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1.  Autophagy and Cancer 
(Macro)autophagy is a cellular membrane trafficking process that serves to deliver cytoplasmic constituents to lysosomes for degradation. At basal levels, it is critical for maintaining cytoplasmic as well as genomic integrity and is therefore key to maintaining cellular homeostasis. Autophagy is also highly adaptable and can be modified to digest specific cargoes to bring about selective effects in response to numerous forms of intracellular and extracellular stress. It is not a surprise, therefore, that autophagy has a fundamental role in cancer and that perturbations in autophagy can contribute to malignant disease. We review here the roles of autophagy in various aspects of tumor suppression including the response of cells to nutrient and hypoxic stress, the control of programmed cell death, and the connection to tumor-associated immune responses.
In healthy cells, autophagy protects against malignant disease by maintaining cellular homeostasis. However, upon transformation, activation of autophagy can promote and suppress cancer progression.
doi:10.1101/cshperspect.a008821
PMCID: PMC3249624  PMID: 22166310
2.  Senescence sensitivity of breast cancer cells is defined by positive feedback loop between CIP2A and E2F1 
Cancer discovery  2013;3(2):182-197.
Senescence induction contributes to cancer therapy responses and is crucial for p53-mediated tumor suppression. However, whether p53 inactivation actively suppresses senescence induction has been unclear. Here we demonstrate that E2F1 overexpression, due to p53 or p21 inactivation, promotes expression of human oncoprotein CIP2A, which in turn, by inhibiting PP2A activity, increases stabilizing serine 364 phosphorylation of E2F1. Several lines of evidence demonstrate that increased activity of E2F1-CIP2A feedback renders breast cancer cells resistant to senescence induction. Importantly, mammary tumorigenesis is impaired in a CIP2A deficient mouse model, and CIP2A deficient tumors display markers of senescence induction. Moreover, high CIP2A expression predicts for poor prognosis in a subgroup of breast cancer patients treated with senescence-inducing chemotherapy. Together these results implicate E2F1-CIP2A feedback loop as a key determinant of breast cancer cell sensitivity to senescence induction. It also constitutes a promising pro-senescence target for therapy of cancers with inactivated p53-p21 pathway.
doi:10.1158/2159-8290.CD-12-0292
PMCID: PMC3572190  PMID: 23306062
3.  Immunohistochemical detection of cytoplasmic LC3 puncta in human cancer specimens 
Autophagy  2012;8(8):1175-1184.
Autophagy is an evolutionarily conserved catabolic process that involves the entrapment of cytoplasmic components within characteristic vesicles for their delivery to and degradation within lysosomes. Alterations in autophagic signaling are found in several human diseases including cancer. Here, we describe a validated immunohistochemical protocol for the detection of LC3 puncta in human formalin-fixed, paraffin-embedded cancer specimens that can also be applied to mouse tissues. In response to systemic chemotherapy, autophagy-competent mouse tumors exhibited LC3 puncta, which did not appear in mouse cancers that had been rendered autophagy-deficient by the knockdown of Atg5 or Atg7. As compared with normal tissues, LC3 staining was moderately to highly elevated in the large majority of human cancers studied, albeit tumors of the same histological type tended to be highly heterogeneous in the number and intensity of LC3 puncta per cell. Moreover, tumor-infiltrating immune cells often were highly positive for LC3. Altogether, this protocol for LC3 staining appears suitable for the specific detection of LC3 puncta in human specimens, including tissue microarrays. We surmise that this technique can be employed for retrospective or prospective studies involving large series of human tumor samples.
doi:10.4161/auto.20353
PMCID: PMC3973657  PMID: 22647537
autophagosomes; CT26; immunohistochemistry; lysosomes; macroautophagy; MCA205
4.  [No title available] 
Panelists will provide brief overviews of new developments and products related to image processing as well as discuss the ethical implications of image manipulation. (1) Kevin Ryan will discuss the advantages and disadvantages of deconvolution versus other techniques, e.g., how do you decide which method to use for a particular sample or experiment system? He will also describe acquisition equipment and criteria for the best deconvolution results. (2) Ed Rader will discuss the Custom Analysis function in MetaMorph NX software, covering tools available in the latest version of the NX software to create your own custom analysis. (3) Meredith Price will describe how Imaris software has continued to provide users with high quality 3D/4D image renderings, reconstructions, and measurements. Bitplane's recent addition of the Vantage view to the Imaris product line now gives users the ability to plot their results using Imaris' reconstructions allowing both the analysis and interpretation of results within Imaris. (4) Doug Cromey will discuss the pitfalls of image analysis that can affect the usefulness of the data and even raise ethical concerns. He will describe best practices that include consistency in sample preparation and image acquisition, protecting and archiving the raw data, and documenting how the images were acquired and manipulated. He will also address important technical issues that also need to be considered to avoid error (e.g., cautions with image processing software tools, calibration and standards, sampling issues, avoiding lossy file compression).
PMCID: PMC3635271
5.  Dose-dependent effects of vitamin D on transdifferentiation of skeletal muscle cells to adipose cells 
The Journal of Endocrinology  2013;217(1):45-58.
Fat infiltration within muscle is one of a number of features of vitamin D deficiency, which leads to a decline in muscle functionality. The origin of this fat is unclear, but one possibility is that it forms from myogenic precursor cells present in the muscle, which transdifferentiate into mature adipocytes. The current study examined the effect of the active form of vitamin D3, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), on the capacity of the C2C12 muscle cell line to differentiate towards the myogenic and adipogenic lineages. Cells were cultured in myogenic or adipogenic differentiation media containing increasing concentrations (0, 10−13, 10−11, 10−9, 10−7 or 10−5 M) of 1,25(OH)2D3 for up to 6 days and markers of muscle and fat development were measured. Mature myofibres were formed in both adipogenic and myogenic media, but fat droplets were only observed in adipogenic media. Relative to controls, low physiological concentrations (10−13 and 10−11 M) of 1,25(OH)2D3 increased fat droplet accumulation, whereas high physiological (10−9 M) and supraphysiological concentrations (≥10−7 M) inhibited fat accumulation. This increased accumulation of fat with low physiological concentrations (10−13 and 10−11 M) was associated with a sequential up-regulation of Pparγ2 (Pparg) and Fabp4 mRNA, indicating formation of adipocytes, whereas higher concentrations (≥10−9 M) reduced all these effects, and the highest concentration (10−5 M) appeared to have toxic effects. This is the first study to demonstrate dose-dependent effects of 1,25(OH)2D3 on the transdifferentiation of muscle cells into adipose cells. Low physiological concentrations (possibly mimicking a deficient state) induced adipogenesis, whereas higher (physiological and supraphysiological) concentrations attenuated this effect.
doi:10.1530/JOE-12-0234
PMCID: PMC3600570  PMID: 23328072
myogenesis; adipogenesis; vitamin D; transdifferentiation
6.  Circularized synthetic oligodeoxynucleotides serve as promoterless RNA polymerase III templates for small RNA generation in human cells 
Nucleic Acids Research  2012;41(4):2552-2564.
Synthetic RNA formulations and viral vectors are the two main approaches for delivering small therapeutic RNA to human cells. Here we report findings supporting an alternative strategy in which an endogenous human RNA polymerase (RNAP) is harnessed to make RNA hairpin-containing small RNA from synthetic single-stranded DNA oligonucleotides. We report that circularizing a DNA template strand encoding a pre-microRNA hairpin mimic can trigger its circumtranscription by human RNAP III in vitro and in human cells. Sequence and secondary structure preferences that appear to promote productive transcription are described. The circular topology of the template is required for productive transcription, at least in part, to stabilize the template against exonucleases. In contrast to bacteriophage and Escherichia coli RNAPs, human RNAPs do not carry out rolling circle transcription on circularized templates. While transfected DNA circles distribute between the nucleus and cytosol, their transcripts are found mainly in the cytosol. Circularized oligonucleotides are synthetic, free of the hazards of viral vectors and maintain small RNA information in a stable form that RNAP III can access in a cellular context with, in some cases, near promoter-like precision and biologically relevant efficiency.
doi:10.1093/nar/gks1334
PMCID: PMC3575851  PMID: 23275570
7.  The cyclin-dependent kinase PITSLRE/CDK11 is required for successful autophagy 
Autophagy  2011;7(11):1295-1301.
(Macro)autophagy is a membrane-trafficking process that serves to sequester cellular constituents in organelles termed autophagosomes, which target their degradation in the lysosome. Autophagy operates at basal levels in all cells where it serves as a homeostatic mechanism to maintain cellular integrity. The levels and cargoes of autophagy can, however, change in response to a variety of stimuli, and perturbations in autophagy are known to be involved in the etiology of various human diseases. Autophagy must therefore be tightly controlled. We report here that the Drosophila cyclindependent kinase PITSLRE is a modulator of autophagy. Loss of the human PITSLRE ortholog, CDK11, initially appears to induce autophagy, but at later time points CDK11 is critically required for autophagic flux and cargo digestion. Since PITSLRE/CDK11 regulates autophagy in both Drosophila and human cells, this kinase represents a novel phylogenetically conserved component of the autophagy machinery.
doi:10.4161/auto.7.11.16646
PMCID: PMC3242795  PMID: 21808150
PITSLRE; CDK11; cyclin-dependent kinase; autophagy; human; Drosophila
8.  MDM2 promotes SUMO-2/3 modification of p53 to modulate transcriptional activity 
Cell Cycle  2011;10(18):3176-3188.
The tumor suppressor p53 is extensively regulated by post-translational modification, including modification by the small ubiquitin-related modifier SUMO. We show here that MDM2, previously shown to promote ubiquitin, Nedd8 and SUMO-1 modification of p53, can also enhance conjugation of endogenous SUMO-2/3 to p53. Sumoylation activity requires p53-MDM2 binding but does not depend on an intact RING finger. Both ARF and L11 can promote SUMO-2/3 conjugation of p53. However, unlike the previously described SUMO-1 conjugation of p53 by an MDM2-ARF complex, this activity does not depend on the ability of MDM2 to relocalize to the nucleolus. Interestingly, the SUMO consensus is not conserved in mouse p53, which is therefore not modified by SUMO-2/3. Finally, we show that conjugation of SUMO-2/3 to p53 correlates with a reduction of both activation and repression of a subset of p53-target genes.
doi:10.4161/cc.10.18.17436
PMCID: PMC3218624  PMID: 21900752
p53; SUMO-2/3; sumoylation; MDM2; ARF; L11
9.  Structure of HIV-1 Reverse Transcriptase with the Inhibitor β-thujaplicinol Bound at the RNase H Active Site 
Structure(London, England:1993)  2009;17(12):1625-1635.
Summary
Novel inhibitors are needed to counteract the rapid emergence of drug-resistant HIV variants. HIV-1 reverse transcriptase (RT) has both DNA polymerase and RNase H (RNH) enzymatic activities, but approved drugs that inhibit RT target the polymerase. Inhibitors that act against new targets, like RNH, would be effective against all of the current drug-resistant variants. Here, we present 2.80 Å and 2.04 Å resolution crystal structures of an RNH inhibitor, β-thujaplicinol, bound at the RNH active site of both HIV-1 RT and an isolated RNH domain. β-thujaplicinol chelates two divalent metal ions at the RNH active site. We provide biochemical evidence that β-thujaplicinol is a slow-binding RNH inhibitor with non-competitive kinetics and suggest that it forms a tropylium ion that interacts favorably with RT and the RNA:DNA substrate.
doi:10.1016/j.str.2009.09.016
PMCID: PMC3365588  PMID: 20004166
10.  Analysis of macroautophagy by immunohistochemistry 
Autophagy  2012;8(6):963-969.
(Macro)Autophagy is a phylogenetically conserved membrane-trafficking process that functions to deliver cytoplasmic cargoes to lysosomes for digestion. The process is a major mechanism for turnover of cellular constituents and is therefore critical for maintaining cellular homeostasis. Macroautophagy is characteristically distinct from other forms of autophagy due to the formation of double-membraned vesicles termed autophagosomes which encapsulate cargoes prior to fusion with lysosomes. Autophagosomes contain an integral membrane-bound form (LC3-II) of the microtubule-associated protein 1 light chain 3 β (MAP1LC3B), which has become a gold-standard marker to detect accumulation of autophagosomes and thereby changes in macroautophagy. Due to the role played by macroautophagy in various diseases, the detection of autophagosomes in tissue sections is frequently desired. To date, however, the detection of endogenous LC3-II on paraffin-embedded tissue sections has proved problematic. We report here a simple, optimized and validated method for the detection of LC3-II by immunohistochemistry in human and mouse tissue samples that we believe will be a useful resource for those wishing to study macroautophagy ex vivo.
doi:10.4161/auto.20186
PMCID: PMC3427261  PMID: 22562096
autophagy; LC3; tissue sections; immunohistochemistry
11.  Inhibition of autophagy impairs tumor cell invasion in an organotypic model 
Cell Cycle  2012;11(10):2022-2029.
Autophagy is a membrane-trafficking process that delivers cytoplasmic constituents to lysosomes for degradation. It contributes to energy and organelle homeostasis and the preservation of proteome and genome integrity. Although a role in cancer is unquestionable, there are conflicting reports that autophagy can be both oncogenic and tumor suppressive, perhaps indicating that autophagy has different roles at different stages of tumor development. In this report, we address the role of autophagy in a critical stage of cancer progression—tumor cell invasion. Using a glioma cell line containing an inducible shRNA that targets the essential autophagy gene Atg12, we show that autophagy inhibition does not affect cell viability, proliferation or migration but significantly reduces cellular invasion in a 3D organotypic model. These data indicate that autophagy may play a critical role in the benign to malignant transition that is also central to the initiation of metastasis.
doi:10.4161/cc.20424
PMCID: PMC3359125  PMID: 22580450
autophagy; cancer; invasion; migration; organotypic model
12.  p53-mediated transcriptional regulation and activation of the actin cytoskeleton regulatory RhoC to LIMK2 signaling pathway promotes cell survival 
Cell Research  2010;21(4):666-682.
The central arbiter of cell fate in response to DNA damage is p53, which regulates the expression of genes involved in cell cycle arrest, survival and apoptosis. Although many responses initiated by DNA damage have been characterized, the role of actin cytoskeleton regulators is largely unknown. We now show that RhoC and LIM kinase 2 (LIMK2) are direct p53 target genes induced by genotoxic agents. Although RhoC and LIMK2 have well-established roles in actin cytoskeleton regulation, our results indicate that activation of LIMK2 also has a pro-survival function following DNA damage. LIMK inhibition by siRNA-mediated knockdown or selective pharmacological blockade sensitized cells to radio- or chemotherapy, such that treatments that were sub-lethal when administered singly resulted in cell death when combined with LIMK inhibition. Our findings suggest that combining LIMK inhibitors with genotoxic therapies could be more efficacious than single-agent administration, and highlight a novel connection between actin cytoskeleton regulators and DNA damage-induced cell survival mechanisms.
doi:10.1038/cr.2010.154
PMCID: PMC3145139  PMID: 21079653
LIMK; RhoC; p53; DNA damage; actin; cofilin; cytoskeleton
13.  The Effects of Prenatal Protein Restriction on β-Adrenergic Signalling of the Adult Rat Heart during Ischaemia Reperfusion 
A maternal low-protein diet (MLP) fed during pregnancy leads to hypertension in adult rat offspring. Hypertension is a major risk factor for ischaemic heart disease. This study examined the capacity of hearts from MLP-exposed offspring to recover from myocardial ischaemia-reperfusion (IR) and related this to cardiac expression of β-adrenergic receptors (β-AR) and their associated G proteins. Pregnant rats were fed control (CON) or MLP diets (n = 12 each group) throughout pregnancy. When aged 6 months, hearts from offspring underwent Langendorff cannulation to assess contractile function during baseline perfusion, 30 min ischemia and 60 min reperfusion. CON male hearts demonstrated impaired recovery in left ventricular pressure (LVP) and dP/dtmax (P < 0.01) during reperfusion when compared to MLP male hearts. Maternal diet had no effect on female hearts to recover from IR. MLP males exhibited greater membrane expression of β2-AR following reperfusion and urinary excretion of noradrenaline and dopamine was lower in MLP and CON female rats versus CON males. In conclusion, the improved cardiac recovery in MLP male offspring following IR was attributed to greater membrane expression of β2-AR and reduced noradrenaline and dopamine levels. In contrast, females exhibiting both decreased membrane expression of β2-AR and catecholamine levels were protected from IR injury.
doi:10.1155/2012/397389
PMCID: PMC3321448  PMID: 22536490
14.  DRAM-1 encodes multiple isoforms that regulate autophagy 
Autophagy  2012;8(1):18-28.
Macro(autophagy) is a cellular mechanism which delivers cytoplasmic constituents to lysosomes for degradation. Due to its role in maintaining cellular integrity, autophagy protects against various diseases including cancer. p53 is a major tumor suppressor gene which can modulate autophagy both positively and negatively. p53 induces autophagy via transcriptional activation of damage-regulated autophagy modulator (DRAM-1). We report here that DRAM-1 encodes not just one mRNA, but a series of p53-inducible splice variants which are expressed at varying levels in multiple human and mouse cell lines. Two of these new splice variants, termed SV4 and SV5, result in mature mRNA species. Different from ‘full-length’ DRAM-1 (SV1), SV4 and SV5 do not localize to lysosomes or endosomes, but instead partially localize to peroxisomes and autophagosomes respectively. In addition, SV4 and SV5 can also be found co-localized with certain markers of the endoplasmic reticulum. Similar to SV1, SV4 and SV5 do not appear to be inducers of programmed cell death, but they do modulate autophagy. In summary, these findings identify new autophagy regulators that provide insight into the control of autophagy downstream of p53.
doi:10.4161/auto.8.1.18077
PMCID: PMC3335989  PMID: 22082963
DRAM-1; mRNA splice variants; p53; cell death; autophagy
15.  p53-mediated transcription and activation of the actin cytoskeleton regulatory RhoC to LIMK2 signaling pathway promotes cell survival 
Cell research  2010;21(4):666-682.
The central arbiter of cell fate in response to DNA damage is p53, which regulates the expression of genes involved in cell cycle arrest, survival and apoptosis. Although many responses initiated by DNA damage have been characterized, the role of actin cytoskeleton regulators is largely unknown. We now show that RhoC and LIMK2 are direct p53 target genes induced by genotoxic agents. Although RhoC and LIMK2 have well-established roles in actin cytoskeleton regulation, our results indicate that activation of LIMK2 also has a pro-survival function following DNA damage. LIMK inhibition by siRNA-mediated knockdown or selective pharmacological blockade sensitized cells to radio- or chemotherapy, such that treatments which were sub-lethal when administered singly resulted in cell death when combined with LIMK inhibition. Our findings suggest that combining LIMK inhibitors with genotoxic therapies could be more efficacious than single-agent administration, and highlight a novel connection between actin cytoskeleton regulators and DNA damage-induced cell survival mechanisms.
doi:10.1038/cr.2010.154
PMCID: PMC3145139  PMID: 21079653
LIMK; RhoC; p53; DNA damage; actin; cofilin; cytoskeleton
16.  Public Policy Versus Individual Rights in Childhood Obesity Interventions: Perspectives From the Arkansas Experience With Act 1220 of 2003 
Preventing Chronic Disease  2011;8(5):A96.
Childhood obesity is a major public health problem. Experts recommend that prevention and control strategies include population-based policies. Arkansas Act 1220 of 2003 is one such initiative and provides examples of the tensions between individual rights and public policy. We discuss concerns raised during the implementation of Act 1220 related to the 2 primary areas in which they emerged: body mass index measurement and reporting to parents and issues related to vending machine access. We present data from the evaluation of Act 1220 that have been used to address concerns and other research findings and conclude with a short discussion of the tension between personal rights and public policy. States considering similar policy approaches should address these concerns during policy development, involve multiple stakeholder groups, establish the legal basis for public policies, and develop consensus on key elements.
PMCID: PMC3181196  PMID: 21843426
17.  Circular Single-Stranded Synthetic DNA Delivery Vectors for MicroRNA 
PLoS ONE  2011;6(2):e16925.
Single-stranded (ss) circular oligodeoxynucleotides were previously found to undergo rolling circle transcription (RCT) by phage and bacterial RNA polymerases (RNAPs) into tandemly repetitive RNA multimers. Here, we redesign them to encode minimal primary miRNA mimics, with the long term aim of intracellular transcription followed by RNA processing and maturation via endogenous pathways. We describe an improved method for circularizing ss synthetic DNA for RCT by using a recently described thermostable RNA ligase, which does not require a splint oligonucleotide to juxtapose the ligating ends. In vitro transcription of four templates demonstrates that the secondary structure inherent in miRNA-encoding vectors does not impair their RCT by RNAPs previously shown to carry out RCT. A typical primary-miRNA rolling circle transcript was accurately processed by a human Drosha immunoprecipitate, indicating that if human RNAPs prove to be capable of RCT, the resulting transcripts should enter the endogenous miRNA processing pathway in human cells. Circular oligonucleotides are therefore candidate vectors for small RNA delivery in human cells, which express RNAPs related to those tested here.
doi:10.1371/journal.pone.0016925
PMCID: PMC3040211  PMID: 21359172
18.  The multiple roles of autophagy in cancer 
Carcinogenesis  2011;32(7):955-963.
Autophagy is an evolutionarily conserved, catabolic process that involves the entrapment of cytoplasmic components within characteristic vesicles for their delivery to and degradation within lysosomes. Autophagy is regulated via a group of genes called AuTophaGy-related genes and is executed at basal levels in virtually all cells as a homeostatic mechanism for maintaining cellular integrity. The levels and cargos of autophagy can be modulated in response to a variety of intra- and extracellular cues to bring about specific and selective events. Autophagy is a multifaceted process and alterations in autophagic signalling pathways are frequently found in cancer and many other diseases. During tumour development and in cancer therapy, autophagy has paradoxically been reported to have roles in promoting both cell survival and cell death. In addition, autophagy has been reported to control other processes relevant to the aetiology of malignant disease, including oxidative stress, inflammation and both innate and acquired immunity. It is the aim of this review to describe the molecular basis and the signalling events that control autophagy in mammalian cells and to summarize the cellular functions that contribute to tumourigenesis when autophagy is perturbed.
doi:10.1093/carcin/bgr031
PMCID: PMC3128556  PMID: 21317301
19.  Oncogene induced sensitization to chemotherapy-induced death requires induction as well as de-regulation of E2F1 
Cancer research  2010;70(10):4074-4080.
The analysis of DNA tumor viruses has provided landmark insights into the molecular pathogenesis of cancer. A paradigm for this field has been the study of the adenoviral E1a protein which has led to identification of proteins such as p300, p400 and members of the retinoblastoma family. Through binding Rb family members, E1a causes deregulation of E2F proteins – an event common to most human cancers and a central pathway in which oncogenes, including E1a, sensitize cells to chemotherapy-induced programmed cell death. We report here, however, that E1a not only causes deregulation of E2F, but importantly that it also causes the post-transcriptional up-regulation of E2F1 protein levels. This effect is distinct from deregulation of E2F1, however, as mutants of E2F1 impaired in pRb binding are induced by E1a and E2F1 induction can also be observed in Rb-null cells. Analysis of E1a mutants selectively deficient in cellular protein binding revealed that induction of E2F1 is instead intrinsically linked to p400. Mutants unable to bind p400, despite being able to deregulate E2F1, do not increase E2F1 protein levels and they do not sensitize cells to apoptotic death. These mutants can, however, be complemented by either knockdown of p400, resulting in restoration of the ability to induce E2F1, or by over expression of E2F1, with both events re-enabling sensitization to chemotherapy-induced death. Due to the frequent deregulation of E2F1 in human cancer, these studies reveal potentially important insights into E2F1-mediated chemotherapeutic responses that may aid the development of novel targeted therapies for malignant disease.
doi:10.1158/0008-5472.CAN-09-2876
PMCID: PMC2892306  PMID: 20460519
E2F1; E1a; apoptosis; protein-stability; p400
20.  Rolling Circle DNA Synthesis: Small Circular Oligonucleotides as Efficient Templates for DNA Polymerases 
We report that small, single-stranded circular DNA oligonucleotides 26 to 74 nucleotides (nt) in size can behave as catalytic templates for DNA synthesis by several DNA polymerase enzymes. The DNA products are repeating end-to-end multimeric copies of the synthetic circular DNAs, and range from 1 000 to > 12 000 nucleotides in length. Several aspects of this reaction are unusual: first, the synthesis proceeds efficiently despite the curvature and small size of the circles, some of which have diameters significantly smaller than that of the enzyme itself. Second, the synthesis can proceed hundreds of times around the circle, while rolling replication of larger circular plasmid DNAs requires other proteins for processive synthesis. Finally, the synthesis scheme produces multiple copies of the template without the requirement for either heating or cooling cycles and requires less than stoichiometric amounts of primer, unlike other DNA synthesis methods. We report on the scope of this reaction, and demonstrate that the multimeric products can be cleaved enzymatically to short, sequence-defined oligodeoxynucleotides. This new approach to DNA synthesis may be a practical way to produce useful repeating DNAs, and combined with DNA cleavage strategies, it may represent a useful enzymatic approach to short, sequence-defined oligodeoxynucleotides.
doi:10.1021/ja952786k
PMCID: PMC2935701  PMID: 20830216
21.  Discrimination of Saturated Aldehydes by the Rat I7 Olfactory Receptor 
Biochemistry  2010;49(30):6302-6304.
The discrimination of n-alkyl saturated aldehydes during the early stage of odorant recognition by the rat I7 olfactory receptor (OR-I7) is investigated. The concentrations of odorants necessary for 50% activation (or inhibition) of the OR-I7 are measured by calcium imaging recordings of dissociated rat olfactory sensory neurons, expressing recombinant OR-I7 from an adenoviral vector. These are correlated to the corresponding binding free energies computed for a homology structural model of OR-I7 built from the crystal structure of bovine visual rhodopsin at 2.2 Å resolution.
doi:10.1021/bi100976w
PMCID: PMC2912408  PMID: 20608641
22.  PUMA and Bax-induced Autophagy Contributes to Apoptosis 
Cell death and differentiation  2009;16(8):1135-1145.
The p53-inducible BH3-only protein PUMA is a key mediator of p53-dependent apoptosis, and PUMA has been shown to function by activating Bax and mitochondrial outer membrane permeabilization. In this study we describe an ability of PUMA to induce autophagy that leads to the selective removal of mitochondria. This function of PUMA depends on Bax/Bak and can be reproduced by overexpression of Bax. The induction of autophagy coincides with cytochrome c release, and taken together the results suggest that PUMA functions through Bax to induce mitochondrial autophagy in response to mitochondrial perturbations. Surprisingly, inhibition of PUMA or Bax-induced autophagy dampens the apoptotic response, suggesting that under some circumstances the selective targeting of mitochondria for autophagy can enhance apoptosis.
doi:10.1038/cdd.2009.28
PMCID: PMC2711052  PMID: 19300452
PUMA; Bax; autophagy
23.  The role of autophagy in tumour development and cancer therapy 
Autophagy is a catabolic membrane-trafficking process that leads to sequestration and degradation of intracellular material within lysosomes. It is executed at basal levels in every cell and promotes cellular homeostasis by regulating organelle and protein turnover. In response to various forms of cellular stress, however, the levels and cargoes of autophagy can be modulated. In nutrient-deprived states, for example, autophagy can be activated to degrade cargoes for cell-autonomous energy production to promote cell survival. In other contexts, in contrast, autophagy has been shown to contribute to cell death. Given these dual effects in regulating cell viability, it is no surprise that autophagy has implications in both the genesis and treatment of malignant disease. In this review, we provide a comprehensive appraisal of the way in which oncogenes and tumour suppressor genes regulate autophagy. In addition, we address the current evidence from human cancer and animal models that has aided our understanding of the role of autophagy in tumour progression. Finally, the potential for targeting autophagy therapeutically is discussed in light of the functions of autophagy at different stages of tumour progression and in normal tissues.
doi:10.1017/S1462399409001306
PMCID: PMC2811398  PMID: 19951459
24.  The Importance of Odorant Conformation to the Binding and Activation of a Representative Olfactory Receptor 
Chemistry & biology  2008;15(12):1317-1327.
SUMMARY
Olfactory receptors (ORs) form a large family of G-protein coupled receptor proteins (GPCRs) responsible for sensing the ambient chemical environment. The molecular recognition strategies used by ORs to detect and distinguish odorant molecules are unclear. Here, we investigated the variable of odorant carbon chain conformation for an established odorant-OR pair: n-octanal and rat OR-I7. A series of conformationally restricted octanal mimics were tested on live olfactory sensory neurons (OSNs). Our results support a model in which unactivated OR-I7 binds aliphatic aldehydes indiscriminately, and then applies conformational and length filters to distinguish agonists from antagonists. Specific conformers are proposed to activate OR-I7 by steric buttressing of an OR activation pocket. Probing endogenously expressed rat OSNs with octanal and constrained mimics furnished evidence that odorant conformation contributes to an odorant’s unique olfactory code signature.
doi:10.1016/j.chembiol.2008.10.014
PMCID: PMC2628580  PMID: 19101476
25.  Vorinostat and sorafenib increase ER stress, autophagy and apoptosis via ceramide-dependent CD95 and PERK activation 
Cancer biology & therapy  2008;7(10):1648-1662.
We recently noted that low doses of sorafenib and vorinostat interact in a synergistic fashion to kill carcinoma cells by activating CD95, and this drug combination is entering phase I trials. The present studies mechanistically extended our initial observations. Low doses of sorafenib and vorinostat, but not the individual agents, caused an acidic sphingomyelinase and fumonisin B1-dependent increase in CD95 surface levels and CD95 association with caspase 8. Knock down of CD95 or FADD expression reduced sorafenib/vorinostat lethality. Signaling by CD95 caused PERK activation that was responsible for both promoting caspase 8 association with CD95 and for increased eIF2α phosphorylation; suppression of eIF2α function abolished drug combination lethality. Cell killing was paralleled by PERK- and eIF2α-dependent lowering of c-FLIP-s protein levels and over-expression of c-FLIP-s maintained cell viability. In a CD95-, FADD- and PERK-dependent fashion, sorafenib and vorinostat increased expression of ATG5 that was responsible for enhanced autophagy. Expression of PDGFRβ and FLT3 were essential for high dose single agent sorafenib treatment to promote autophagy. Suppression of PERK function reduced sorafenib and vorinostat lethality whereas suppression of ATG5 levels elevated sorafenib and vorinostat lethality. Over-expression of c-FLIP-s blocked apoptosis and enhanced drug-induced autophagy. Thus sorafenib and vorinostat promote ceramide-dependent CD95 activation followed by induction of multiple downstream survival regulatory signals: ceramide-CD95-PERK-FADD-pro-caspase 8 (death); ceramide-CD95-PERK-eIF2α -↓c-FLIP-s (death); ceramide-CD95-PERK-ATG5-autophagy (survival).
PMCID: PMC2674577  PMID: 18787411
Vorinostat; Sorafenib; CD95; c-FLIP-s; PDGFRβ; FLT3; autophagy; ceramide; cell death; ASMase

Results 1-25 (35)