered and widened the BP range but adding AuNPs functionalized with the same ligand had little effect. Higher concentrations or molecular weights of the ligands, free or tethered to the AuNPs, completely destabilized the BP. Mini-AuNRs functionalized with the same ligands lowered and widened the BP temperature range with longer mini-AuNRs having a larger effect. In contrast to the AuNPs, the mini-AuNRs with the higher molecular weight ligands widened rather than destabilized the BP, though the lowest MW ligand yielded the largest BP range, (ΔTBP > 13 °C). The different effects on the BP may be due to the AuNPs accumulating at singular defect sites whereas the mini-AuNRs, with diameters smaller than that of the disclination lines, can more efficiently fill in the BP defects.

5.
J Appl Microbiol ; 129(2): 162-174, 2020 Aug.
Article in English | MEDLINE | ID: mdl-31758754

ABSTRACT

Collections of micro-organisms are a crucial element of life science research infrastructure but are vulnerable to loss and damage caused by natural or man-made disasters, the untimely death or retirement of personnel, or the loss of research funding. Preservation of biological collections has risen in priority due to a new appreciation for discoveries linked to preserved specimens, emerging hurdles to international collecting and decreased funding for new collecting. While many historic collections have been lost, several have been preserved, some with dramatic rescue stories. Rescued microbes have been used for discoveries in areas of health, biotechnology and basic life science. Suggestions for long-term planning for microbial stocks are listed, as well as inducements for long-term preservation.


Subject(s)
Preservation, Biological , Biomedical Research , Biotechnology , Environmental Microbiology , Humans , Preservation, Biological/methods , Preservation, Biological/trends , United States
6.
Int J Comput Assist Radiol Surg ; 13(3): 479-490, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29143240

ABSTRACT

PURPOSE: Complications in wound healing after neurosurgical operations occur often due to scarred dehiscence with skin blood perfusion disturbance. The standard imaging method for intraoperative skin perfusion assessment is the invasive indocyanine green video angiography (ICGA). The noninvasive dynamic infrared thermography (DIRT) is a promising alternative modality that was evaluated by comparison with ICGA. METHODS: The study was carried out in two parts: (1) investigation of technical conditions for intraoperative use of DIRT for its comparison with ICGA, and (2) visual and quantitative comparison of both modalities in a proof of concept on nine patients. Time-temperature curves in DIRT and time-intensity curves in ICGA for defined regions of interest were analyzed. New perfusion parameters were defined in DIRT and compared with the usual perfusion parameters in ICGA. RESULTS: The visual observation of the image data in DIRT and ICGA showed that operation material, anatomical structures and skin perfusion are represented similarly in both modalities. Although the analysis of the curves and perfusion parameter values showed differences between patients, no complications were observed clinically. These differences were represented in DIRT and ICGA equivalently. CONCLUSIONS: DIRT has shown a great potential for intraoperative use, with several advantages over ICGA. The technique is passive, contactless and noninvasive. The practicability of the intraoperative recording of the same operation field section with ICGA and DIRT has been demonstrated. The promising results of this proof of concept provide a basis for a trial with a larger number of patients.


Subject(s)
Angiography/methods , Indocyanine Green/pharmacology , Plastic Surgery Procedures/methods , Skull/diagnostic imaging , Surgery, Computer-Assisted/methods , Thermography/methods , Video Recording/methods , Coloring Agents/pharmacology , Female , Humans , Male , Middle Aged , Neurosurgical Procedures/methods , Skin/blood supply , Skin/diagnostic imaging , Skull/surgery
7.
Oecologia ; 179(3): 889-900, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26201261

ABSTRACT

Pulses of respiration from coarse woody debris (CWD) have been observed immediately following canopy disturbances, but it is unclear how long these pulses are sustained. Several factors are known to influence carbon flux rates from CWD, but few studies have evaluated more than temperature and moisture. We experimentally manipulated forest structure in a second-growth northern hardwood forest and measured CO2 flux periodically for seven growing seasons following gap creation. We present an analysis of which factors, including the composition of the wood-decay fungal community influence CO2 flux. CO2 flux from CWD was strongly and positively related to wood temperature and varied significantly between substrate types (logs vs. stumps). For five growing seasons after treatment, the CO2 flux of stumps reached rates up to seven times higher than that of logs. CO2 flux of logs did not differ significantly between canopy-gap and closed-canopy conditions in the fourth through seventh post-treatment growing seasons. By the seventh season, the seasonal carbon flux of both logs and stumps had decreased significantly from prior years. Linear mixed models indicated the variation in the wood inhabiting fungal community composition explained a significant portion of variability in the CO2 flux along with measures of substrate conditions. CO2 flux rates were inversely related to fungal diversity, with logs hosting more species but emitting less CO2 than stumps. Overall, our results suggest that the current treatment of CWD in dynamic forest carbon models may be oversimplified, thereby hampering our ability to predict realistic carbon fluxes associated with wood decomposition.


Subject(s)
Carbon Cycle , Carbon/analysis , Forests , Carbon/metabolism , Carbon Dioxide/analysis , Carbon Dioxide/metabolism , Fungi , Trees/microbiology , Wood/microbiology
8.
Leukemia ; 29(9): 1857-67, 2015 Sep.
Article in English | MEDLINE | ID: mdl-25801911

ABSTRACT

Diffuse large B-cell lymphoma (DLBCL) is a hematological cancer associated with an aggressive clinical course. The predominant subtypes of DLBCL display features of chronic or tonic B-cell antigen receptor (BCR) signaling. However, it is not known whether the spatial organization of the BCR contributes to the regulation of pro-survival signaling pathways and cell growth. Here, we show that primary DLBCL tumors and patient-derived DLBCL cell lines contain high levels of phosphorylated Ezrin-Radixin-Moesin (ERM) proteins. The surface BCRs in both activated B cell and germinal B cell subtype DLBCL cells co-segregate with phosphoERM suggesting that the cytoskeletal network may support localized BCR signaling and contribute to pathogenesis. Indeed, ablation of membrane-cytoskeletal linkages by dominant-negative mutants, pharmacological inhibition and knockdown of ERM proteins disrupted cell surface BCR organization, inhibited proximal and distal BCR signaling, and reduced the growth of DLBCL cell lines. In vivo administration of the ezrin inhibitor retarded the growth of DLBCL tumor xenografts, concomitant with reduction in intratumor phosphoERM levels, dampened pro-survival signaling and induction of apoptosis. Our results reveal a novel ERM-based spatial mechanism that is coopted by DLBCL cells to sustain tumor cell growth and survival.


Subject(s)
DNA-Binding Proteins/metabolism , Lymphoma, Large B-Cell, Diffuse/metabolism , Lymphoma, Large B-Cell, Diffuse/pathology , Receptors, Antigen, B-Cell/metabolism , Signal Transduction , Transcription Factors/metabolism , Animals , Apoptosis , Biopsy , Cell Line, Tumor , Cell Proliferation/drug effects , DNA-Binding Proteins/antagonists & inhibitors , Disease Models, Animal , Female , Heterografts , Humans , Immunohistochemistry , Lymphoma, Large B-Cell, Diffuse/genetics , Mice , Microvilli/metabolism , Phenols/pharmacology , Phosphorylation/drug effects , Protein Binding , Protein Transport , Quinolones/pharmacology , Signal Transduction/drug effects , Transcription Factors/antagonists & inhibitors , Tumor Burden/drug effects
9.
Nervenarzt ; 85(12): 1561-8, 2014 Dec.
Article in German | MEDLINE | ID: mdl-25431126

ABSTRACT

BACKGROUND: Deep brain stimulation (DBS) has become a reliable method in the treatment of movement disorders, e.g. idiopathic Parkinson's disease (IPD) and is technically based on stereotaxy. The Starfix® platform is a new type of stereotactic frame that allows an individualized and patient-optimized therapeutic regimen in IPD. OBJECTIVES: The aim of this study was to retrospectively compare the outcomes of IPD patients who underwent surgery with the use of conventional stereotactic frames (31 patients) to those who underwent implantation of DBS with the use of Starfix® frames (29 patients). MATERIAL AND METHODS: Surgery time, the unified Parkinson's disease rating scale III (UPDRS/III) score, L-dopa and L-dopa equivalent doses (LED) were compared prior to surgery as well as 4 weeks, 12 weeks, 6 months and 1 year postoperatively. RESULTS: The IPD-related symptoms improved significantly in both groups with respect to the UPDRS III score (conventional 69.6% vs. 72.4% Starfix®). After surgery significant reductions of L-dopa and LED were seen in both groups. Inherent advantages of the Starfix® platform included simultaneous positioning of the stimulating electrodes and a significant reduction in surgical time. CONCLUSION: In summary, both stereotactic procedures are reliable and safe procedures for the placement of stimulating electrodes as well as the stimulation effect achieved. The logistical uncoupling of presurgical planning from surgical therapy emphasizes the benefits of the individualized stereotactic procedure.


Subject(s)
Deep Brain Stimulation/instrumentation , Deep Brain Stimulation/methods , Electrodes, Implanted , Movement Disorders/therapy , Parkinson Disease/therapy , Prosthesis Implantation/instrumentation , Stereotaxic Techniques/instrumentation , Adult , Aged , Equipment Design , Equipment Failure Analysis , Female , Humans , Longitudinal Studies , Male , Middle Aged , Movement Disorders/etiology , Parkinson Disease/complications , Prosthesis Implantation/methods , Treatment Outcome
10.
Am J Physiol Heart Circ Physiol ; 306(8): H1246-52, 2014 Apr 15.
Article in English | MEDLINE | ID: mdl-24531807

ABSTRACT

Recent studies suggest that the signal molecules cAMP and cGMP have antifibrotic effects by negatively regulating pathways associated with fibroblast to myofibroblast (MyoCF) conversion. The phosphodiesterase 2 (PDE2) has the unique property to be stimulated by cGMP, which leads to a remarkable increase in cAMP hydrolysis and thus mediates a negative cross-talk between both pathways. PDE2 has been recently investigated in cardiomyocytes; here we specifically addressed its role in fibroblast conversion and cardiac fibrosis. PDE2 is abundantly expressed in both neonatal rat cardiac fibroblasts (CFs) and cardiomyocytes. The overexpression of PDE2 in CFs strongly reduced basal and isoprenaline-induced cAMP synthesis, and this decrease was sufficient to induce MyoCF conversion even in the absence of exogenous profibrotic stimuli. Functional stress-strain experiments with fibroblast-derived engineered connective tissue (ECT) demonstrated higher stiffness in ECTs overexpressing PDE2. In regard to cGMP, neither basal nor atrial natriuretic peptide-induced cGMP levels were affected by PDE2, whereas the response to nitric oxide donor sodium nitroprusside was slightly but significantly reduced. Interestingly, despite persistently depressed cAMP levels, both cGMP-elevating stimuli were able to completely prevent the PDE2-induced MyoCF phenotype, arguing for a double-tracked mechanism. In conclusion, PDE2 accelerates CF to MyoCF conversion, which leads to greater stiffness in ECTs. Atrial natriuretic peptide- and sodium nitroprusside-mediated cGMP synthesis completely reverses PDE2-induced fibroblast conversion. Thus PDE2 may augment cardiac remodeling, but this effect can also be overcome by enhanced cGMP. The redundant role of cAMP and cGMP as antifibrotic meditators may be viewed as a protective mechanism in heart failure.


Subject(s)
Cyclic AMP/metabolism , Cyclic GMP/physiology , Cyclic Nucleotide Phosphodiesterases, Type 2/physiology , Myocardium/cytology , Myofibroblasts/physiology , Signal Transduction/physiology , Animals , Animals, Newborn , Atrial Natriuretic Factor/pharmacology , Cells, Cultured , Cyclic Nucleotide Phosphodiesterases, Type 2/genetics , Fibroblasts/drug effects , Fibroblasts/enzymology , Fibroblasts/physiology , Gene Expression , Hydrolysis , Myocytes, Cardiac/enzymology , Nitric Oxide Donors/pharmacology , Nitroprusside/pharmacology , Rats , Receptors, Adrenergic, beta/physiology
11.
Leukemia ; 28(7): 1486-93, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24406841

ABSTRACT

Pulmonary hypertension (PH) is a frequently under recognized complication of myelofibrosis (MF). The pathophysiology of PH in MF is unknown and no definitive therapies have been established. We studied 15 patients with MF-associated PH and compared their echocardiographic and PH relevant biomarkers (nitric oxide (NO), N-terminal pro-hormone of brain natriuretic peptide (NT-pro BNP), von Willebrand antigen (vWB), ristocetin-cofactor activity (RCA) and uric acid (UA)) pre- and post-ruxolitinib treatment. Ruxolitinib decreased the plasma levels of NT-pro BNP (73%; P=0.043), UA (60%), vWB (86%) and RCA (73%; P=0.036). Improvements in echocardiographic findings were also seen in 66% of patients (P=0.022). Furthermore, marked increase in NO compared with baseline (69.75 vs 40.1 picomolar (pM); P=0.001) was observed post-ruxolitinib therapy, whereas no changes were noted with conventional therapies. Treatment with ruxolitinib also resulted in the reduction of key cytokines (tumor necrosis factor alpha, interleukin-4 (IL-4), IL-6 and IL-8) and induction of interferon-gamma. Animal studies further supported the role of ruxolitinib in the induction of NO levels. In conclusion, aberrant Janus kinase (JAK)-signal transducer and activator of transcription signaling in MF may mediate PH through dysregulation of NO and cytokine levels, which can be restored by therapy with JAK inhibitors suggesting that inhibition of this pathway is a novel target for the management of patients with PH.


Subject(s)
Hypertension, Pulmonary/drug therapy , Hypertension, Pulmonary/etiology , Primary Myelofibrosis/complications , Pyrazoles/therapeutic use , Aged , Aged, 80 and over , Animals , Biomarkers/blood , Cytokines/blood , Disease Models, Animal , Echocardiography , Female , Ferritins/blood , Humans , Hypertension, Pulmonary/diagnosis , Janus Kinases/antagonists & inhibitors , Male , Mice, Knockout , Middle Aged , Nitric Oxide/blood , Nitriles , Primary Myelofibrosis/blood , Primary Myelofibrosis/genetics , Pyrimidines
12.
Oncogene ; 33(24): 3195-204, 2014 Jun 12.
Article in English | MEDLINE | ID: mdl-23851499

ABSTRACT

The non-receptor tyrosine kinase Src is a major player in multiple physiological responses including growth, survival and differentiation. Overexpression and/or oncogenic mutation in the Src gene have been documented in human tumors. The v-Src protein is an oncogenic mutant of Src, which promotes cell survival, migration, invasion and division. GRIM-19 is an antioncogene isolated using a genome-wide knockdown screen. Genes associated with Retinoid-IFN-induced Mortality (GRIM)-19 binds to transcription factor STAT3 and ablates its pro-oncogenic effects while v-Src activates STAT3 to promote its oncogenic effects. However, we found that GRIM-19 inhibits the pro-oncogenic effects of v-Src independently of STAT3. Here, we report the identification of functionally inactivating GRIM-19 mutations in a set of head and neck cancer patients. While wild-type GRIM-19 strongly ablated v-Src-induced cell migration, cytoskeletal remodeling and tumor metastasis, the tumor-derived mutants (L(71)P, L(91)P and A(95)T) did not. These mutants were also incapable of inhibiting the drug resistance of v-Src-transformed cells. v-Src downregulated the expression of Pag1, a lipid raft-associated inhibitor of Src, which was restored by wild-type GRIM-19. The tumor-derived mutant GRIM-19 proteins failed to upregulate Pag1. These studies show a novel mechanism that deregulates Src activity in cancer cells.


Subject(s)
Apoptosis Regulatory Proteins/genetics , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/pathology , Cell Transformation, Neoplastic/pathology , Mouth Neoplasms/genetics , Mouth Neoplasms/pathology , Mutation/genetics , NADH, NADPH Oxidoreductases/genetics , Oncogene Protein pp60(v-src)/metabolism , Animals , Apoptosis , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Blotting, Western , Cell Movement , Cell Proliferation , Fluorescent Antibody Technique , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Immunoenzyme Techniques , Mice , Mice, Nude , Oligonucleotide Array Sequence Analysis , Oncogene Protein pp60(v-src)/genetics , Phosphorylation , RNA, Messenger/genetics , Rats , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , STAT3 Transcription Factor/genetics , STAT3 Transcription Factor/metabolism , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
13.
Int J Mol Med ; 32(1): 158-64, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23652584

ABSTRACT

In this study, we examined cardiac inflammation, fibrosis and left ventricular (LV) function during the development of streptozotocin (STZ)-induced diabetic cardiomyopathy using an animal model of diabetes mellitus (DM). Diabetes was induced in 22 Sprague­Dawley rats by an intraperitoneal single injection of STZ (70 mg/kg). Non-diabetic animals served as the controls (n=6). LV function was documented using the conductance catheter technique 2 and 6 weeks after the induction of diabetes. Cardiac tissue was analyzed for cardiac immune cell infiltration, oxidative stress and remodeling in rats with STZ-induced diabetes at 2 different time points by immunohistochemistry. Cardiac function was significantly impaired in the diabetic animals. After 2 weeks, the induction of diabetes resulted in impaired cardiac function indexed by a decrease in systolic and diastolic LV function. This impairment of LV performance continued for up to 6 weeks after the STZ injection. This was associated with an increase in cardiac CD3+ and CD8a+ immune cell invasion and fibrosis, indexed by an increase in collagen content (p<0.05). Furthermore, oxidative stress response and matrix remodeling were increased after 2 weeks and this continued for up to 6 weeks after the induction of diabetes. In conclusion, cardiac dysfunction is associated with cardiac inflammation and adverse remodeling in experimental diabetic cardiomyopathy. Our results suggest that the model of STZ-induced diabetic cardiomyopathy is a robust model for investigating cardiac immune response and LV remodeling processes under diabetic conditions.


Subject(s)
Antibiotics, Antineoplastic/adverse effects , Diabetic Cardiomyopathies/chemically induced , Diabetic Cardiomyopathies/pathology , Inflammation/pathology , Streptozocin/adverse effects , Ventricular Remodeling , Animals , Diabetes Mellitus, Experimental , Diabetic Cardiomyopathies/immunology , Diabetic Cardiomyopathies/physiopathology , Extracellular Matrix/metabolism , Fibrosis , Hemodynamics , Inflammation/immunology , Oxidative Stress , Rats , Time Factors
14.
Oncogene ; 31(6): 776-86, 2012 Feb 09.
Article in English | MEDLINE | ID: mdl-21725364

ABSTRACT

In clear-cell renal cell carcinoma (ccRCC), inactivation of the tumor suppressor von Hippel-Lindau (VHL) occurs in the majority of the tumors and is causal for the pathogenesis of ccRCC. Recently, a large-scale genomic sequencing study of ccRCC tumors revealed that enzymes that regulate histone H3 lysine 4 trimethylation (H3K4Me3), such as JARID1C/KDM5C/SMCX and MLL2, were mutated in ccRCC tumors, suggesting that H3K4Me3 might have an important role in regulating gene expression and tumorigenesis. In this study we report that in VHL-deficient ccRCC cells, the overall H3K4Me3 levels were significantly lower than that of VHL+/+ counterparts. Furthermore, this was hypoxia-inducible factor (HIF) dependent, as depletion of HIF subunits by small hairpin RNA in VHL-deficient ccRCC cells restored H3K4Me3 levels. In addition, we demonstrated that only loss of JARID1C, not JARID1A or JARID1B, abolished the difference of H3K4Me3 levels between VHL-/- and VHL+/+ cells, and JARID1C displayed HIF-dependent expression pattern. JARID1C in VHL-/- cells was responsible for the suppression of HIF-responsive genes insulin-like growth factor-binding protein 3 (IGFBP3), DNAJC12, COL6A1, growth and differentiation factor 15 (GDF15) and density-enhanced phosphatase 1. Consistent with these findings, the H3K4Me3 levels at the promoters of IGFBP3, DNAJC12, COL6A1 and GDF15 were lower in VHL-/- cells than in VHL+/+ cells, and the differences disappeared after JARID1C depletion. Although HIF2α is an oncogene in ccRCC, some of its targets might have tumor suppressive activity. Consistent with this, knockdown of JARID1C in 786-O VHL-/- ccRCC cells significantly enhanced tumor growth in a xenograft model, suggesting that JARID1C is tumor suppressive and its mutations are tumor promoting in ccRCC. Thus, VHL inactivation decreases H3K4Me3 levels through JARID1C, which alters gene expression and suppresses tumor growth.


Subject(s)
Carcinoma, Renal Cell/metabolism , Kidney Neoplasms/metabolism , Oxidoreductases, N-Demethylating/metabolism , Von Hippel-Lindau Tumor Suppressor Protein/metabolism , Animals , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Blotting, Western , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/pathology , Cell Line, Tumor , Cell Proliferation , Collagen Type VI/genetics , Collagen Type VI/metabolism , Gene Expression Regulation, Neoplastic , HEK293 Cells , Histone Demethylases , Histones/metabolism , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Insulin-Like Growth Factor Binding Protein 3/genetics , Insulin-Like Growth Factor Binding Protein 3/metabolism , Kidney Neoplasms/genetics , Kidney Neoplasms/pathology , Lysine/metabolism , Methylation , Mice , Mice, Nude , Mutation , Oxidoreductases, N-Demethylating/genetics , RNA Interference , Reverse Transcriptase Polymerase Chain Reaction , Transplantation, Heterologous , Tumor Burden , Von Hippel-Lindau Tumor Suppressor Protein/genetics
15.
Cell Death Differ ; 18(5): 829-40, 2011 May.
Article in English | MEDLINE | ID: mdl-21127501

ABSTRACT

Malignant gliomas are lethal cancers that display cellular hierarchies with cancer stem cells at the apex. Glioma stem cells (GSCs) are not uniformly distributed, but rather located in specialized niches, suggesting that the cancer stem cell phenotype is regulated by the tumor microenvironment. Indeed, recent studies show that hypoxia and its molecular responses regulate cancer stem cell maintenance. We now demonstrate that acidic conditions, independent of restricted oxygen, promote the expression of GSC markers, self-renewal and tumor growth. GSCs exert paracrine effects on tumor growth through elaboration of angiogenic factors, and low pH conditions augment this expression associated with induction of hypoxia inducible factor 2α (HIF2α), a GSC-specific regulator. Induction of HIF2α and other GSC markers by acidic stress can be reverted by elevating pH in vitro, suggesting that raising intratumoral pH may be beneficial for targeting the GSC phenotype. Together, our results suggest that exposure to low pH promotes malignancy through the induction of a cancer stem cell phenotype, and that culturing cancer cells at lower pH reflective of endogenous tumor conditions may better retain the cellular heterogeneity found in tumors.


Subject(s)
Brain Neoplasms/pathology , Glioma/pathology , Neoplastic Stem Cells/pathology , Acidosis , Angiogenesis Inducing Agents/metabolism , Antigens, Differentiation/metabolism , Basic Helix-Loop-Helix Transcription Factors/genetics , Basic Helix-Loop-Helix Transcription Factors/metabolism , Biomarkers, Tumor/metabolism , Brain Neoplasms/metabolism , Gene Expression Regulation, Neoplastic , Glioma/metabolism , Glucose Transporter Type 1/genetics , Homeodomain Proteins/metabolism , Humans , Hydrogen-Ion Concentration , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Nanog Homeobox Protein , Neoplasm Transplantation , Neoplastic Stem Cells/metabolism , Nerve Tissue Proteins/metabolism , Octamer Transcription Factor-3/metabolism , Oligodendrocyte Transcription Factor 2 , Phenotype , Serpins/genetics , Stress, Physiological , Transcription, Genetic , Tumor Microenvironment/physiology , Vascular Endothelial Growth Factor A/genetics , Vascular Endothelial Growth Factor A/metabolism
16.
Protein Pept Lett ; 17(5): 605-9, 2010 May.
Article in English | MEDLINE | ID: mdl-19689227

ABSTRACT

We describe the recombinant production of the human Y(1) receptor from inclusion bodies of E. coli cultures. The in vitro refolding was carried out in the presence of lipids from bovine brain extracts. Y(1) receptors in brain lipids compete for cellular receptors in competitive binding experiments.


Subject(s)
Membrane Lipids/metabolism , Receptors, Neuropeptide Y/metabolism , Recombinant Proteins/metabolism , Animals , Binding, Competitive , Brain Chemistry , Cattle , Cell Line, Tumor , Escherichia coli/genetics , Humans , Neuroblastoma , Neuropeptide Y/metabolism , Phosphorus Isotopes , Protein Folding , Receptors, Neuropeptide Y/chemistry , Receptors, Neuropeptide Y/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Swine , Tritium
17.
Oncogene ; 28(25): 2383-92, 2009 Jun 25.
Article in English | MEDLINE | ID: mdl-19430495

ABSTRACT

Inositol hexakisphosphate kinase 2 (IP6K2), a member of the inositol hexakisphosphate kinase family, functions as a growth suppressive and apoptosis-enhancing kinase during cell stress. We created mice with a targeted deletion of IP6K2; these mice display normal embryogenesis, development, growth and fertility. Chronic exposure to the carcinogen 4-nitroquinoline 1-oxide (4-NQO, a UV-mimetic compound) in drinking water resulted in fourfold increased incidence of invasive squamous cell carcinoma (SCC) formation in the oral cavity and esophagus of the knockout (KO) mice compared to the wild-type (WT) littermates. Paradoxically, KO mice displayed relative resistance to ionizing radiation and exhibit enhanced survival following 8-10 Gy total body irradiation. Primary KO fibroblasts displayed resistance to antiproliferative effects of interferon-beta and increased colony forming units following ionizing radiation. Radioresistance of KO fibroblasts was associated with accelerated DNA repair measured by comet assay. Direct microinjection of 5-PP-Ins(1,2,3,4,6)P(5) (the enzymatic product of IP6K2), but not InsP(6) (the substrate of IP6K2) induced cell death in SCC22A squamous carcinoma cells.


Subject(s)
Carcinoma, Squamous Cell/genetics , Esophageal Neoplasms/genetics , Gene Deletion , Genetic Predisposition to Disease/genetics , Mouth Neoplasms/genetics , Phosphotransferases (Phosphate Group Acceptor)/genetics , 4-Nitroquinoline-1-oxide/toxicity , Animals , Apoptosis , Carcinogens/toxicity , Carcinoma, Squamous Cell/radiotherapy , Female , Fibroblasts/cytology , Fibroblasts/metabolism , Fibroblasts/radiation effects , Gamma Rays , Gene Expression Profiling , Immunoblotting , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Microinjections , Radiation Tolerance , Radiation, Ionizing , Reverse Transcriptase Polymerase Chain Reaction
18.
Br J Cancer ; 100(8): 1287-91, 2009 Apr 21.
Article in English | MEDLINE | ID: mdl-19367285

ABSTRACT

Reliable surrogate markers of response to anticancer therapy remain a desirable tool for preclinical modelling and clinical practice in oncology. Clinical evaluation is relatively unreliable when attempting to assess rapidly and prospectively the outcome of treatment. Fluxes in released or circulating tumour marker levels are a useful but inconsistent marker of cytotoxic response. Serial measurement of circulating tumour cells appears to have some utility as a surrogate marker, but assay systems are expensive, and many cancers are not associated with the presence of circulating tumour cells. Because tissue breakdown is associated with release of nucleic acids and other cellular products, we reasoned that serial measurement of intra-tumoural pH may correlate with the extent of tumour lysis, and thus with outcomes of cytotoxic chemotherapy. Doxorubicin-sensitive and doxorubicin-resistant sublines of P388 murine monocytic leukaemia in C57BL/6 mice were treated with increasing concentrations of doxorubicin. Tumours were serially measured by conventional bi-dimensional methods and pH was sampled using a bevelled tip electrode. Mean and median pH changes were statistically different in responsive and resistant tumours, and amplitude of change correlated with long-term responses to doxorubicin. Serial sampling of pH in tumour masses may provide a useful surrogate of long-term response to chemotherapy.


Subject(s)
Antineoplastic Agents/therapeutic use , Biomarkers, Tumor/analysis , Hydrogen-Ion Concentration , Leukemia P388/drug therapy , Animals , Cell Division/drug effects , Cell Line, Tumor , Cyclophosphamide/therapeutic use , Doxorubicin/therapeutic use , Drug Resistance, Neoplasm , Drug Tolerance , Humans , Kinetics , Leukemia P388/pathology , Mice , Mice, Inbred C57BL
19.
Oncogene ; 28(10): 1339-47, 2009 Mar 12.
Article in English | MEDLINE | ID: mdl-19151760

ABSTRACT

GRIM-19 (Gene associated with Retinoid-Interferon-induced Mortality 19) is a novel tumor suppressor regulated by interferon/retinoid combination. We have recently shown that GRIM-19 inhibits v-Src-induced oncogenic transformation and metastatic behavior of cells. Oncogenic v-Src induces cell motility by cytoskeletal remodeling, especially the formation of podosomes and. Here, we show that GRIM-19 inhibited the v-Src-induced cell motility by inhibiting cytoskeletal remodeling, that is, podosome formation. We also show that the N terminus of GRIM-19 played a major role in this process and identified critical residues in this region. More importantly, we show that tumor-associated GRIM-19 mutations disrupted its ability to inhibit v-Src-induced cell motility. These actions appear to occur independently of STAT3, a known target of GRIM-19-mediated inhibition. Lastly, tumor-associated GRIM-19 mutants significantly lost their ability to control v-Src-induced metastases in vivo, indicating the biological and pathological significance of these observations.


Subject(s)
Cell Movement , Cytoskeleton/chemistry , NADH, NADPH Oxidoreductases/physiology , Oncogene Protein pp60(v-src)/antagonists & inhibitors , Animals , Cell Transformation, Neoplastic , Cortactin/metabolism , Mice , NADH, NADPH Oxidoreductases/chemistry , NADH, NADPH Oxidoreductases/genetics , Phosphorylation , Structure-Activity Relationship
20.
Oncogene ; 26(20): 2894-901, 2007 May 03.
Article in English | MEDLINE | ID: mdl-17130843

ABSTRACT

Ovarian cancer is a highly metastatic disease. Lysophosphatidic acid (LPA) levels are elevated in ascites from ovarian cancer patients, but its potential role in ovarian cancer metastasis has just begun to be revealed. In this work, we show that LPA stimulates invasion of primary ovarian cancer cells, but not ovarian epithelial or borderline ovarian tumor cells, although these benign cells indeed respond to LPA in cell migration. We have found that LPA downregulates tissue inhibitor of metalloproteinases (TIMPs). TIMP2 and TIMP3 play functional role in LPA-induced invasion as negative regulators. G(i) protein, phosphatidylinositol-3 kinase (PI3K), p38 mitogen-activated protein kinase (MAPK), cytosolic phospholipase A(2) and urokinase type plasminogen activator (uPA) are required for LPA-induced cells invasion. TIMP3 may affect two independent downstream targets, vascular endothelial growth factor receptor and p38 MAPK. In vivo, LPA stimulates tumor metastasis in an orthotopic ovarian tumor model, which can be inhibited by a PI3K inhibitor, LY294002. In summary, LPA is likely a key component for promoting ovarian metastasis in vivo. LPA downregulates TIMP3, which may have targets other than metalloproteinases. Our in vivo metastasis mouse model is useful for studying the efficacy of therapeutic regimes of ovarian cancer.


Subject(s)
Cell Movement/drug effects , Gene Expression Regulation, Neoplastic/drug effects , Lysophospholipids/pharmacology , Ovarian Neoplasms/genetics , Tissue Inhibitor of Metalloproteinases/genetics , Animals , Epithelial Cells/drug effects , Female , GTP-Binding Protein alpha Subunits, Gi-Go/metabolism , Humans , Mice , Neoplasm Invasiveness , Neoplasm Metastasis , Ovarian Neoplasms/pathology , Phosphatidylinositol 3-Kinases/metabolism , Phosphoinositide-3 Kinase Inhibitors , Tissue Inhibitor of Metalloproteinases/metabolism , Tumor Cells, Cultured , Xenograft Model Antitumor Assays , p38 Mitogen-Activated Protein Kinases/metabolism
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