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1.
Am J Physiol Heart Circ Physiol ; 320(1): H52-H65, 2021 01 01.
Article in English | MEDLINE | ID: mdl-33373275

ABSTRACT

Vascular cells restructure extracellular matrix in response to aging or changes in mechanical loading. Here, we characterized collagen architecture during age-related aortic remodeling in atherosclerosis-prone mice. We hypothesized that changes in collagen fiber orientation reflect an altered balance between passive and active forces acting on the arterial wall. We examined two factors that can alter this balance, endothelial dysfunction and reduced smooth muscle cell (SMC) contractility. Collagen fiber organization was visualized by second-harmonic generation microscopy in aortic adventitia of apolipoprotein E (apoE) knockout (KO) mice at 6 wk and 6 mo of age on a chow diet and at 7.5 mo of age on a Western diet (WD), using image analysis to yield mean fiber orientation. Adventitial collagen fibers became significantly more longitudinally oriented with aging in apoE knockout mice on chow diet. Conversely, fibers became more circumferentially oriented with aging in mice on WD. Total collagen content increased significantly with age in mice fed WD. We compared expression of endothelial nitric oxide synthase and acetylcholine-mediated nitric oxide release but found no evidence of endothelial dysfunction in older mice. Time-averaged volumetric blood flow in all groups showed no significant changes. Wire myography of aortic rings revealed decreases in active stress generation with age that were significantly exacerbated in WD mice. We conclude that the aorta displays a distinct remodeling response to atherogenic stimuli, indicated by altered collagen organization. Collagen reorganization can occur in the absence of altered hemodynamics and may represent an adaptive response to reduced active stress generation by vascular SMCs.NEW & NOTEWORTHY The following major observations were made in this study: 1) aortic adventitial collagen fibers become more longitudinally oriented with aging in apolipoprotein E knockout mice fed a chow diet; 2) conversely, adventitial collagen fibers become more circumferentially oriented with aging in apoE knockout mice fed a high-fat diet; 3) adventitial collagen content increases significantly with age in mice on a high-fat diet; 4) these alterations in collagen organization occur largely in the absence of hemodynamic changes; and 5) circumferential reorientation of collagen is associated with decreased active force generation (contractility) in aged mice on a high-fat diet.


Subject(s)
Aorta, Abdominal/pathology , Aorta, Thoracic/pathology , Aortic Diseases/pathology , Atherosclerosis/pathology , Diet, Western , Fibrillar Collagens/metabolism , Vascular Remodeling , Age Factors , Animals , Aorta, Abdominal/metabolism , Aorta, Abdominal/physiopathology , Aorta, Thoracic/metabolism , Aorta, Thoracic/physiopathology , Aortic Diseases/genetics , Aortic Diseases/metabolism , Aortic Diseases/physiopathology , Atherosclerosis/genetics , Atherosclerosis/metabolism , Atherosclerosis/physiopathology , Disease Models, Animal , Female , Male , Mice, Knockout, ApoE , Vasoconstriction
2.
J Cardiovasc Dev Dis ; 7(2)2020 May 24.
Article in English | MEDLINE | ID: mdl-32456345

ABSTRACT

Transforming growth factor beta3 (TGFB3) gene mutations in patients of arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD1) and Loeys-Dietz syndrome-5 (LDS5)/Rienhoff syndrome are associated with cardiomyopathy, cardiac arrhythmia, cardiac fibrosis, cleft palate, aortic aneurysms, and valvular heart disease. Although the developing heart of embryos express Tgfb3, its overarching role remains unclear in cardiovascular development and disease. We used histological, immunohistochemical, and molecular analyses of Tgfb3-/- fetuses and compared them to wildtype littermate controls. The cardiovascular phenotypes were diverse with approximately two thirds of the Tgfb3-/- fetuses having one or more cardiovascular malformations, including abnormal ventricular myocardium (particularly of the right ventricle), outflow tract septal and alignment defects, abnormal aortic and pulmonary trunk walls, and thickening of semilunar and/or atrioventricular valves. Ventricular septal defects (VSD) including the perimembranous VSDs were observed in Tgfb3-/- fetuses with myocardial defects often accompanied by the muscular type VSD. In vitro studies using TGFß3-deficient fibroblasts in 3-D collagen lattice formation assays indicated that TGFß3 was required for collagen matrix reorganization. Biochemical studies indicated the 'paradoxically' increased activation of canonical (SMAD-dependent) and noncanonical (MAP kinase-dependent) pathways. TGFß3 is required for cardiovascular development to maintain a balance of canonical and noncanonical TGFß signaling pathways.

3.
J Neurochem ; 153(1): 33-50, 2020 04.
Article in English | MEDLINE | ID: mdl-31419307

ABSTRACT

It is important to monitor serotonin neurochemistry in the context of brain disorders. Specifically, a better understanding of biophysical alterations and associated biochemical functionality within subregions of the brain will enable better of understanding of diseases such as depression. Fast voltammetric tools at carbon fiber microelectrodes provide an opportunity to make direct evoked and ambient serotonin measurements in vivo in mice. In this study, we characterize novel stimulation and measurement circuitries for serotonin analyses in brain regions relevant to psychiatric disease. Evoked and ambient serotonin in these brain areas, the CA2 region of the hippocampus and the medial prefrontal cortex, are compared to ambient and evoked serotonin in the substantia nigra pars reticulata, an area well established previously for serotonin measurements with fast voltammetry. Stimulation of a common axonal location evoked serotonin in all three brain regions. Differences are observed in the serotonin release and reuptake profiles between these three brain areas which we hypothesize to arise from tissue physiology heterogeneity around the carbon fiber microelectrodes. We validate this hypothesis mathematically and via confocal imaging. We thereby show that fast voltammetric methods can provide accurate information about local physiology and highlight implications for chemical mapping. Cover Image for this issue: doi: 10.1111/jnc.14739.


Subject(s)
Brain/physiopathology , Electrochemical Techniques/methods , Mental Disorders/physiopathology , Serotonin/analysis , Serotonin/metabolism , Animals , Axons/physiology , Brain Chemistry/physiology , Carbon Fiber , Electric Stimulation , Evoked Potentials , Hippocampus/chemistry , Male , Medial Forebrain Bundle , Mice , Mice, Inbred C57BL , Microelectrodes , Models, Theoretical , Prefrontal Cortex/chemistry , Substantia Nigra/chemistry
4.
J Neuroimmune Pharmacol ; 15(2): 209-223, 2020 06.
Article in English | MEDLINE | ID: mdl-31802418

ABSTRACT

HIV-1 Associated Neurocognitive Disorder (HAND) is a common and clinically detrimental complication of HIV infection. Viral proteins, including Tat, released from infected cells, cause neuronal toxicity. Substance abuse in HIV-infected patients greatly influences the severity of neuronal damage. To repurpose small molecule inhibitors for anti-HAND therapy, we employed MOLIERE, an AI-based literature mining system that we developed. All human genes were analyzed and prioritized by MOLIERE to find previously unknown targets connected to HAND. From the identified high priority genes, we narrowed the list to those with known small molecule ligands developed for other applications and lacking systemic toxicity in animal models. To validate the AI-based process, the selective small molecule inhibitor of DDX3 helicase activity, RK-33, was chosen and tested for neuroprotective activity. The compound, previously developed for cancer treatment, was tested for the prevention of combined neurotoxicity of HIV Tat and cocaine. Rodent cortical cultures were treated with 6 or 60 ng/ml of HIV Tat and 10 or 25 µM of cocaine, which caused substantial toxicity. RK-33 at doses as low as 1 µM greatly reduced the neurotoxicity of Tat and cocaine. Transcriptome analysis showed that most Tat-activated transcripts are microglia-specific genes and that RK-33 blocks their activation. Treatment with RK-33 inhibits the Tat and cocaine-dependent increase in the number and size of microglia and the proinflammatory cytokines IL-6, TNF-α, MCP-1/CCL2, MIP-2, IL-1α and IL-1ß. These findings reveal that inhibition of DDX3 may have the potential to treat not only HAND but other neurodegenerative diseases. Graphical Abstract RK-33, selective inhibitor of Dead Box RNA helicase 3 (DDX3) protects neurons from combined Tat and cocaine neurotoxicity by inhibition of microglia activation and production of proinflammatory cytokines.


Subject(s)
Azepines/pharmacology , Cocaine/toxicity , DEAD-box RNA Helicases/antagonists & inhibitors , Imidazoles/pharmacology , Microglia/drug effects , tat Gene Products, Human Immunodeficiency Virus/toxicity , AIDS Dementia Complex/drug therapy , AIDS Dementia Complex/enzymology , Animals , Azepines/therapeutic use , Cells, Cultured , DEAD-box RNA Helicases/metabolism , Dopamine Uptake Inhibitors/toxicity , Dose-Response Relationship, Drug , Female , Imidazoles/therapeutic use , Male , Microglia/enzymology , Rats , Rats, Sprague-Dawley
5.
PLoS One ; 14(9): e0222001, 2019.
Article in English | MEDLINE | ID: mdl-31490998

ABSTRACT

A number of viruses and bacterial species have been implicated as contributors to atherosclerosis, potentially providing novel pathways for prevention. Epidemiological studies examining the association between Helicobacter pylori and cardiovascular disease have yielded variable results and no studies have been conducted in nonhuman primates. In this investigation, we examined the relationship between H. pylori infection and atherosclerosis development in socially housed, pre- and postmenopausal cynomolgus macaques consuming human-like diets. Ninety-four premenopausal cynomolgus monkeys (Macaca fascicularis) were fed for 36 months an atherogenic diet deriving its protein from either casein lactalbumin(CL) or high isoflavone soy (SOY). Animals were then ovariectomized and fed either the same or the alternate diet for an additional 36 months. Iliac artery biopsies were obtained at the time of ovariectomy and iliac and coronary artery sections were examined at the end of the study. Evidence of H. pylori infection was found in 64% of the monkeys and 46% of animals had live H. pylori within coronary atheromas as determined by mRNA-specific in situ hybridization. There was a significant linear relationship between the densities of gastric and atheroma organisms. Helicobactor pylori infection correlated with increased intimal plaque area and thickness at both the premenopausal and postmenopausal time points and regardless of diet (p< 0.01), although animals consuming the SOY diet throughout had the least amount of atherosclerosis. Additionally, plasma lipid profiles, intimal collagen accumulation, ICAM-1, and plaque macrophage densities were adversely affected by H. pylori infection among animals consuming the CL diet, while the SOY diet had the opposite effect. Plaque measurements were more highly associated with the densities of cagA-positive H. pylori within coronary atheromas than with the densities of gastric organisms, whereas plasma lipid changes were associated with H. pylori infection, but not cagA status. This study provides strong evidence that live H. pylori infects atheromas, exacerbates atherosclerotic plaque development, and alters plasma lipid profiles independently of diet or hormonal status. Finally, socially subordinate animals relative to their dominant counterparts had a greater prevalence of H. pylori, suggesting a stress effect. The results indicate that early H. pylori eradication could prevent or delay development of cardiovascular disease.


Subject(s)
Atherosclerosis , Diet , Helicobacter Infections , Helicobacter pylori , Postmenopause , Premenopause , Animals , Female , Arteries/metabolism , Arteries/pathology , Atherosclerosis/epidemiology , Atherosclerosis/etiology , Atherosclerosis/metabolism , Atherosclerosis/microbiology , Biomarkers/metabolism , Helicobacter Infections/complications , Helicobacter pylori/physiology , Lipids/blood , Macaca fascicularis , Prevalence
6.
Curr Biol ; 29(14): 2307-2321.e5, 2019 07 22.
Article in English | MEDLINE | ID: mdl-31303492

ABSTRACT

Systems consolidation is a process by which memories initially require the hippocampus for recent long-term memory (LTM) but then become increasingly independent of the hippocampus and more dependent on the cortex for remote LTM. Here, we study the role of phosphodiesterase 11A4 (PDE11A4) in systems consolidation. PDE11A4, which degrades cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), is preferentially expressed in neurons of CA1, the subiculum, and the adjacently connected amygdalohippocampal region. In male and female mice, deletion of PDE11A enhances remote LTM for social odor recognition and social transmission of food preference (STFP) despite eliminating or silencing recent LTM for those same social events. Measurement of a surrogate marker of neuronal activation (i.e., Arc mRNA) suggests the recent LTM deficits observed in Pde11 knockout mice correspond with decreased activation of ventral CA1 relative to wild-type littermates. In contrast, the enhanced remote LTM observed in Pde11a knockout mice corresponds with increased activation and altered functional connectivity of anterior cingulate cortex, frontal association cortex, parasubiculum, and the superficial layer of medial entorhinal cortex. The apparent increased neural activation observed in prefrontal cortex of Pde11a knockout mice during remote LTM retrieval may be related to an upregulation of the N-methyl-D-aspartate receptor subunits NR1 and NR2A. Viral restoration of PDE11A4 to vCA1 alone is sufficient to rescue both the LTM phenotypes and upregulation of NR1 exhibited by Pde11a knockout mice. Together, our findings suggest remote LTM can be decoupled from recent LTM, which may have relevance for cognitive deficits associated with aging, temporal lobe epilepsy, or transient global amnesia.


Subject(s)
3',5'-Cyclic-GMP Phosphodiesterases/genetics , Hippocampus/physiology , Memory Disorders/physiopathology , Memory, Long-Term/physiology , Neurons/metabolism , 3',5'-Cyclic-GMP Phosphodiesterases/metabolism , Animals , Female , Male , Mice , Mice, Knockout
7.
J Biopharm Stat ; 29(1): 82-97, 2019.
Article in English | MEDLINE | ID: mdl-29985739

ABSTRACT

In clinical trials, longitudinally assessed ordinal outcomes are commonly dichotomized and only the final measure is used for primary analysis, partly for ease of clinical interpretation. Dichotomization of the ordinal scale and failure to utilize the repeated measures can reduce statistical power. Additionally, in certain emergent settings, the same measure cannot be assessed at baseline prior to treatment. For such a data set, a piecewise-constant multistate Markov model that incorporates a latent model for the unobserved baseline measure is proposed. These models can be useful in analyzing disease history data and are advantageous in clinical applications where a disease process naturally moves through increasing stages of severity. Two examples are provided using acute stroke clinical trials data. Conclusions drawn in this article are consistent with those from the primary analysis for treatment effect in both of the motivating examples. Use of these models allows for a more refined examination of treatment effect and describes the movement between health states from baseline to follow-up visits which may provide more clinical insight into the treatment effect.


Subject(s)
Biostatistics/methods , Clinical Trials, Phase III as Topic/statistics & numerical data , Endpoint Determination/statistics & numerical data , Research Design/statistics & numerical data , Data Interpretation, Statistical , Humans , Markov Chains , Stroke/diagnosis , Stroke/physiopathology , Stroke/therapy , Treatment Outcome
8.
ACS Appl Mater Interfaces ; 10(50): 43363-43374, 2018 Dec 19.
Article in English | MEDLINE | ID: mdl-30462474

ABSTRACT

As biomaterial therapies emerge to address adipose tissue dysfunction that underlies metabolic disease, the immune response to these systems must be established. As a potential therapy, we are investigating resveratrol delivery from porous poly(lactide- co-glycolide) scaffolds designed to integrate with adipose tissue. Resveratrol was selected for its ability to protect mice and primates from high fat diet and broad anti-inflammatory properties. Herein, we report fabrication of scaffolds with high resveratrol loading that are stable and active for up to one year. In vitro release profiles indicate that drug release is biphasic with a burst release over 3 days followed by a plateau. Surprisingly, we find that PLG scaffolds implanted into adipose tissue of mice promote an anti-inflammatory environment characterized by high arginase-1 and low TNF-α and IL-6 compared to naïve unmanipulated fat. Resveratrol delivery from the scaffold augments this anti-inflammatory environment by decreasing monocyte and lymphocyte numbers at the implant site and increasing expression of IL-10 and IL-13, cytokines that promote healthy adipose tissue. In terms of therapeutic applications, implant of scaffolds designed to release resveratrol into the visceral fat decreases MCP-1 expression in mice fed a high fat diet, a molecule that drives both local and systemic inflammation during obesity. Taken together, resveratrol delivery to adipose tissue using poly(lactide- co-glycolide) scaffolds is a promising therapeutic strategy for the treatment of adipose tissue inflammation that drives metabolic disease.


Subject(s)
Intra-Abdominal Fat/metabolism , Panniculitis/drug therapy , Polyglactin 910 , Resveratrol , 3T3-L1 Cells , Animals , Arginase/metabolism , Cytokines/metabolism , Drug Implants/chemistry , Drug Implants/pharmacology , Inflammation/drug therapy , Inflammation/metabolism , Inflammation/pathology , Intra-Abdominal Fat/pathology , Male , Mice , Panniculitis/metabolism , Panniculitis/pathology , Polyglactin 910/chemistry , Polyglactin 910/pharmacology , Porosity , Resveratrol/chemistry , Resveratrol/pharmacology
9.
Nat Commun ; 9(1): 3358, 2018 08 22.
Article in English | MEDLINE | ID: mdl-30135423

ABSTRACT

Critical functions of intra-axonally synthesized proteins are thought to depend on regulated recruitment of mRNA from storage depots in axons. Here we show that axotomy of mammalian neurons induces translation of stored axonal mRNAs via regulation of the stress granule protein G3BP1, to support regeneration of peripheral nerves. G3BP1 aggregates within peripheral nerve axons in stress granule-like structures that decrease during regeneration, with a commensurate increase in phosphorylated G3BP1. Colocalization of G3BP1 with axonal mRNAs is also correlated with the growth state of the neuron. Disrupting G3BP functions by overexpressing a dominant-negative protein activates intra-axonal mRNA translation, increases axon growth in cultured neurons, disassembles axonal stress granule-like structures, and accelerates rat nerve regeneration in vivo.


Subject(s)
Axons/metabolism , Cytoplasmic Granules/metabolism , Nerve Regeneration/physiology , Poly-ADP-Ribose Binding Proteins/metabolism , RNA, Messenger/metabolism , Animals , Cells, Cultured , Female , Fluorescence Recovery After Photobleaching , HEK293 Cells , Humans , Male , Mice , Microscopy, Fluorescence , NIH 3T3 Cells , Nerve Regeneration/genetics , Poly-ADP-Ribose Binding Proteins/genetics , RNA, Messenger/genetics , Rats , Rats, Sprague-Dawley
10.
Cancer ; 124(9): 1912-1920, 2018 05 01.
Article in English | MEDLINE | ID: mdl-29415338

ABSTRACT

BACKGROUND: Cancer screening rates are lowest in those without insurance or a regular provider. Since 2008, the Colorectal Cancer Prevention Network (CCPN) has provided open access colonoscopy to uninsured residents of South Carolina through established, statewide partnerships and patient navigation. Herein, we describe the structure, implementation, and clinical outcomes of this program. METHODS: The CCPN provides access to colonoscopy screening at no cost to uninsured, asymptomatic patients aged 50-64 years (African Americans age 45-64 years are eligible) who live at or below 150% of the poverty line and seek medical care in free medical clinics, federally qualified health centers, or hospital-based indigent practices in South Carolina. Screening is performed by board-certified gastroenterologists. Descriptive statistics and regression analysis are used to describe the population screened, and to assess compliance rates and colonoscopy quality metrics. RESULTS: Out of >4000 patients referred to the program, 1854 were deemed eligible, 1144 attended an in-person navigation visit, and 1030 completed a colonoscopy; 909 were included in the final sample. Nearly 90% of participants exhibited good-to-excellent bowel preparation. An overall cecal intubation rate of 99% was measured. The polyp detection rate and adenoma detection rate were 63% and 36%, respectively, with male sex and urban residence positively associated with adenoma detection. Over 13% of participants had an advanced polyp, and 1% had a cancer diagnosis or surgical intervention. CONCLUSION: The CCPN program is characterized by strong collaboration with clinicians statewide, low no-show rates, and high colonoscopy quality. Future work will assess the effectiveness of the navigation approach and will explore the mechanisms driving higher adenoma detection in urban participants. Cancer 2018;124:1912-20. © 2018 American Cancer Society.


Subject(s)
Colorectal Neoplasms/diagnostic imaging , Early Detection of Cancer/statistics & numerical data , Health Services Accessibility/statistics & numerical data , Mass Screening/statistics & numerical data , Medically Uninsured/statistics & numerical data , State Health Plans/statistics & numerical data , Asymptomatic Diseases , Colonoscopy/statistics & numerical data , Colorectal Neoplasms/epidemiology , Female , Humans , Male , Middle Aged , No-Show Patients/statistics & numerical data , Patient Navigation/statistics & numerical data , Poverty/statistics & numerical data , Program Evaluation , Rural Population/statistics & numerical data , Sex Factors , South Carolina/epidemiology , Urban Population/statistics & numerical data
11.
Commun Stat Simul Comput ; 46(9): 7040-7061, 2017.
Article in English | MEDLINE | ID: mdl-29225407

ABSTRACT

Ordinal outcomes collected at multiple follow-up visits are common in clinical trials. Sometimes, one visit is chosen for the primary analysis and the scale is dichotomized amounting to loss of information. Multistate Markov models describe how a process moves between states over time. Here, simulation studies are performed to investigate the type I error and power characteristics of multistate Markov models for panel data with limited non-adjacent state transitions. The results suggest that the multistate Markov models preserve the type I error and adequate power is achieved with modest sample sizes for panel data with limited non-adjacent state transitions.

12.
PLoS One ; 12(10): e0187050, 2017.
Article in English | MEDLINE | ID: mdl-29073195

ABSTRACT

Historically, ordinal measures of functional outcome have been dichotomized for the primary analysis in acute stroke therapy trials. A number of alternative methods to analyze the ordinal scales have been proposed, with an emphasis on maintaining the ordinal structure as much as possible. In addition, despite the availability of longitudinal outcome data in many trials, the primary analysis consists of a single endpoint. Inclusion of information about the course of disease progression allows for a more complete understanding of the treatment effect. Multistate Markov modeling, which allows for the full ordinal scale to be analyzed longitudinally, is compared with previously suggested analytic techniques for the ordinal modified Rankin Scale (dichotomous-logistic regression; continuous-linear regression; ordinal- shift analysis, proportional odds model, partial proportional odds model, adjacent categories logit model; sliding dichotomy; utility weights; repeated measures). In addition, a multistate Markov model utilizing an estimate of the unobservable baseline outcome derived from principal component analysis is compared Each of the methods is used to re-analyze the National Institute of Neurological Diseases and Stroke tissue plasminogen activator study which showed a consistently significant effect of tissue plasminogen activator using a global test of four dichotomized outcomes in the analysis of the primary outcome at 90 days post-stroke in the primary analysis. All methods detected a statistically significant treatment effect except the multistate Markov model without predicted baseline (p = 0.053). This provides support for the use of the estimated baseline in the multistate Markov model since the treatment effect is able to be detected with its inclusion. Multistate Markov modeling allows for a more refined examination of treatment effect and describes the movement between modified Rankin Scale states over time which may provide more clinical insight into the treatment effect. Multistate Markov models are feasible and desirable in describing treatment effect in acute stroke therapy trials.


Subject(s)
Stroke/drug therapy , Tissue Plasminogen Activator/therapeutic use , Humans , Markov Chains
13.
Anal Chem ; 89(18): 9703-9711, 2017 09 19.
Article in English | MEDLINE | ID: mdl-28795565

ABSTRACT

The mechanisms that control extracellular serotonin levels in vivo are not well-defined. This shortcoming makes it very challenging to diagnose and treat the many psychiatric disorders in which serotonin is implicated. Fast-scan cyclic voltammetry (FSCV) can measure rapid serotonin release and reuptake events but cannot report critically important ambient serotonin levels. In this Article, we use fast-scan controlled adsorption voltammetry (FSCAV), to measure serotonin's steady-state, extracellular chemistry. We characterize the "Jackson" voltammetric waveform for FSCAV and show highly stable, selective, and sensitive ambient serotonin measurements in vitro. In vivo, we report basal serotonin levels in the CA2 region of the hippocampus as 64.9 ± 2.3 nM (n = 15 mice, weighted average ± standard error). We electrochemically and pharmacologically verify the selectivity of the serotonin signal. Finally, we develop a statistical model that incorporates the uncertainty in in vivo measurements, in addition to electrode variability, to more critically analyze the time course of pharmacological data. Our novel method is a uniquely powerful analysis tool that can provide deeper insights into the mechanisms that control serotonin's extracellular levels.


Subject(s)
Carbon Fiber/chemistry , Electrochemical Techniques , Serotonin/analysis , Animals , Male , Mice , Mice, Inbred C57BL , Microelectrodes
14.
Sci Rep ; 7: 43023, 2017 02 22.
Article in English | MEDLINE | ID: mdl-28223711

ABSTRACT

Targeted cancer therapeutics aim to exploit tumor-specific, genetic vulnerabilities specifically affecting neoplastic cells without similarly affecting normal cells. Here we performed sequencing-based screening of an shRNA library on a panel of cancer cells of different origins as well as normal cells. The shRNA library was designed to target a subset of genes previously identified using a whole genome screening approach. This focused shRNA library was infected into cells followed by analysis of enrichment and depletion of the shRNAs over the course of cell proliferation. We developed a bootstrap likelihood ratio test for the interpretation of the effects of multiple shRNAs over multiple cell line passages. Our analysis identified 44 genes whose depletion preferentially inhibited the growth of cancer cells. Among these genes ribosomal protein RPL35A, putative RNA helicase DDX24, and coatomer complex I (COPI) subunit ARCN1 most significantly inhibited growth of multiple cancer cell lines without affecting normal cell growth and survival. Further investigation revealed that the growth inhibition caused by DDX24 depletion is independent of p53 status underlining its value as a drug target. Overall, our study establishes a new approach for the analysis of proliferation-based shRNA selection strategies and identifies new targets for the development of cancer therapeutics.


Subject(s)
Drug Design , RNA, Small Interfering/metabolism , Cell Line, Tumor , Cell Proliferation/drug effects , Coatomer Protein/antagonists & inhibitors , Coatomer Protein/genetics , Coatomer Protein/metabolism , DEAD-box RNA Helicases/antagonists & inhibitors , DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Gene Library , Humans , Likelihood Functions , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/pathology , RNA Interference , RNA, Small Interfering/pharmacology , RNA, Small Interfering/therapeutic use , Ribosomal Proteins/antagonists & inhibitors , Ribosomal Proteins/genetics , Ribosomal Proteins/metabolism , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism
15.
Risk Anal ; 37(4): 716-732, 2017 04.
Article in English | MEDLINE | ID: mdl-27322778

ABSTRACT

This article describes several approaches for estimating the benchmark dose (BMD) in a risk assessment study with quantal dose-response data and when there are competing model classes for the dose-response function. Strategies involving a two-step approach, a model-averaging approach, a focused-inference approach, and a nonparametric approach based on a PAVA-based estimator of the dose-response function are described and compared. Attention is raised to the perils involved in data "double-dipping" and the need to adjust for the model-selection stage in the estimation procedure. Simulation results are presented comparing the performance of five model selectors and eight BMD estimators. An illustration using a real quantal-response data set from a carcinogenecity study is provided.


Subject(s)
Dose-Response Relationship, Drug , Risk Assessment/methods , Carcinogens , Computer Simulation , Humans , Models, Statistical , No-Observed-Adverse-Effect Level , Regression Analysis
16.
Oncotarget ; 8(1): 228-237, 2017 Jan 03.
Article in English | MEDLINE | ID: mdl-27974688

ABSTRACT

Ulcerative colitis (UC) is a chronic lifelong inflammatory disorder of the colon, which, while untreated, has a relapsing and remitting course with increasing risk of progression toward colorectal cancer. Current medical treatment strategies of UC mostly focus on inhibition of the signs and symptoms of UC to induce remission and prevent relapse of disease activity, minimizing the impact on quality of life, but not affecting the cause of disease. To date, however, there is no single reliable treatment agent and/or strategy capable of effectively controlling colitis progression throughout the patient's life without side effects, remission, or resistance. Taking into consideration an urgent need for the new colitis treatment strategies, targets and/or modulators of inflammation, we have tested current and prospective compounds for colitis treatment and directly compared their anti-colitis potency using a dextran sulfate sodium (DSS) mouse model of colitis. We have introduced a composite score - a multi-parameters comparison tool - to assess biological potency of different compounds.


Subject(s)
Colitis/drug therapy , Colitis/etiology , Disease Models, Animal , Drug Discovery , Animals , Biomarkers , Body Weight/drug effects , Colitis/metabolism , Dextran Sulfate/adverse effects , Male , Mice , Stress, Physiological
17.
Stat (Int Stat Inst) ; 5(1): 119-131, 2016.
Article in English | MEDLINE | ID: mdl-27330743

ABSTRACT

This article proposes multinomial probit Bayesian additive regression trees (MPBART) as a multinomial probit extension of BART - Bayesian additive regression trees. MPBART is flexible to allow inclusion of predictors that describe the observed units as well as the available choice alternatives. Through two simulation studies and four real data examples, we show that MPBART exhibits very good predictive performance in comparison to other discrete choice and multiclass classification methods. To implement MPBART, the R package mpbart is freely available from CRAN repositories.

18.
Microsc Microanal ; 22(1): 55-62, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26739629

ABSTRACT

Characterization of collagen fiber angle distribution throughout the blood vessel wall provides insight into the mechanical behavior of healthy and diseased arteries and their capacity to remodel. Atherosclerotic plaque contributes to the overall mechanical behavior, yet little is known experimentally about how collagen fiber orientation is influenced by atherogenesis. We hypothesized that atherosclerotic lesion development, and the factors contributing to lesion development, leads to a shift in collagen fiber angles within the aorta. Second-harmonic generation microscopy was used to visualize the three-dimensional organization of collagen throughout the aortic wall and to examine structural differences in mice maintained on high-fat Western diet versus age-matched chow diet mice in a model of atherosclerosis. Image analysis was performed on thoracic and abdominal sections of the aorta from each mouse to determine fiber orientation, with the circumferential (0°) and blood flow directions (axial ±90°) as the two reference points. All measurements were used in a multiple regression analysis to determine the factors having a significant influence on mean collagen fiber angle. We found that mean absolute angle of collagen fibers is 43° lower in Western diet mice compared with chow diet mice. Mice on a chow diet have a mean collagen fiber angle of ±63°, whereas mice on a Western diet have a more circumferential fiber orientation (~20°). This apparent shift in absolute angle coincides with the development of extensive aortic atherosclerosis, suggesting that atherosclerotic factors contribute to collagen fiber angle orientation.


Subject(s)
Aorta/pathology , Atherosclerosis/pathology , Fibrillar Collagens/analysis , Microscopy , Animals , Diet/methods , Disease Models, Animal , Image Processing, Computer-Assisted , Mice
19.
Am Stat ; 70(4): 413-423, 2016.
Article in English | MEDLINE | ID: mdl-29104295

ABSTRACT

In this pedagogical article, distributional properties, some surprising, pertaining to the homogeneous Poisson process (HPP), when observed over a possibly random window, are presented. Properties of the gap-time that covered the termination time and the correlations among gap-times of the observed events are obtained. Inference procedures, such as estimation and model validation, based on event occurrence data over the observation window, are also presented. We envision that through the results in this paper, a better appreciation of the subtleties involved in the modeling and analysis of recurrent events data will ensue, since the HPP is arguably one of the simplest among recurrent event models. In addition, the use of the theorem of total probability, Bayes theorem, the iterated rules of expectation, variance and covariance, and the renewal equation could be illustrative when teaching distribution theory, mathematical statistics, and stochastic processes at both the undergraduate and graduate levels. This article is targeted towards both instructors and students.

20.
J Nonparametr Stat ; 28(4): 716-735, 2016.
Article in English | MEDLINE | ID: mdl-28761316

ABSTRACT

Asymptotic properties, both consistency and weak convergence, of estimators arising in a general class of dynamic recurrent event models are presented. The class of models take into account the impact of interventions after each event occurrence, the impact of accumulating event occurrences, the induced informative and dependent right-censoring mechanism due to the data-accrual scheme, and the effect of covariate processes on the recurrent event occurrences. The class of models subsumes as special cases many of the recurrent event models that have been considered in biostatistics, reliability, and in the social sciences. The asymptotic properties presented have the potential of being useful in developing goodness-of-fit and model validation procedures, confidence intervals and confidence bands constructions, and hypothesis testing procedures for the finite- and infinite-dimensional parameters of a general class of dynamic recurrent event models, albeit the models without frailties.

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