bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effects of Control Domain Position on Optimal Control of Cardiac Arrhythmia
Authors: Ng Kin Wei , Rohanin Ahmad
Published: December 2012

We study the effects of control domain position on optimal control problem of cardiac arrhythmia. The well‐established mathematical model, namely, the monodomain model, is used to represent the electrical behavior of the cardiac tissue. Two test cases are considered in this paper: the control domain for Test Case 1 is close to the excitation domain, while the control domain for Test Case 2 is a little bit far away from the excitation domain. The modified Dai‐Yuan nonlinear conjugate gradient method is employed for computing the optimal applied extracellular current. Our experiment results show that the excitation wavefronts are successfully dampened out for both test cases. Also, experiment results show that the position of the control domain for Test Case 1 is preferable than that of Test Case 2 during the defibrillation process.
Analysis of the Travel Intent for Park and Ride Based on Perception
Authors: Qin Huanmei , Guan Hongzhi , Zhang Guang
Published: December 2012

As a multimodal travel behavior, park and ride includes several trip modes such as car, walking, bus, or railway. And people’s choice of park and ride is influenced by many factors. This paper, based on the park and ride behavior survey in Beijing, will analyze the relationship between the perception of the influencing factors and the behavior intent for park and ride by using structural equation modeling. The conclusions suggest that the park and ride choice for travelers is a passive behavior which means giving up driving the car is mainly caused by the serious traffic congestion. Furthermore, improving the service level of the park and ride facilities and the comfort for riding bus or railway will increase the utilization of park and ride facilities. The perceptions of the influencing factors have both direct and indirect effects on the travel intent for park and ride by the interaction among the influencing factors.
PPAR Could Contribute to the Pathogenesis of Hepatocellular Carcinoma
Authors: Kimura Osamu , Kondo Yasuteru , Shimosegawa Tooru
Published: December 2012

Viral hepatitis with hepatitis C virus or hepatitis B virus and chronic liver disease such as alcoholic or nonalcoholic steatohepatitis are critical factors in the development of hepatocellular carcinoma (HCC). Furthermore, diabetes is known as an independent risk factor for HCC. Peroxisome proliferator-activated receptor (PPAR) is known to have an important role in fatty liver, and the mechanism of carcinogenesis has been clarified. PPAR controls ligand-dependent transcription, and three subtypes (α,δ, andγ) in humans are known. PPARs could contribute to the mechanisms of cell cycling, anti-inflammatory responses, and apoptosis. Therefore, to clarify the pathogenesis of HCC, we should examine PPAR signaling. In this paper, we have summarized the relevance of PPARs to the pathogenesis of HCC and cancer stem cells and possible therapeutic options through modifying PPAR signaling.
Short Communication: A Simple Method for Performing Worm-Egg Counts on Sodium Acetate Formaldehyde-Preserved Samples
Authors: Melrose Wayne , Menzies Holly , Boer Melissa , Joseph Hayley , Reeve David , Speare Richard
Published: December 2012

The Kato Katz method is the most common way of performing worm-egg counts on human faecal samples, but it must be done in the field using freshly collected samples. This makes it difficult to use in remote, poorly accessible situations. This paper describes a simple method for egg counts on preserved samples collected in the field and sent to a central location for further processing.
Phylogenomic Investigation of Phospholipid Synthesis in Archaea
Authors: Lombard Jonathan , López-García Purificación , Moreira David
Published: December 2012

Archaea have idiosyncratic cell membranes usually based on phospholipids containing glycerol-1-phosphate linked by ether bonds to isoprenoid lateral chains. Since these phospholipids strongly differ from those of bacteria and eukaryotes, the origin of the archaeal membranes (and by extension, of all cellular membranes) was enigmatic and called for accurate evolutionary studies. In this paper we review some recent phylogenomic studies that have revealed a modified mevalonate pathway for the synthesis of isoprenoid precursors in archaea and suggested that this domain uses an atypical pathway of synthesis of fatty acids devoid of any acyl carrier protein, which is essential for this activity in bacteria and eukaryotes. In addition, we show new or updated phylogenetic analyses of enzymes likely responsible for the isoprenoid chain synthesis from their precursors and the phospholipid synthesis from glycerol phosphate, isoprenoids, and polar head groups. These results support that most of these enzymes can be traced back to the last archaeal common ancestor and, in many cases, even to the last common ancestor of all living organisms.
Almost Periodic Solutions of a Discrete Mutualism Model with Variable Delays
Authors: Liao Yongzhi , Zhang Tianwei
Published: December 2012

We discuss a discrete mutualism model with variable delays of the formsN1(n + 1) = N1(n)exp  {r1(n)[(K1(n) + α1(n)N2(n − μ2(n))) /1 + N2(n − μ2(n))) − N1(n − ν1(n))]}, N2(n + 1) = N2(n)exp  {r2(n)[(K2(n) + α2(n)N1(n − μ1(n)))/(1 + N1(n − μ1(n))) − N2(n − ν2(n))]}. By means of an almost periodic functional hull theory, sufficient conditions are established for the existence and uniqueness of globally attractive almost periodic solution to the previous system. Our results complement and extend some scientific work in recent years. Finally, some examples and numerical simulations are given to illustrate the effectiveness of our main results.
Oxidative Stress Markers in Prostate Cancer Patients after HDR Brachytherapy Combined with External Beam Radiation
Authors: Woźniak Alina , Masiak Rafał , Szpinda Michał , Mila-Kierzenkowska Celestyna , Woźniak Bartosz , Makarewicz Roman , Szpinda Anna
Published: December 2012

Assessment of oxidative stress markers was perfomed in prostate cancer (PCa) patients subjected to high-dose brachytherapy (HDR) with external beam radiotherapy (EBRT). Sixty men with PCa were subjected to combined two-fraction treatment with HDR (tot. 20 Gy) and EBRT (46 Gy). Blood samples were taken before treatment, immediately afterwards, after 1.5–3 months, and approx. 2 years. Control group consisted of 30 healthy men. Erythrocyte glutathione peroxidase activity in the patients was lower than in healthy subjects by 34% (, 50% (, 30% (, and 61% (, respectively, at all periods. No significant differences were found by comparing superoxide dismutase and catalase activity in PCa patients with that of the controls. After 2 years of the end of treatment, the activity of studied enzymes demonstrated a decreasing tendency versus before therapy. Blood plasma thiobarbituric acid reactive substances (TBARS) concentration was higher than in the controls at all periods, while erythrocyte TBARS decreased after 2 years to control levels. The results confirm that in the course of PCa, imbalance of oxidant-antioxidant processes occurs. The therapy did not alter the levels of oxidative stress markers, which may prove its applicability. Two years is too short a period to restore the oxidant-antioxidant balance.
Fundus Autofluorescence Imaging in an Ocular Screening Program
Authors: Kolomeyer A. M. , Nayak N. V. , Szirth B. C. , Khouri A. S.
Published: December 2012

Purpose. To describe integration of fundus autofluorescence (FAF) imaging into an ocular screening program.Methods. Fifty consecutive screening participants were included in this prospective pilot imaging study. Color and FAF (530/640 nm exciter/barrier filters) images were obtained with a 15.1MP Canon nonmydriatic hybrid camera. A clinician evaluated the images on site to determine need for referral. Visual acuity (VA), intraocular pressure (IOP), and ocular pathology detected by color fundus and FAF imaging modalities were recorded.Results. Mean ± SD age was 47.4 ± 17.3 years. Fifty-two percent were female and 58% African American. Twenty-seven percent had a comprehensive ocular examination within the past year. Mean VA was 20/39 in the right eye and 20/40 in the left eye. Mean IOP was 15 mmHg bilaterally. Positive color and/or FAF findings were identified in nine (18%) individuals with diabetic retinopathy or macular edema (n=4), focal RPE defects (n=2), age-related macular degeneration (n=1), central serous retinopathy (n=1), and ocular trauma (n=1).Conclusions. FAF was successfully integrated in our ocular screening program and aided in the identification of ocular pathology. Larger studies examining the utility of this technology in screening programs may be warranted.
A 5-Year Retrospective Review of Fungal Keratitis at Hospital Universiti Sains Malaysia
Authors: Mohd-Tahir Fadzillah , Norhayati A. , Siti-Raihan Ishak , Ibrahim M.
Published: December 2012

Background. Corneal blindness from healed infected keratitis is one of the most preventable causes of monocular blindness in developing countries, including Malaysia. Our objectives were to identify the causative fungi, predisposing risk factors, the proportion of correct clinical diagnosis, and visual outcome of patients treated in our hospital.Methods. A retrospective review of medical and microbiology records was conducted for all patients who were treated for fungal keratitis at Hospital Universiti Sains Malaysia from January 2007 until December 2011.Results. Forty-seven patients (47/186, 25.27%) were treated for fungal keratitis during the study period. This demonstrated that the incidence of fungal keratitis has increased each year from 2007 to 2011 by 12.50%, 17.65%, 21.21%, 26.83%, and 28.57%, respectively. The most common predisposing factors were injury to the eye followed by use of topical steroid, and preexisting ocular surface disease.Fusariumspecies were the most common fungal isolated, followed byCandidaspecies. Clinical diagnosis of fungal keratitis was made in 26 of the 41 (63.41%) cases of positive isolates. Of these, in eleven cases (23.40%) patients required surgical intervention. Clinical outcome of healed scar was achieved in 34 (72.34%) cases.Conclusions. The percentage of positive fungal isolated has steadily increased and the trend of common fungal isolated has changed. The latest review regarding fungal keratitis is important for us to improve patients' outcome in the future.
A Comparative Analysis of Subjective Quality of the Mobility between a New Portable Electric Transportation Mode and Walking
Authors: Ohta Hiroyuki , Matsumoto Haruyuki , Fukuda Daisuke , Fujii Satoshi
Published: December 2012

To analyze the psychological impacts of the introduction of new portable electric transportation modes, we implemented an experiment using a personal mobile vehicle (PMV). We investigated its effects on 2 types of the subjective quality of mobility (SQM): instrumental aspects including “easiness” and “speed”: and affective aspects including “enjoyment,” “seeing scenery,” and “enjoying the atmosphere.” The result indicated that PMV might contribute to the improvement of the instrumental aspects of SQM, but walking was regarded as more preferable in terms of the affective aspects. The results suggest that such a new transportation mode could contribute to the improvement of subjective quality of mobility, if and only if it can be introduced in an appropriate situation.
Chemical Tuning of Adsorption Properties of Titanate Nanotubes
Authors: Grigorieva Anastasia V. , Yuschenko Valentina V. , Ivanova Irina I. , Goodilin Eugene A. , Tretyakov Yuri D.
Published: December 2012

A conventional hydrothermal method widely used for the preparation of titania‐based nanotubes still generates many unsolved questions. One of them is definitely connected with the influence of a posthydrothermal treatment of titania nanotubes on their micromorphology, structure, and adsorption characteristics. Here, it was analyzed systematically by a group of methods including nitrogen adsorption and temperature‐programmed desorption of ammonia and carbon dioxide. It is proved that adsorption characteristics and the surface state of titania nanotubes correlate with a sodium content, since sodium ions act as Lewis acid sites and shield Ti4+ acid sites of the nanotubes. To obey a balance between chemical and heat treatments of the nanotubes to design their functional properties has been suggested.
Efficacy and Safety of Rituximab in the Treatment of Vasculitic Leg Ulcers Associated with Hepatitis C Virus Infection
Authors: Bonilla-Abadía Fabio , Echeverri Andrés F. , Izquierdo Jorge H. , Cañas Felipe , Cañas Carlos A.
Published: December 2012

Vasculitic leg ulcers are a cutaneous manifestation of hepatitis C virus (HCV) infection often associated with cryoglobulinemia. Their treatment is difficult and is based on steroids and immunosuppressive drugs with an erratic response and a high probability of adverse reaction. We report three patients with vasculitic leg ulcers associated with hepatitis C virus infection who were treated successfully with rituximab. The pain control and healing were achieved quickly. No adverse effects with rituximab in these patients were presented.
Newton Method to Recover the Phase Accumulated during MRI Data Acquisition
Authors: Kwon Oh-In , Park Chunjae
Published: December 2012

For an internal conductivity image, magnetic resonance electrical impedance tomography (MREIT) injects an electric current into an object and measures the induced magnetic flux density, which appears in the phase part of the acquired MR image data. To maximize signal intensity, the injected current nonlinear encoding (ICNE) method extends the duration of the current injection until the end of the MR data reading. It disturbs the usual linear encoding of the MR k‐space data used in the inverse Fourier transform. In this study, we estimate the magnetic flux density, which is recoverable from nonlinearly encoded MR k‐space data by applying a Newton method.
Disperse Dyes Based on Thiazole, Their Dyeing Application on Polyester Fiber and Their Antimicrobial Activity
Authors: Zadafiya S. K. , Tailor J. H. , Malik G. M.
Published: December 2012

Various diazotized aryl amines were coupled with N‐(4‐nitrophenyl)‐2‐[(4‐phenyl‐1,3‐thiazol‐2‐yl)amino]acetamide to give the corresponding various azo disperse dyes (D1‐D13). These dyes were applied to polyester fiber by HTHP method and their fastness properties were evaluated. Dyes were characterized by IR, elemental analysis, and NMR spectral studies. These dyes showed very good antibacterial and antifungal activities.
Ionic‐Liquid‐Mediated MacMillan’s Catalyst for Diels‐Alder Reaction
Authors: Srivastava Vivek
Published: December 2012

Ionic liquids were used to enhance as well as recycle the MacMillan′s catalyst 1 for the Diels‐Alder reaction. Using our developed protocol, Diels‐Alder adducts were obtained in good yields and selectivities along the 6 times recycling of MacMillan′s imidazolidinone catalyst 1. Synthesis of steroid 4 is the major outcome of our developed protocol.
Endocan Is Upregulated on Tumor Vessels in Invasive Bladder Cancer Where It Mediates VEGF-A–Induced Angiogenesis
Authors: Roudnicky Filip , Poyet Cedric , Wild Peter , Krampitz Sarah , Negrini Fabrizia , Huggenberger Reto , Rogler Anja , Stöhr Robert , Hartmann Arndt , Provenzano Maurizio , Otto Vivianne I. , Detmar Michael
Published: December 2012

Tumor-associated blood vessels differ from normal vessels and proteins present only on tumor vessels may serve as biomarkers or targets for antiangiogenic therapy in cancer. Comparing the transcriptional profiles of blood vascular endothelium from human invasive bladder cancer with normal bladder tissue, we found that the endothelial cell-specific molecule endocan (ESM1) was highly elevated on tumor vessels. Endocan was associated with filopodia of angiogenic endothelial tip cells in invasive bladder cancer. Notably, endocan expression on tumor vessels correlated strongly with staging and invasiveness, predicting a shorter recurrence-free survival time in noninvasive bladder cancers. Both endocan and VEGF-A levels were higher in plasma of patients with invasive bladder cancer than healthy individuals. Mechanistic investigations in cultured blood vascular endothelial cells or transgenic mice revealed that endocan expression was stimulated by VEGF-A through the phosphorylation and activation of VEGFR-2, which was required to promote cell migration and tube formation by VEGF-A. Taken together, our findings suggest that disrupting endocan interaction with VEGFR-2 or VEGF-A could offer a novel rational strategy to inhibit tumor angiogenesis. Furthermore, they suggest that endocan might serve as a useful biomarker to monitor disease progression and the efficacy of VEGF-A–targeting therapies in patients with bladder cancer. Cancer Res; 73(3); 1097–106. ©2012 AACR.
STC1 Expression By Cancer-Associated Fibroblasts Drives Metastasis of Colorectal Cancer
Authors: Peña Cristina , Céspedes María Virtudes , Lindh Maja Bradic , Kiflemariam Sara , Mezheyeuski Artur , Edqvist Per-Henrik , Hägglöf Christina , Birgisson Helgi , Bojmar Linda , Jirström Karin , Sandström Per , Olsson Eleonor , Veerla Srinivas , Gallardo Alberto , Sjöblom Tobias , Chang Andy C.-M. , Reddel Roger R. , Mangues Ramón , Augsten Martin , Östman Arne
Published: December 2012

Platelet-derived growth factor (PDGF) receptor signaling is a major functional determinant of cancer-associated fibroblasts (CAF). Elevated expression of PDGF receptors on stromal CAFs is associated with metastasis and poor prognosis, but mechanism(s) that underlie these connections are not understood. Here, we report the identification of the secreted glycoprotein stanniocalcin-1 (STC1) as a mediator of metastasis by PDGF receptor function in the setting of colorectal cancer. PDGF-stimulated fibroblasts increased migration and invasion of cocultured colorectal cancer cells in an STC1-dependent manner. Analyses of human colorectal cancers revealed significant associations between stromal PDGF receptor and STC1 expression. In an orthotopic mouse model of colorectal cancer, tumors formed in the presence of STC1-deficient fibroblasts displayed reduced intravasation of tumor cells along with fewer and smaller distant metastases formed. Our results reveal a mechanistic basis for understanding the contribution of PDGF-activated CAFs to cancer metastasis. Cancer Res; 73(4); 1287–97. ©2012 AACR.
Myeloid-Derived Suppressor Cells Function as Novel Osteoclast Progenitors Enhancing Bone Loss in Breast Cancer
Authors: Sawant Anandi , Deshane Jessy , Jules Joel , Lee Carnella M. , Harris Brittney A. , Feng Xu , Ponnazhagan Selvarangan
Published: December 2012

Enhanced bone destruction is a hallmark of various carcinomas such as breast cancer, where osteolytic bone metastasis is associated with increased morbidity and mortality. Immune cells contribute to osteolysis in cancer growth, but the factors contributing to aggressive bone destruction are not well understood. In this study, we show the importance of myeloid-derived suppressor cells (MDSC) in this process at bone metastatic sites. Because MDSC originate from the same myeloid lineage as macrophages, which are osteoclast precursors, we hypothesized that MDSC may undergo osteoclast differentiation and contribute to enhanced bone destruction and tumor growth. Using an immunocompetent mouse model of breast cancer bone metastasis, we confirmed that MDSC isolated from the tumor-bone microenvironment differentiated into functional osteoclasts both in vitro and in vivo. Mechanistic investigations revealed that nitric oxide signaling was critical for differentiation of MDSC into osteoclasts. Remarkably, osteoclast differentiation did not occur in MDSC isolated from control or tumor-bearing mice that lacked bone metastasis, signifying the essential cross-talk between tumor cells and myeloid progenitors in the bone microenvironment as a requirement for osteoclast differentiation of MDSC. Overall, our results identify a wholly new facet to the multifunctionality of MDSC in driving tumor progression, in this case as a novel osteoclast progenitor that specifically drives bone metastasis during cancer progression. Cancer Res; 73(2); 672–82. ©2012 AACR.
The Noncoding RNA MALAT1 Is a Critical Regulator of the Metastasis Phenotype of Lung Cancer Cells
Authors: Gutschner Tony , Hämmerle Monika , Eißmann Moritz , Hsu Jeff , Kim Youngsoo , Hung Gene , Revenko Alexey , Arun Gayatri , Stentrup Marion , Groß Matthias , Zörnig Martin , MacLeod A. Robert , Spector David L. , Diederichs Sven
Published: December 2012

The long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1), also known as MALAT-1 or NEAT2 (nuclear-enriched abundant transcript 2), is a highly conserved nuclear noncoding RNA (ncRNA) and a predictive marker for metastasis development in lung cancer. To uncover its functional importance, we developed a MALAT1 knockout model in human lung tumor cells by genomically integrating RNA destabilizing elements using zinc finger nucleases. The achieved 1,000-fold MALAT1 silencing provides a unique loss-of-function model. Proposed mechanisms of action include regulation of splicing or gene expression. In lung cancer, MALAT1 does not alter alternative splicing but actively regulates gene expression including a set of metastasis-associated genes. Consequently, MALAT1-deficient cells are impaired in migration and form fewer tumor nodules in a mouse xenograft. Antisense oligonucleotides (ASO) blocking MALAT1 prevent metastasis formation after tumor implantation. Thus, targeting MALAT1 with ASOs provides a potential therapeutic approach to prevent lung cancer metastasis with this ncRNA serving as both predictive marker and therapeutic target. Finally, regulating gene expression, but not alternative splicing, is the critical function of MALAT1 in lung cancer metastasis. In summary, 10 years after the discovery of the lncRNA MALAT1 as a biomarker for lung cancer metastasis, our loss-of-function model unravels the active function of MALAT1 as a regulator of gene expression governing hallmarks of lung cancer metastasis. Cancer Res; 73(3); 1180–9. ©2012 AACR.
ΔNp63α-Mediated Activation of Bone Morphogenetic Protein Signaling Governs Stem Cell Activity and Plasticity in Normal and Malignant Mammary Epithelial Cells
Authors: Balboni Amanda L. , Hutchinson Justine A. , DeCastro Andrew J. , Cherukuri Pratima , Liby Karen , Sporn Michael B. , Schwartz Gary N. , Wells Wendy A. , Sempere Lorenzo F. , Yu Paul B. , DiRenzo James
Published: December 2012

Genetic analysis of TP63 indicates that ΔNp63 isoforms are required for preservation of regenerative stasis within diverse epithelial tissues. In squamous carcinomas, TP63 is commonly amplified, and ΔNp63α confers a potent survival advantage. Genome-wide occupancy studies show that ΔNp63 promotes bidirectional target gene regulation by binding more than 5,000 sites throughout the genome; however, the subset of targets mediating discreet activities of TP63 remains unclear. We report that ΔNp63α activates bone morphogenic proteins (BMP) signaling by inducing the expression of BMP7. Immunohistochemical analysis indicates that hyperactivation of BMP signaling is common in human breast cancers, most notably in the basal molecular subtype, as well as in several mouse models of breast cancer. Suppression of BMP signaling in vitro with LDN193189, a small-molecule inhibitor of BMP type I receptor kinases, represses clonogenicity and diminishes the cancer stem cell–enriched ALDH1+ population. Importantly, LDN193189 blocks reconstitution of mixed ALDH1+/ALDH1− cultures indicating that BMP signaling may govern aspects of cellular plasticity within tumor hierarchies. These results show that BMP signaling enables reversion of committed populations to a stem-like state, potentially supporting progression and maintenance of tumorigenesis. Treatment of a mouse model of breast cancer with LDN193189 caused reduced expression of markers associated with epithelial-to-mesenchymal transition (EMT). Furthermore, in vivo limiting dilution analysis assays revealed that LDN193189 treatment suppressed tumor-initiating capacity and increased tumor latency. These studies support a model in which ΔNp63α-mediated activation of BMP signaling governs epithelial cell plasticity, EMT, and tumorigenicity during breast cancer initiation and progression. Cancer Res; 73(2); 1020–30. ©2012 AACR.
Midkine Promotes Neuroblastoma through Notch2 Signaling
Authors: Kishida Satoshi , Mu Ping , Miyakawa Shin , Fujiwara Masatoshi , Abe Tomoyuki , Sakamoto Kazuma , Onishi Akira , Nakamura Yoshikazu , Kadomatsu Kenji
Published: December 2012

Midkine is a heparin-binding growth factor highly expressed in various cancers, including neuroblastoma, the most common extracranial pediatric solid tumor. Prognosis of patients with neuroblastoma in which MYCN is amplified remains particularly poor. In this study, we used a MYCN transgenic model for neuroblastoma in which midkine is highly expressed in precancerous lesions of sympathetic ganglia. Genetic ablation of midkine in this model delayed tumor formation and reduced tumor incidence. Furthermore, an RNA aptamer that specifically bound midkine suppressed the growth of neuroblastoma cells in vitro and in vivo in tumor xenografts. In precancerous lesions, midkine-deficient MYCN transgenic mice exhibited defects in activation of Notch2, a candidate midkine receptor, and expression of the Notch target gene HES1. Similarly, RNA aptamer-treated tumor xenografts also showed attenuation of Notch2-HES1 signaling. Our findings establish a critical role for the midkine-Notch2 signaling axis in neuroblastoma tumorigenesis, which implicates new strategies to treat neuroblastoma. Cancer Res; 73(4); 1318–27. ©2012 AACR.
Opportunities and Challenges for Selected Emerging Technologies in Cancer Epidemiology: Mitochondrial, Epigenomic, Metabolomic, and Telomerase Profiling
Authors: Verma Mukesh , Khoury Muin J. , Ioannidis John P.A.
Published: December 2012

Remarkable progress has been made in the last decade in new methods for biologic measurements using sophisticated technologies that go beyond the established genome, proteome, and gene expression platforms. These methods and technologies create opportunities to enhance cancer epidemiologic studies. In this article, we describe several emerging technologies and evaluate their potential in epidemiologic studies. We review the background, assays, methods, and challenges and offer examples of the use of mitochondrial DNA and copy number assessments, epigenomic profiling (including methylation, histone modification, miRNAs, and chromatin condensation), metabolite profiling (metabolomics), and telomere measurements. We map the volume of literature referring to each one of these measurement tools and the extent to which efforts have been made at knowledge integration (e.g., systematic reviews and meta-analyses). We also clarify strengths and weaknesses of the existing platforms and the range of type of samples that can be tested with each of them. These measurement tools can be used in identifying at-risk populations and providing novel markers of survival and treatment response. Rigorous analytic and validation standards, transparent availability of massive data, and integration in large-scale evidence are essential in fulfilling the potential of these technologies. Cancer Epidemiol Biomarkers Prev; 22(2); 189–200. ©2012 AACR.
Detection of miR-34a Promoter Methylation in Combination with Elevated Expression of c-Met and β-Catenin Predicts Distant Metastasis of Colon Cancer
Authors: Siemens Helge , Neumann Jens , Jackstadt Rene , Mansmann Ulrich , Horst David , Kirchner Thomas , Hermeking Heiko
Published: December 2012

Purpose: Here, we determined whether epigenetic inactivation of miR-34a and miR-34b/c genes may serve as a prognostic marker for distant metastases in colon cancer.

Experimental Design: Using a case–control study design of 94 primary colon cancer samples with and without liver metastases, we determined CpG methylation frequencies of miR-34a and miR-34b/c promoters, expression of miR-34a, and its targets c-Met, Snail, and β-catenin and their prognostic value.

Results: miR-34a methylation was detected in 45.1% (n = 42 of 93) of the samples and strongly associated with metastases to the liver (P = 0.003) and lymph nodes (P = 0.006). miR-34b/c methylation was detected in 91.9% of the samples (n = 79/86). A significant inverse correlation between miR-34a methylation and expression of mature miR-34a (P = 0.018) was detected. Decreased miR-34a expression was associated with upregulation of c-Met, Snail, and β-catenin protein levels (P = 0.031, 0.132, and 0.004), which were associated with distant metastases (P = 0.001, 0.017, and 0.005). In a confounder-adjusted multivariate regression model miR-34a methylation, high c-Met and β-catenin levels provided the most significant prognostic information about metastases to the liver (P = 0.014, 0.031, and 0.058) and matched pairs showed a higher prevalence of these risk factors in the samples with distant spread (P = 0.029). Finally, we obtained statistical evidence indicating that the simultaneous detection of these three markers has the highest prognostic value.

Conclusions: Silencing of miR-34a and upregulation of c-Met, Snail, and β-catenin expression is associated with liver metastases of colon cancer. Detection of miR-34a silencing in resected primary colon cancer may be of prognostic value, especially in combination with detection of c-Met and β-catenin expression. Clin Cancer Res; 19(3); 710–20. ©2012 AACR.
Effective Assessment of egfr Mutation Status in Bronchoalveolar Lavage and Pleural Fluids by Next-Generation Sequencing
Authors: Buttitta Fiamma , Felicioni Lara , Del Grammastro Maela , Filice Giampaolo , Di Lorito Alessia , Malatesta Sara , Viola Patrizia , Centi Irene , D'Antuono Tommaso , Zappacosta Roberta , Rosini Sandra , Cuccurullo Franco , Marchetti Antonio
Published: December 2012

Purpose: The therapeutic choice for patients with lung adenocarcinoma depends on the presence of EGF receptor (EGFR) mutations. In many cases, only cytologic samples are available for molecular diagnosis. Bronchoalveolar lavage (BAL) and pleural fluid, which represent a considerable proportion of cytologic specimens, cannot always be used for molecular testing because of low rate of tumor cells.

Experimental Design: We tested the feasibility of EGFR mutation analysis on BAL and pleural fluid samples by next-generation sequencing (NGS), an innovative and extremely sensitive platform. The study was devised to extend the EGFR test to those patients who could not get it due to the paucity of biologic material. A series of 830 lung cytology specimens was used to select 48 samples (BAL and pleural fluid) from patients with EGFR mutations in resected tumors. These samples included 36 cases with 0.3% to 9% of neoplastic cells (series A) and 12 cases without evidence of tumor (series B). All samples were analyzed by Sanger sequencing and NGS on 454 Roche platform. A mean of 21,130 ± 2,370 sequences per sample were obtained by NGS.

Results: In series A, EGFR mutations were detected in 16% of cases by Sanger sequencing and in 81% of cases by NGS. Seventy-seven percent of cases found to be negative by Sanger sequencing showed mutations by NGS. In series B, all samples were negative for EGFR mutation by Sanger sequencing whereas 42% of them were positive by NGS.

Conclusions: The very sensitive EGFR-NGS assay may open up to the possibility of specific treatments for patients otherwise doomed to re-biopsies or nontargeted therapies. Clin Cancer Res; 19(3); 691–8. ©2012 AACR.
Influence of Human OATP1B1, OATP1B3, and OATP1A2 on the Pharmacokinetics of Methotrexate and Paclitaxel in Humanized Transgenic Mice
Authors: van de Steeg Evita , van Esch Anita , Wagenaar Els , Kenworthy Kathryn E. , Schinkel Alfred H.
Published: December 2012

Purpose: Organic anion-transporting polypeptide (OATP) drug uptake transporters are thought to play an important role in drug pharmacokinetics and toxicokinetics. We aimed to determine the influence of the individual human OATP1B1, OATP1B3, and OATP1A2 transporters on the in vivo disposition of the anticancer drugs methotrexate and paclitaxel by using liver-specific humanized OATP1A/1B transgenic mice.

Experimental Design: Wild-type, Slco1a/1b−/− (Oatp1a/1b knockout), Slco1a/1b−/−;1B1tg, Slco1a/1b−/−;1B3tg, and newly generated Slco1a/1b−/−;1A2tg (humanized OATP1B1, OATP1B3, and OATP1A2 transgenic) mice were characterized biochemically and physiologically, and subsequently intravenously dosed with methotrexate or paclitaxel (2 or 10 mg/kg each) for pharmacokinetic analyses.

Results: Humanized OATP1B1, OATP1B3, and OATP1A2 transgenic mice all showed partial or complete rescue of increased plasma bilirubin levels, but also of the increased plasma levels and decreased liver and small intestinal accumulation of methotrexate observed in Slco1a/1b−/− mice. Furthermore, hepatic expression of OATP1B3 and OATP1A2, but not OATP1B1, resulted in increased liver uptake of paclitaxel (2 mg/kg). At 10 mg/kg, a modest effect of only OATP1A2 on paclitaxel liver uptake was observed.

Conclusion: Human OATP1A/1B transporters play an important role in plasma and tissue distribution of the structurally diverse chemotherapeutics methotrexate (organic anion) and paclitaxel (hydrophobic, bulky). Variation in OATP1A/1B activity due to genetic variation and pharmacologic inhibition, or differences in tumor-specific expression levels might therefore affect plasma, tissue, and tumor levels of these drugs in patients, and hence their therapeutic efficacy. Humanized transgenic OATP1A/1B mice will provide excellent tools to further study these aspects in vivo for many (anticancer) drugs. Clin Cancer Res; 19(4); 821–32. ©2012 AACR.
DNA Methylation as an Adjunct to Histopathology to Detect Prevalent, Inconspicuous Dysplasia and Early-Stage Neoplasia in Barrett's Esophagus
Authors: Alvi Muhammad A. , Liu Xinxue , O'Donovan Maria , Newton Richard , Wernisch Lorenz , Shannon Nicholas B. , Shariff Kareem , di Pietro Massimiliano , Bergman Jacques J.G.H.M. , Ragunath Krish , Fitzgerald Rebecca C.
Published: December 2012

Purpose: Endoscopic surveillance of Barrett's esophagus is problematic because dysplasia/early-stage neoplasia is frequently invisible and likely to be missed because of sampling bias. Molecular abnormalities may be more diffuse than dysplasia. The aim was therefore to test whether DNA methylation, especially on imprinted and X-chromosome genes, is able to detect dysplasia/early-stage neoplasia.

Experimental design: 27K methylation arrays were used to find genes best able to differentiate between 22 Barrett's esophagus and 24 esophageal adenocarcinoma (EAC) samples. These were validated using pyrosequencing on a retrospective cohort (60 Barrett's esophagus, 36 dysplastic, and 90 EAC) and then in a prospective multicenter study (98 Barrett's esophagus patients, including 28 dysplastic and 9 early EAC) designed to utilize biomarkers to stratify patients according to their prevalent dysplasia/EAC status.

Results: Genes (23%) on the array, including 7% of X-linked and 69% of imprinted genes, have shown statistically significant changes in methylation in EAC versus Barrett's esophagus (Wilcoxon P < 0.05). 6/7 selected candidate genes were successfully internally (Pearson's P < 0.01) and externally validated (ANOVA P < 0.001). Four genes (SLC22A18, PIGR, GJA12, and RIN2) showed the greatest area under curve (0.988) to distinguish between Barrett's esophagus and dysplasia/EAC in the retrospective cohort. This methylation panel was able to stratify patients from the prospective cohort into three risk groups based on the number of genes methylated (low risk: <2 genes, intermediate: 2, and high: >2).

Conclusion: Widespread DNA methylation changes were observed in Barrett's carcinogenesis including ≈70% of known imprinted genes. A four-gene methylation panel stratified patients with Barrett's esophagus into three risk groups with potential clinical utility. Clin Cancer Res; 19(4); 878–88. ©2012 AACR.
Inhibiting EGF Receptor or SRC Family Kinase Signaling Overcomes BRAF Inhibitor Resistance in Melanoma
Authors: Girotti Maria R. , Pedersen Malin , Sanchez-Laorden Berta , Viros Amaya , Turajlic Samra , Niculescu-Duvaz Dan , Zambon Alfonso , Sinclair John , Hayes Andrew , Gore Martin , Lorigan Paul , Springer Caroline , Larkin James , Jorgensen Claus , Marais Richard
Published: December 2012

We generated cell lines resistant to BRAF inhibitors and show that the EGF receptor (EGFR)–SRC family kinase (SFK)–STAT3 signaling pathway was upregulated in these cells. In addition to driving proliferation of resistant cells, this pathway also stimulated invasion and metastasis. EGFR inhibitors cooperated with BRAF inhibitors to block the growth of the resistant cells in vitro and in vivo, and monotherapy with the broad specificity tyrosine kinase inhibitor dasatinib blocked growth and metastasis in vivo. We analyzed tumors from patients with intrinsic or acquired resistance to vemurafenib and observed increased EGFR and SFK activity. Furthermore, dasatinib blocked the growth and metastasis of one of the resistant tumors in immunocompromised mice. Our data show that BRAF inhibitor-mediated activation of EGFR–SFK–STAT3 signaling can mediate resistance in patients with BRAF-mutant melanoma. We describe 2 treatments that seem to overcome this resistance and could deliver therapeutic efficacy in patients with drug-resistant BRAF-mutant melanoma.

Significance: Therapies that target the driver oncogenes in cancer can achieve remarkable responses if patients are stratified for treatment. However, as with conventional therapies, patients often develop acquired resistance to targeted therapies, and a proportion of patients are intrinsically resistant and fail to respond despite the presence of an appropriate driver oncogene mutation. We found that the EGFR/SFK pathway mediated resistance to vemurafenib in BRAF-mutant melanoma and that BRAF and EGFR or SFK inhibition blocked proliferation and invasion of these resistant tumors, providing potentially effective therapeutic options for these patients. Cancer Discov; 3(2); 158–67. ©2012 AACR.

This article is highlighted in the In This Issue feature, p. 125
The mTORC1 Inhibitor Everolimus Prevents and Treats Eμ-Myc Lymphoma by Restoring Oncogene-Induced Senescence
Authors: Wall Meaghan , Poortinga Gretchen , Stanley Kym L. , Lindemann Ralph K. , Bots Michael , Chan Christopher J. , Bywater Megan J. , Kinross Kathryn M. , Astle Megan V. , Waldeck Kelly , Hannan Katherine M. , Shortt Jake , Smyth Mark J. , Lowe Scott W. , Hannan Ross D. , Pearson Richard B. , Johnstone Ricky W. , McArthur Grant A.
Published: December 2012

MYC deregulation is common in human cancer. IG-MYC translocations that are modeled in Eμ-Myc mice occur in almost all cases of Burkitt lymphoma as well as in other B-cell lymphoproliferative disorders. Deregulated expression of MYC results in increased mTOR complex 1 (mTORC1) signaling. As tumors with mTORC1 activation are sensitive to mTORC1 inhibition, we used everolimus, a potent and specific mTORC1 inhibitor, to test the requirement for mTORC1 in the initiation and maintenance of Eμ-Myc lymphoma. Everolimus selectively cleared premalignant B cells from the bone marrow and spleen, restored a normal pattern of B-cell differentiation, and strongly protected against lymphoma development. Established Eμ-Myc lymphoma also regressed after everolimus therapy. Therapeutic response correlated with a cellular senescence phenotype and induction of p53 activity. Therefore, mTORC1-dependent evasion of senescence is critical for cellular transformation and tumor maintenance by MYC in B lymphocytes.

Significance: This work provides novel insights into the requirements for MYC-induced oncogenesis by showing that mTORC1 activity is necessary to bypass senescence during transformation of B lymphocytes. Furthermore, tumor eradication through senescence elicited by targeted inhibition of mTORC1 identifies a previously uncharacterized mechanism responsible for significant anticancer activity of rapamycin analogues and serves as proof-of-concept that senescence can be harnessed for therapeutic benefit. Cancer Discov; 3(1); 82–95. ©2012 AACR.

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The Impact of Partial and Complete Loss-of-Function Mutations in Endothelial Lipase on High-Density Lipoprotein Levels and Functionality in Humans
Authors: Singaraja Roshni R. , Sivapalaratnam Suthesh , Hovingh Kees , Dubé Marie-Pierre , Castro-Perez José , Collins Heidi L. , Adelman Steven J. , Riwanto Meliana , Manz Jasmin , Hubbard Brian , Tietjen Ian , Wong Kenny , Mitnaul Lyndon J. , van Heek Margaret , Lin Linus , Roddy Thomas A. , McEwen Jason , Dallinge-Thie Geesje , van Vark-van der Zee Leonie , Verwoert Germaine , Winther Michael , van Duijn Cornelia , Hofman Albert , Trip Mieke D. , Marais A. David , Asztalos Bela , Landmesser Ulf , Sijbrands Eric , Kastelein John J. , Hayden Michael R.
Published: December 2012

Background—

Endothelial lipase is a phospholipase with activity against high-density lipoprotein. Although a small number of mutations in
LIPG
have been described, the role of
LIPG
in protection against atherosclerosis is unclear.

Methods and Results—

We identified 8 loss-of-function (LOF) mutations in
LIPG
in individuals with high-density lipoprotein cholesterol. Functional analysis confirmed that most rare mutations abolish lipase activity in vitro, indicating complete LOF, whereas 2 more common mutations N396S and R476W reduce activity by ≈50%, indicating partial LOF and implying ≈50% and ≈75% remaining endothelial lipase function in heterozygous complete LOF and partial LOF mutation carriers, respectively. complete LOF mutation carriers had significantly higher plasma high-density lipoprotein cholesterol levels compared with partial LOF mutation carriers. Apolipoprotein B-depleted serum from complete LOF carriers showed significantly enhanced cholesterol efflux acceptor capacity, whereas only trends were observed in partial LOF carriers. Carriers of
LIPG
mutations exhibited trends toward reduced coronary artery disease in 4 independent cohorts (meta-analysis odds ratio, 0.7;
P
=0.04).

Conclusions—

Our data suggest that the impact of
LIPG
mutations is directly related to their effect on endothelial lipase function and support that antagonism of endothelial lipase function improves cardioprotection.
Measuring Local Gradients of Intramitochondrial [Ca
2+
] in Cardiac Myocytes During Sarcoplasmic Reticulum Ca
2+
Release
Authors: Lu Xiyuan , Ginsburg Kenneth S. , Kettlewell Sarah , Bossuyt Julie , Smith Godfrey L. , Bers Donald M.
Published: December 2012

Rationale:

Mitochondrial [Ca
2+
] ([Ca
2+
]
mito
) regulates mitochondrial energy production, provides transient Ca
2+
buffering under stress, and can be involved in cell death. Mitochondria are near the sarcoplasmic reticulum (SR) in cardiac myocytes, and evidence for crosstalk exists. However, quantitative measurements of [Ca
2+
]
mito
are limited, and spatial [Ca
2+
]
mito
gradients have not been directly measured.

Objective:

To directly measure local [Ca
2+
]
mito
during normal SR Ca release in intact myocytes, and evaluate potential subsarcomeric spatial [Ca
2+
]
mito
gradients.

Methods and Results:

Using the mitochondrially targeted inverse pericam indicator Mitycam, calibrated in situ, we directly measured [Ca
2+
]
mito
during SR Ca
2+
release in intact rabbit ventricular myocytes by confocal microscopy. During steady state pacing, Δ[Ca
2+
]
mito
amplitude was 29±3 nmol/L, rising rapidly (similar to cytosolic free [Ca
2+
]) but declining much more slowly. Taking advantage of the structural periodicity of cardiac sarcomeres, we found that [Ca
2+
]
mito
near SR Ca
2+
release sites (Z-line) versus mid-sarcomere (M-line) reached a high peak amplitude (37±4 versus 26±4 nmol/L, respectively
P
<0.05) which occurred earlier in time. This difference was attributed to ends of mitochondria being physically closer to SR Ca
2+
release sites, because the mitochondrial Ca
2+
uniporter was homogeneously distributed, and elevated [Ca
2+
] applied laterally did not produce longitudinal [Ca
2+
]
mito
gradients.

Conclusions:

We developed methods to measure spatiotemporal [Ca
2+
]
mito
gradients quantitatively during excitation–contraction coupling. The amplitude and kinetics of [Ca
2+
]
mito
transients differ significantly from those in the cytosol and are respectively higher and faster near the Z-line versus M-line. This approach will help clarify SR-mitochondrial Ca
2+
signaling.
β-Adrenergic Regulation of Cardiac Progenitor Cell Death Versus Survival and Proliferation
Authors: Khan Mohsin , Mohsin Sadia , Avitabile Daniele , Siddiqi Sailay , Nguyen Jonathan , Wallach Kathleen , Quijada Pearl , McGregor Michael , Gude Natalie , Alvarez Roberto , Tilley Douglas G. , Koch Walter J. , Sussman Mark A.
Published: December 2012

Rationale:

Short-term β-adrenergic stimulation promotes contractility in response to stress but is ultimately detrimental in the failing heart because of accrual of cardiomyocyte death. Endogenous cardiac progenitor cell (CPC) activation may partially offset cardiomyocyte losses, but consequences of long-term β-adrenergic drive on CPC survival and proliferation are unknown.

Objective:

We sought to determine the relationship between β-adrenergic activity and regulation of CPC function.

Methods and Results:

Mouse and human CPCs express only β2 adrenergic receptor (β2-AR) in conjunction with stem cell marker c-kit. Activation of β2-AR signaling promotes proliferation associated with increased AKT, extracellular signal-regulated kinase 1/2, and endothelial NO synthase phosphorylation, upregulation of cyclin D1, and decreased levels of G protein–coupled receptor kinase 2. Conversely, silencing of β2-AR expression or treatment with β2-antagonist ICI 118, 551 impairs CPC proliferation and survival. β1-AR expression in CPC is induced by differentiation stimuli, sensitizing CPC to isoproterenol-induced cell death that is abrogated by metoprolol. Efficacy of β1-AR blockade by metoprolol to increase CPC survival and proliferation was confirmed in vivo by adoptive transfer of CPC into failing mouse myocardium.

Conclusions:

β-adrenergic stimulation promotes expansion and survival of CPCs through β2-AR, but acquisition of β1-AR on commitment to the myocyte lineage results in loss of CPCs and early myocyte precursors.