bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatitis B Virus Inhibits Apoptosis of Hepatoma Cells by Sponging the MicroRNA 15a/16 Cluster
Authors: Liu Ningning , Zhang Jinfang , Jiao Tong , Li Zhiwei , Peng Jirun , Cui Zhuqingqing , Ye Xin 
Published: October 2013

ABSTRACT
Hepatitis B virus (HBV) causes chronic hepatitis in hundreds of millions of people worldwide, which can eventually lead to hepatocellular carcinoma (HCC). The molecular mechanisms underlying HBV persistence are not well understood. In this study, we found that HBV inhibited the chemotherapy drug etoposide-induced apoptosis of hepatoma cells. Further analysis revealed that HBV mRNAs possess a microRNA 15a/16 (miR-15a/16)-complementary site (HBV nucleotides [nt] 1362 to 1383) that acts as a sponge to bind and sequester endogenous miR-15a/16. Consequently, Bcl-2, known as the target of miR-15a/16, was upregulated in HBV-infected cells. The data from HBV-transgenic mice further confirmed that HBV transcripts cause the reduction of miR-15a/16 and increase of Bcl-2. More importantly, we examined the levels of HBV transcripts and miR-15a/16 in HBV-infected HCC from patients and found that the amount of HBV mRNA and the level of miR-15a/16 were negatively correlated. Consistently, the level of Bcl-2 mRNA was upregulated in HBV-infected patients. In conclusion, we identified a novel HBV mRNA–miR-15a/16–Bcl-2 regulatory pathway that is involved in inhibiting etoposide-induced apoptosis of hepatoma cells, which may contribute to facilitating chronic HBV infection and hepatoma development.
Characteristics of Oncolytic Vesicular Stomatitis Virus Displaying Tumor-Targeting Ligands
Authors: Ammayappan Arun , Peng Kah-Whye , Russell Stephen J. 
Published: October 2013

ABSTRACT

We sought proof of principle that tumor-targeting ligands can be displayed on the surface of vesicular stomatitis virus (VSV) by engineering its glycoprotein. Here, we successfully rescued VSVs displaying tumor vasculature-targeting ligands. By using a rational approach, we investigated various feasible insertion sites on the G protein of VSV (VSV-G) for display of tumor vasculature-targeting ligands, cyclic RGD (cRGD) and echistatin. We found seven sites on VSV-G that tolerated insertion of the 9-residue cRGD peptide, two of which could tolerate insertion of the 49-amino acid echistatin domain. All of the ligand-displaying viruses replicated as well as the parental virus.
In vitro
studies demonstrated that the VSV-echistatin viruses specifically bound to targeted integrins. Since the low-density lipoprotein receptor (LDLR) was recently identified as a major receptor for VSV, we investigated the entry of ligand-displaying viruses after masking LDLR. The experiment showed that the modified viruses can enter the cell independently of LDLR, whereas entry of unmodified virus is significantly blocked by a specific monoclonal antibody against LDLR. Both parental and ligand-displaying viruses displayed equal oncolytic efficacies in a syngeneic mouse myeloma model. We further demonstrated that single-chain antibody fragments against tumor-specific antigens can be inserted at the N terminus of the G protein and that corresponding replication-competent VSVs can be rescued efficiently. Overall, we demonstrated that functional tumor-targeting ligands can be displayed on replication-competent VSVs without perturbing viral growth and oncolytic efficacy. This study provides a rational foundation for the future development of fully retargeted oncolytic VSVs.
5-HT
2
Receptors Facilitate JC Polyomavirus Entry
Authors: Assetta Benedetta , Maginnis Melissa S. , Gracia Ahufinger Irene , Haley Sheila A. , Gee Gretchen V. , Nelson Christian D. S. , O'Hara Bethany A. , Allen Ramdial Stacy-ann A. , Atwood Walter J. 
Published: October 2013

ABSTRACT

The human JC polyomavirus (JCPyV) causes the rapidly progressing demyelinating disease progressive multifocal leukoencephalopathy (PML). The disease occurs most often in individuals with AIDS but also occurs in individuals receiving immunomodulatory therapies for immune-related diseases such as multiple sclerosis. JCPyV infection of host cells requires the pentasaccharide lactoseries tetrasaccharide c (LSTc) and the serotonin receptor 5-hydroxytryptamine (5-HT) receptor 5-HT
2A
R. While LSTc is involved in the initial attachment of virus to cells via interactions with VP1, the mechanism by which 5-HT
2A
R contributes to infection is not clear. To further define the roles of serotonin receptors in infection, HEK293A cells, which are poorly permissive to JCPyV, were transfected with 14 different isoforms of serotonin receptor. Only 5-HT
2
receptors were found to support infection by JCPyV. None of the other 11 isoforms of serotonin receptor supported JCPyV infection. Expression of 5-HT
2
receptors did not increase binding of JCPyV to cells, but this was not unexpected, given that the cells uniformly expressed the major attachment receptor, LSTc. Infection of these cells remained sensitive to inhibition with soluble LSTc, confirming that LSTc recognition is required for JCPyV infection. Virus internalization into HEK293A cells was significantly and specifically enhanced when 5HT
2
receptors were expressed. Taken together, these data confirm that the carbohydrate LSTc is the attachment receptor for JCPyV and that the type 2 serotonin receptors contribute to JCPyV infection by facilitating entry.
LINE-1 Retrotransposable Element DNA Accumulates in HIV-1-Infected Cells
Authors: Jones R. Brad , Song Haihan , Xu Yang , Garrison Keith E. , Buzdin Anton A. , Anwar Naveed , Hunter Diana V. , Mujib Shariq , Mihajlovic Vesna , Martin Eric , Lee Erika , Kuciak Monika , Raposo Rui André Saraiva , Bozorgzad Ardalan , Meiklejohn Duncan A. , Ndhlovu Lishomwa C. , Nixon Douglas F. , Ostrowski Mario A. 
Published: October 2013

ABSTRACT

Type 1 long-interspersed nuclear elements (L1s) are autonomous retrotransposable elements that retain the potential for activity in the human genome but are suppressed by host factors. Retrotransposition of L1s into chromosomal DNA can lead to genomic instability, whereas reverse transcription of L1 in the cytosol has the potential to activate innate immune sensors. We hypothesized that HIV-1 infection would compromise cellular control of L1 elements, resulting in the induction of retrotransposition events. Here, we show that HIV-1 infection enhances L1 retrotransposition in Jurkat cells in a Vif- and Vpr-dependent manner. In primary CD4
+
cells, HIV-1 infection results in the accumulation of L1 DNA, at least the majority of which is extrachromosomal. These data expose an unrecognized interaction between HIV-1 and endogenous retrotransposable elements, which may have implications for the innate immune response to HIV-1 infection, as well as for HIV-1-induced genomic instability and cytopathicity.
Rescue of Maturation Off-Pathway Products in the Assembly of Pseudomonas Phage ϕ6
Authors: Sun Xiaoyu , Pirttimaa Markus J. , Bamford Dennis H. , Poranen Minna M. 
Published: October 2013

ABSTRACT

Many complex viruses use an assembly pathway in which their genome is packaged into an empty procapsid which subsequently matures into its final expanded form. We utilized
Pseudomonas
phage ϕ6, a well-established virus assembly model, to probe the plasticity of the procapsid maturation pathway. The ϕ6 packaging nucleoside triphosphatase (NTPase), which powers sequential translocation of the three viral genomic single-stranded RNA molecules to the procapsid during capsid maturation, is part of the mature ϕ6 virion but may spontaneously be dissociated from the procapsid shell. We demonstrate that the dissociation of NTPase subunits results in premature capsid expansion, which is detected as a change in the sedimentation velocity and as defects in RNA packaging and transcription activity. However, this dead-end conformation of the procapsids was rescued by the addition of purified NTPase hexamers, which efficiently associated on the NTPase-deficient particles and subsequently drove their contraction to the compact naive conformation. The resulting particles regained their biological and enzymatic activities, directing them into a productive maturation pathway. These observations imply that the maturation pathways of complex viruses may contain reversible steps that allow the rescue of the off-pathway conformation in an overall unidirectional virion assembly pathway. Furthermore, we provide direct experimental evidence that particles which have different physical properties (distinct sedimentation velocities and conformations) display different stages of the genome packaging program and show that the transcriptional activity of the ϕ6 procapsids correlates with the number of associated NTPase subunits.
Highly Sensitive Real-Time
In Vivo
Imaging of an Influenza Reporter Virus Reveals Dynamics of Replication and Spread
Authors: Tran Vy , Moser Lindsey A. , Poole Daniel S. , Mehle Andrew 
Published: October 2013

ABSTRACT

The continual public health threat posed by the emergence of novel influenza viruses necessitates the ability to rapidly monitor infection and spread in experimental systems. To analyze real-time infection dynamics, we have created a replication-competent influenza reporter virus suitable for
in vivo
imaging. The reporter virus encodes the small and bright NanoLuc luciferase whose activity serves as an extremely sensitive readout of viral infection. This virus stably maintains the reporter construct and replicates in culture and in mice with near-native properties. Bioluminescent imaging of the reporter virus permits serial observations of viral load and dissemination in infected animals, even following clearance of a sublethal challenge. We further show that the reporter virus recapitulates known restrictions due to host range and antiviral treatment, suggesting that this technology can be applied to studying emerging influenza viruses and the impact of antiviral interventions on infections
in vivo
. These results describe a generalizable method to quickly determine the replication and pathogenicity potential of diverse influenza strains in animals.
Epstein-Barr Virus Coinfection in Children Boosts Cytomegalovirus-Induced Differentiation of Natural Killer Cells
Authors: Saghafian-Hedengren Shanie , Sohlberg Ebba , Theorell Jakob , Carvalho-Queiroz Claudia , Nagy Noémi , Persson Jan-Olov , Nilsson Caroline , Bryceson Yenan T. , Sverremark-Ekström Eva 
Published: October 2013

ABSTRACT

During childhood, infections with cytomegalovirus (CMV) and Epstein-Barr virus (EBV) can occur in close temporal proximity. Active, as well as latent, CMV infection is associated with enlarged subsets of differentiated natural killer (NK) and cytotoxic T cells. How EBV infection may influence CMV-driven immune differentiation is not known. We found that EBV coinfection selectively influenced the NK cell compartment of CMV-seropositive (CMV
+
) children. Coinfected children had significantly higher proportions of peripheral-blood NKG2C
+
NK cells than CMV
+
EBV
−
children.
Ex vivo
NK cell degranulation after target cell stimulation and plasma IL-15 levels were significantly higher in CMV
+
children. EBV coinfection was related to the highest levels of plasma interleukin-15 (IL-15) and IL-12p70. Remarkably,
in vitro
EBV infection of peripheral blood mononuclear cells (PBMC) from EBV
−
CMV
+
children increased NKG2C
+
NK cell proportions. A similar tendency was seen in cocultures of PBMC with EBV
+
lymphoblastoid B-cell lines (LCL) and IL-15. After K562 challenge, NKG2C
+
NK cells excelled in regard to degranulation and production of gamma interferon, regardless of whether there was previous coculture with LCL. Taken together, our data suggest that dual latency with these herpesviruses during childhood could contribute to an
in vivo
environment supporting differentiation and maintenance of distinct NK cell populations. This viral imprint may affect subsequent immune responses through altered distributions of effector cells.
Alpha Interferon Restricts Human T-Lymphotropic Virus Type 1 and 2
De Novo
Infection through PKR Activation
Authors: Cachat Anne , Chevalier Sébastien Alain , Alais Sandrine , Ko Nga Ling , Ratner Lee , Journo Chloé , Dutartre Hélène , Mahieux Renaud 
Published: October 2013

ABSTRACT

Type I interferon (IFN-I) inhibits the replication of different viruses. However, the effect of IFN-I on the human T-lymphotropic virus type 1 (HTLV-1) viral cycle is controversial. Here, we investigated the consequences of IFN-α addition for different steps of HTLV-1 and HTLV-2 infection. We first show that alpha interferon (IFN-α) efficiently impairs HTLV-1 and HTLV-2
de novo
infection in a T cell line and in primary lymphocytes. Using pseudotyped viruses expressing HTLV-1 envelope, we then show that cell-free infection is insensitive to IFN-α, demonstrating that the cytokine does not affect the early stages of the viral cycle. In contrast, intracellular levels of Gag, Env, or Tax protein are affected by IFN-α treatment in T cells, primary lymphocytes, or 293T cells transfected with HTLV-1 or HTLV-2 molecular clones, demonstrating that IFN-α acts during the late stages of infection. We show that IFN-α does not affect Tax-mediated transcription and acts at a posttranscriptional level. Using either small interfering RNA (siRNA) directed against PKR or a PKR inhibitor, we demonstrate that PKR, whose expression is induced by interferon, plays a major role in IFN-α-induced HTLV-1/2 inhibition. These results indicate that IFN-α has a strong repressive effect on the HTLV-1 and HTLV-2 viral cycle during
de novo
infection of cells that are natural targets of the viruses.
Annihilation and coalescence on binary trees
Authors: Benjamini Itai , Lima Yuri 
Published: October 2013

An infection spreads in a binary tree [Formula: see text] of height n as follows: initially, each leaf is either infected by one of k states or it is not infected at all. The infection state of each leaf is independently distributed according to a probability vector p = (p1, …, pk+1). The remaining nodes become infected or not via annihilation and coalescence: nodes whose two children have the same state (infected or not) are infected (or not) by this state; nodes whose two children have different states are not infected; nodes such that only one of the children is infected are infected by this state. In this paper we characterize, for every p, the limiting distribution at the root node of [Formula: see text] as n goes to infinity. We also consider a variant of the model when k = 2 and a mutation can happen, with a fixed probability q, at each infection step. We characterize, in terms of p and q, the limiting distribution at the root node of [Formula: see text] as n goes to infinity. The distribution at the root node is driven by a dynamical system, and the proofs rely on the analysis of this dynamics.
Identification of Breast Cancer DNA Methylation Markers Optimized for Fine-Needle Aspiration Samples
Authors: Bu Dawei , Lewis Cheryl M. , Sarode Venetia , Chen Min , Ma Xiaotu , Lazorwitz Aaron M. , Rao Roshni , Leitch Marilyn , Moldrem Amy , Andrews Valerie , Gazdar Adi , Euhus David 
Published: October 2013

AbstractBackground: Random periareolar fine-needle aspiration (RP-FNA) is increasingly used in trials of breast cancer prevention for biomarker assessments. DNA methylation markers may have value as surrogate endpoint biomarkers, but this requires identification of biologically relevant markers suitable for paucicellular, lymphocyte-contaminated clinical samples.Methods: Unbiased whole-genome 5-aza-2′-deoxycytidine (5AZA)–induced gene expression assays, followed by several phases of qualitative and quantitative methylation-specific PCR (MSP) testing, were used to identify novel breast cancer DNA methylation markers optimized for clinical FNA samples.Results: The initial 5AZA experiment identified 453 genes whose expression was potentially regulated by promoter region methylation. Informatics filters excluded 273 genes unlikely to yield useful DNA methylation markers. MSP assays were designed for 271 of the remaining genes and, ultimately, 33 genes were identified that were differentially methylated in clinical breast cancer samples, as compared with benign RP-FNA samples, and never methylated in lymphocytes. A subset of these markers was validated by quantitative multiplex MSP in extended clinical sample sets. Using a novel permutation method for analysis of quantitative methylation data, PSAT1, GNE, CPNE8, and CXCL14 were found to correlate strongly with specific clinical and pathologic features of breast cancer. In general, our approach identified markers methylated in a smaller subpopulation of tumor cells than those identified in published methylation array studies.Conclusions: Clinically relevant DNA methylation markers were identified using a 5AZA-induced gene expression approach.Impact: These breast cancer-relevant, FNA-optimized DNA methylation markers may have value as surrogate endpoint biomarkers in RP-FNA studies. Cancer Epidemiol Biomarkers Prev; 22(12); 2212–21. ©2013 AACR.
Novel Methylation Biomarker Panel for the Early Detection of Pancreatic Cancer
Authors: Yi Joo Mi , Guzzetta Angela A. , Bailey Vasudev J. , Downing Stephanie R. , Van Neste Leander , Chiappinelli Katherine B. , Keeley Brian P. , Stark Alejandro , Herrera Alexander , Wolfgang Christopher , Pappou Emmanouil P. , Iacobuzio-Donahue Christine A. , Goggins Michael G. , Herman James G. , Wang Tza-Huei , Baylin Stephen B. , Ahuja Nita 
Published: October 2013

Abstract
Purpose: Pancreatic cancer is the fourth leading cause of cancer deaths and there currently is no reliable modality for the early detection of this disease. Here, we identify cancer-specific promoter DNA methylation of BNC1 and ADAMTS1 as a promising biomarker detection strategy meriting investigation in pancreatic cancer.
Experimental Design: We used a genome-wide pharmacologic transcriptome approach to identify novel cancer-specific DNA methylation alterations in pancreatic cancer cell lines. Of eight promising genes, we focused our studies on BNC1 and ADAMTS1 for further downstream analysis, including methylation and expression. We used a nanoparticle-enabled methylation on beads (MOB) technology to detect early-stage pancreatic cancers by analyzing DNA methylation in patient serum.
Results: We identified two novel genes, BNC1 (92%) and ADAMTS1 (68%), that showed a high frequency of methylation in pancreatic cancers (n = 143), up to 100% in PanIN-3 and 97% in stage I invasive cancers. Using the nanoparticle-enabled MOB technology, these alterations could be detected in serum samples (n = 42) from patients with pancreatic cancer, with a sensitivity for BNC1 of 79% [95% confidence interval (CI), 66%–91%] and for ADAMTS1 of 48% (95% CI, 33%–63%), whereas specificity was 89% for BNC1 (95% CI, 76%–100%) and 92% for ADAMTS1 (95% CI, 82%–100%). Overall sensitivity using both markers is 81% (95% CI, 69%–93%) and specificity is 85% (95% CI, 71%–99%).
Conclusions: Promoter DNA methylation of BNC1 and ADAMTS1 is a potential biomarker to detect early-stage pancreatic cancers. Assaying the promoter methylation status of these genes in circulating DNA from serum is a promising strategy for early detection of pancreatic cancer and has the potential to improve mortality from this disease. Clin Cancer Res; 19(23); 6544–55. ©2013 AACR.
Photodynamic Therapy with 3-(1′-Hexyloxyethyl) Pyropheophorbide a for Cancer of the Oral Cavity
Authors: Rigual Nestor , Shafirstein Gal , Cooper Michele T. , Baumann Heinz , Bellnier David A. , Sunar Ulas , Tracy Erin C. , Rohrbach Daniel J. , Wilding Gregory , Tan Wei , Sullivan Maureen , Merzianu Mihai , Henderson Barbara W. 
Published: October 2013

Abstract
Purpose: The primary objective was to evaluate safety of 3-(1′-hexyloxyethyl)pyropheophorbide-a (HPPH) photodynamic therapy (HPPH-PDT) for dysplasia and early squamous cell carcinoma of the head and neck (HNSCC). Secondary objectives were the assessment of treatment response and reporters for an effective PDT reaction.
Experimental Design: Patients with histologically proven oral dysplasia, carcinoma in situ, or early-stage HNSCC were enrolled in two sequentially conducted dose escalation studies with an expanded cohort at the highest dose level. These studies used an HPPH dose of 4 mg/m2 and light doses from 50 to 140 J/cm2. Pathologic tumor responses were assessed at 3 months. Clinical follow up range was 5 to 40 months. PDT induced cross-linking of STAT3 were assessed as potential indicators of PDT effective reaction.
Results: Forty patients received HPPH-PDT. Common adverse events were pain and treatment site edema. Biopsy proven complete response rates were 46% for dysplasia and carcinoma in situ and 82% for squamous cell carcinomas (SCC) lesions at 140 J/cm2. The responses in the carcinoma in situ/dysplasia cohort are not durable. The PDT-induced STAT3 cross-links is significantly higher (P = 0.0033) in SCC than in carcinoma in situ/dysplasia for all light doses.
Conclusion: HPPH-PDT is safe for the treatment of carcinoma in situ/dysplasia and early-stage cancer of the oral cavity. Early-stage oral HNSCC seems to respond better to HPPH-PDT in comparison with premalignant lesions. The degree of STAT3 cross-linking is a significant reporter to evaluate HPPH-PDT–mediated photoreaction. Clin Cancer Res; 19(23); 6605–13. ©2013 AACR.
Ten-Year Experience With Extended Criteria Cardiac Transplantation
Authors: Samsky Marc D. , Patel Chetan B. , Owen Ashleigh , Schulte Phillip J. , Jentzer Jacob , Rosenberg Paul B. , Felker G. Michael , Milano Carmelo A. , Hernandez Adrian F. , Rogers Joseph G. 
Published: October 2013

Background—
Extended criteria cardiac transplant (ECCT) programs expand the transplant pool by matching donors and recipients typically excluded from the transplant process because of age or comorbidity. There is a paucity of data examining long-term outcomes with this strategy.

Methods and Results—

Between January 2000 and December 2009, adult patients undergoing isolated heart transplant were prospectively classified as ECCT based on prespecified criteria. Baseline characteristics and outcomes were compared between ECCT and standard criteria cardiac transplant recipients. Two Cox proportional hazards models were developed. The first to identify clinical variables contributing to survival between the 2 groups, and the second to determine the additional risk associated with assignment to ECCT. Among the 454 patients who underwent heart transplant, 84 (18.5%) were ECCT. Compared with the patients who underwent standard criteria cardiac transplant, ECCT patients were older (median, 66.6 years versus 53.2 years;
P
<0.001), with higher frequency of diabetes mellitus (46.4% versus 24.6%;
P
<0.001) and chronic kidney disease (median estimated glomerular filtration rate, 55 versus 61.6 mL/min;
P
=0.001). After adjustment for baseline characteristics, standard criteria cardiac transplant survival was higher than ECCT at 1 (89% versus 86%;
P
=0.18) and 5 (77% versus 66%;
P
=0.035) years. In a multivariate model that included listing criteria, creatinine (hazard ratio, 1.05 per 0.1 mg/dL; 95% confidence interval, 1.02–1.09;
P
=0.001) was a significant predictor of post-transplant mortality.

Conclusions—
ECCT is an acceptable alternative for advanced heart failure therapy in select patients. Age and renal dysfunction are important determinants of long-term survival and post-transplant morbidity.