bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Breadth of Expandable Memory CD8
+
T Cells Inversely Correlates with Residual Viral Loads in HIV Elite Controllers
Authors: Ndhlovu Zaza M. , Stampouloglou Eleni , Cesa Kevin , Mavrothalassitis Orestes , Alvino Donna Marie , Li Jonathan Z. , Wilton Shannon , Karel Daniel , Piechocka-Trocha Alicja , Chen Huabiao , Pereyra Florencia , Walker Bruce D. 
Published: August 2015

ABSTRACT

Previous studies have shown that elite controllers with minimal effector T cell responses harbor a low-frequency, readily expandable, highly functional, and broadly directed memory population. Here, we interrogated the
in vivo
relevance of this cell population by investigating whether the breadth of expandable memory responses is associated with the magnitude of residual viremia in individuals achieving durable suppression of HIV infection. HIV-specific memory CD8
+
T cells were expanded by using autologous epitopic and variant peptides. Viral load was measured by an ultrasensitive single-copy PCR assay. Following expansion, controllers showed a greater increase in the overall breadth of Gag responses than did untreated progressors (
P
= 0.01) as well as treated progressors (
P
= 0.0003). Nef- and Env-specific memory cells expanded poorly for all groups, and their expanded breadths were indistinguishable among groups (
P
= 0.9 for Nef as determined by a Kruskal-Wallis test;
P
= 0.6 for Env as determined by a Kruskal-Wallis test). More importantly, we show that the breadth of expandable, previously undetectable Gag-specific responses was inversely correlated with residual viral load (
r
= −0.6;
P
= 0.009). Together, these data reveal a direct link between the abundance of Gag-specific expandable memory responses and prolonged maintenance of low-level viremia. Our studies highlight a CD8
+
T cell feature that would be desirable in a vaccine-induced T cell response.

IMPORTANCE
Many studies have shown that the rare ability of some individuals to control HIV infection in the absence of antiretroviral therapy appears to be heavily dependent upon special HIV-specific killer T lymphocytes that are able to inhibit viral replication. The identification of key features of these immune cells has the potential to inform rational HIV vaccine design. This study shows that a special subset of killer lymphocytes, known as central memory CD8
+
T lymphocytes, is at least partially involved in the durable control of HIV replication. HIV controllers maintain a large proportion of Gag-specific expandable memory CD8
+
T cells involved in ongoing viral suppression. These data suggest that induction of this cell subset by future HIV vaccines may be important for narrowing possible routes of rapid escape from vaccine-induced CD8
+
T cell responses.
Replication-Competent Controlled Herpes Simplex Virus
Authors: Bloom David C. , Feller Joyce , McAnany Peterjon , Vilaboa Nuria , Voellmy Richard 
Published: August 2015

ABSTRACT
We present the development and characterization of a replication-competent controlled herpes simplex virus 1 (HSV-1). Replication-essential ICP4 and ICP8 genes of HSV-1 wild-type strain 17syn+ were brought under the control of a dually responsive gene switch. The gene switch comprises (i) a transactivator that is activated by a narrow class of antiprogestins, including mifepristone and ulipristal, and whose expression is mediated by a promoter cassette that comprises an HSP70B promoter and a transactivator-responsive promoter and (ii) transactivator-responsive promoters that drive the ICP4 and ICP8 genes. Single-step growth experiments in different cell lines demonstrated that replication of the recombinant virus, HSV-GS3, is strictly dependent on an activating treatment consisting of administration of a supraphysiological heat dose in the presence of an antiprogestin. The replication-competent controlled virus replicates with an efficiency approaching that of the wild-type virus from which it was derived. Essentially no replication occurs in the absence of activating treatment or if HSV-GS3-infected cells are exposed only to heat or antiprogestin. These findings were corroborated by measurements of amounts of viral DNA and transcripts of the regulated ICP4 gene and the glycoprotein C (gC) late gene, which was not regulated. Similar findings were made in experiments with a mouse footpad infection model.

IMPORTANCE
The alphaherpesviruses have long been considered vectors for recombinant vaccines and oncolytic therapies. The traditional approach uses vector backbones containing attenuating mutations that restrict replication to ensure safety. The shortcoming of this approach is that the attenuating mutations tend to limit both the immune presentation and oncolytic properties of these vectors. HSV-GS3 represents a novel type of vector that, when activated, replicates with the efficiency of a nonattenuated virus and whose safety is derived from deliberate, stringent regulation of multiple replication-essential genes. By directing activating heat to the region of virus administration, replication is strictly confined to infected cells within this region. The requirement for antiprogestin provides an additional level of safety, ensuring that virus replication cannot be triggered inadvertently. Replication-competent controlled vectors such as HSV-GS3 may have the potential to be superior to conventional attenuated HSV vaccine and oncolytic vectors without sacrificing safety.
Nef Is Dispensable for Resistance of Simian Immunodeficiency Virus-Infected Macrophages to CD8
+
T Cell Killing
Authors: Rainho Jennifer N. , Martins Mauricio A. , Cunyat Francesc , Watkins Ian T. , Watkins David I. , Stevenson Mario 
Published: August 2015

ABSTRACT

Simian immunodeficiency virus (SIV)-specific CD8
+
T cells kill SIV-infected CD4
+
T cells in an major histocompatibility complex class I (MHC-I)-dependent manner. However, they are reportedly less efficient at killing SIV-infected macrophages. Since the viral accessory protein Nef has been shown to downregulate MHC-I molecules and enhance cytotoxic T lymphocyte (CTL) evasion in human immunodeficiency virus type 1 (HIV-1)-infected CD4
+
T cells, we examined whether Nef played a role in protecting SIV-infected macrophages from killing by SIV-specific CD8
+
T cells. To explore the role of Nef in CD8
+
T cell evasion, we compared the ability of freshly sorted SIV-specific CD8
+
T cells to readily suppress viral replication or eliminate CD4
+
T cells or monocyte-derived macrophages infected with SIV variants containing wild-type (WT) or mutated
nef
genes. As expected, SIV-specific CD8
+
T cells suppressed viral replication and eliminated the majority of SIV-infected CD4
+
T cells, and this killing was enhanced in CD4
+
T cells infected with the
nef
variants. However, macrophages infected with
nef
variants that disrupt MHC-I downregulation did not promote rapid killing by freshly isolated CD8
+
T cells. These results suggest that mechanisms other than Nef-mediated MHC-I downregulation govern the resistance of SIV-infected macrophages to CD8
+
T cell-mediated killing. This study has implications for viral persistence and suggests that macrophages may afford primate lentiviruses some degree of protection from immune surveillance.

IMPORTANCE
Myeloid cells are permissive for HIV/SIV replication
in vitro
and may contribute to viral persistence
in vivo
. While many studies have been geared to understanding how CD8
+
T cells control viral replication in CD4
+
T cells, the role of these cells in controlling viral replication in macrophages is less clear. Primary, unstimulated CD8
+
T cells insignificantly suppress viral replication or eliminate SIV-infected macrophages. Since the viral Nef protein downregulates MHC-I and provides infected cells some degree of protection from CD8
+
T cell-mediated effector functions, we evaluated whether Nef may be contributing to the resistance of macrophages to CD8
+
T cell suppression. Our results suggest that Nef is not involved in protecting infected macrophages from CD8
+
T cell killing and suggest that other mechanisms are involved in macrophage evasion from CD8 surveillance.
Actin-Modulating Protein Cofilin Is Involved in the Formation of Measles Virus Ribonucleoprotein Complex at the Perinuclear Region
Authors: Koga Ritsuko , Sugita Yukihiko , Noda Takeshi , Yanagi Yusuke , Ohno Shinji 
Published: August 2015

ABSTRACT
In measles virus (MV)-infected cells, the ribonucleoprotein (RNP) complex, comprised of the viral genome and the nucleocapsid (N) protein, phosphoprotein (P protein), and large protein, assembles at the perinuclear region and synthesizes viral RNAs. The cellular proteins involved in the formation of the RNP complex are largely unknown. In this report, we show that cofilin, an actin-modulating host protein, interacts with the MV N protein and aids in the formation of the RNP complex. Knockdown of cofilin using the short hairpin RNA reduces the formation of the RNP complex after MV infection and that of the RNP complex-like structure after plasmid-mediated expression of MV N and P proteins. A lower level of formation of the RNP complex results in the reduction of viral RNA synthesis. Cofilin phosphorylation on the serine residue at position 3, an enzymatically inactive form, is increased after MV infection and the phosphorylated form of cofilin is preferentially included in the complex. These results indicate that cofilin plays an important role in MV replication by increasing formation of the RNP complex and viral RNA synthesis.

IMPORTANCE
Many RNA viruses induce within infected cells the structure called the ribonucleoprotein (RNP) complex in which viral RNA synthesis occurs. It is comprised of the viral genome and proteins that include the viral RNA polymerase. The cellular proteins involved in the formation of the RNP complex are largely unknown. In this report, we show that cofilin, an actin-modulating host protein, binds to the measles virus (MV) nucleocapsid protein and plays an important role in the formation of the MV RNP complex and MV RNA synthesis. The level of the phosphorylated form of cofilin, enzymatically inactive, is increased after MV infection, and the phosphorylated form is preferentially associated with the RNP complex. Our findings determined with cofilin will help us better understand the mechanism by which the RNP complex is formed in virus-infected cells and develop new antiviral drugs targeting the RNP complex.
Improvement of HIV-1 and Human T Cell Lymphotropic Virus Type 1 Replication-Dependent Vectors via Optimization of Reporter Gene Reconstitution and Modification with Intronic Short Hairpin RNA
Authors: Shunaeva Anastasia , Potashnikova Daria , Pichugin Alexey , Mishina Alexandra , Filatov Alexander , Nikolaitchik Olga , Hu Wei-Shau , Mazurov Dmitriy 
Published: August 2015

ABSTRACT
Cell-to-cell transmission is an efficient mechanism to disseminate human immunodeficiency virus type 1 (HIV-1) and human T cell lymphotropic virus type 1 (HTLV-1). However, it has been challenging to quantify the level of cell-to-cell transmission because the virus-producing cells cannot be easily distinguished from infected target cells. We have previously described replication-dependent vectors that can quantify infection events in cocultured cells. These vectors contain an antisense-oriented promoter and reporter gene interrupted by a sense-oriented intron from the human gamma-globin gene. This strategy prevents expression of the reporter gene in the transfected cells but permits its expression in target cells after infection. However, the gamma-globin intron is not efficiently removed by splicing in the aforementioned vectors, thereby reducing the level of reporter gene expression after transduction into target cells. Here, we used two approaches to improve the replication-dependent vectors. First, we improved the splicing events that remove the gamma-globin intron by optimizing the intron insertion site within the reporter gene. Second, we improved the packaging of the spliced RNA without the gamma-globin intron by targeting the intron-containing RNA via microRNA 30 (miR30)-based short hairpin RNAs. Using two optimized fluorescent reporter vectors and flow cytometry, we determined that multiply HIV-1-infected cells were generated at a higher frequency in coculture than in cell-free infection; furthermore, this increase was dependent upon viruses bearing HIV-1 Env. Compared with previously described vectors, these improved vectors can quantify the infection in lymphocytes and in primary cells with a higher sensitivity and allow the detection and quantitation of multiply infected cells, providing better tools to study retroviral cell-mediated infection.

IMPORTANCE
The human-pathogenic retroviruses HTLV-1 and HIV-1 can be transmitted more efficiently
in vivo
via direct contact of infected cells with healthy target cells than through cell-free virion-mediated infection. Despite its importance, cell-to-cell transmission has been difficult to quantify because the previously infected cells and the newly infected cells are mixed together in the same culture. In the current study, we generated vectors that are significantly improved over the previously described replication-dependent vectors. As a result, these improved vectors can efficiently detect and quantify cell-to-cell transmission or new infection events in cells in mixed culture. These luciferase- or fluorescence protein-based reporter vectors can be used to quantify and study HIV-1 or HTLV-1 cell-mediated infection in a simple one-step transfection/infection assay.
Parametric unfolding of flexural folds using palaeomagnetic vectors
Authors: Ramón Maria José , Pueyo Emilio L. , Caumon Guillaume , Briz José Luis 
Published: August 2015

Abstract
Providing that a primary and reliable record of the magnetic field and its reference in a deformed area exists, the incorporation of palaeomagnetic constraints in restoration methods reduces uncertainty of rotation because such constraints can be applied both before and after deformation. In this paper, we utilize palaeomagnetic data to improve an unfolding algorithm based on the parameterization of the surface using isometric constraints. This method is more robust than others based on piecewise restoration of a triangulated surface, which are dependent on the meshing and, especially, on the pin-element. A disadvantage of this approach is that parametric restoration is sensitive to the initial solution, which hampers results for complex non-coaxial or non-cylindrical structures. We show that the use of palaeomagnetism as the initial gradient of one of the parameters improves the results of the method. We use analogue models to test the method because the expected restoration result can be stated, since the initial surface is known. We study the restoration sensitivity to surface meshing and the initial palaeomagnetic orientation. All in all, the use of palaeomagnetic vectors in the studied analogue models achieves the best restoration results. The implementation of palaeomagnetic vectors is crucial to obtain reliable 3D restorations of complex structures.
Perivascular M2 Macrophages Stimulate Tumor Relapse after Chemotherapy
Authors: Hughes Russell , Qian Bin-Zhi , Rowan Charlotte , Muthana Munitta , Keklikoglou Ioanna , Olson Oakley C. , Tazzyman Simon , Danson Sarah , Addison Christina , Clemons Mark , Gonzalez-Angulo Ana Maria , Joyce Johanna A. , De Palma Michele , Pollard Jeffrey W. , Lewis Claire E. 
Published: August 2015

Abstract
Tumor relapse after chemotherapy-induced regression is a major clinical problem, because it often involves inoperable metastatic disease. Tumor-associated macrophages (TAM) are known to limit the cytotoxic effects of chemotherapy in preclinical models of cancer. Here, we report that an alternatively activated (M2) subpopulation of TAMs (MRC1+TIE2HiCXCR4Hi) accumulate around blood vessels in tumors after chemotherapy, where they promote tumor revascularization and relapse, in part, via VEGF-A release. A similar perivascular, M2-related TAM subset was present in human breast carcinomas and bone metastases after chemotherapy. Although a small proportion of M2 TAMs were also present in hypoxic tumor areas, when we genetically ablated their ability to respond to hypoxia via hypoxia-inducible factors 1 and 2, tumor relapse was unaffected. TAMs were the predominant cells expressing immunoreactive CXCR4 in chemotherapy-treated mouse tumors, with the highest levels expressed by MRC1+ TAMs clustering around the tumor vasculature. Furthermore, the primary CXCR4 ligand, CXCL12, was upregulated in these perivascular sites after chemotherapy, where it was selectively chemotactic for MRC1+ TAMs. Interestingly, HMOX-1, a marker of oxidative stress, was also upregulated in perivascular areas after chemotherapy. This enzyme generates carbon monoxide from the breakdown of heme, a gas known to upregulate CXCL12. Finally, pharmacologic blockade of CXCR4 selectively reduced M2-related TAMs after chemotherapy, especially those in direct contact with blood vessels, thereby reducing tumor revascularization and regrowth. Our studies rationalize a strategy to leverage chemotherapeutic efficacy by selectively targeting this perivascular, relapse-promoting M2-related TAM cell population. Cancer Res; 75(17); 3479–91. ©2015 AACR.
Serum Retinol and Carotenoid Concentrations and Prostate Cancer Risk: Results from the Prostate Cancer Prevention Trial
Authors: Nash Sarah H. , Till Cathee , Song Xiaoling , Lucia M. Scott , Parnes Howard L. , Thompson Ian M. , Lippman Scott M. , Platz Elizabeth A. , Schenk Jeannette 
Published: August 2015

Abstract
Background: Findings from epidemiologic studies examining associations of serum retinol and carotenoids with prostate cancer risk have been inconsistent. This case–control study nested in the Prostate Cancer Prevention Trial evaluated associations of serum retinol and carotenoids with total, low-, and high-grade prostate cancer risk in a highly screened study population.
Methods: We used logistic regression adjusting for age, family history of prostate cancer, race, body mass index, and serum cholesterol to estimate ORs and 95% confidence intervals (CI) of prostate cancer by quartiles of serum retinol and carotenoids, separately in the placebo (975 cases/1,009 frequency-matched controls) and finasteride (708 cases/743 frequency-matched controls) arms of the trial.
Results: Serum retinol concentrations were associated with increased risk of total prostate cancer [OR (95% CI) comparing the highest quartile of serum retinol with the lowest: 1.30 (1.00–1.68)] and high-grade prostate cancer [OR (95% CI), 1.74 (1.14–2.68)] in the placebo arm of the trial only. Also in the placebo arm, there was a moderate positive association of α-carotene with risk of total prostate cancer [OR (95% CI), 1.32 (1.01–1.73)]. None of the other carotenoids was associated with prostate cancer risk in the placebo arm. No associations were observed for retinol and carotenoids in the finasteride arm.
Conclusion: In the placebo arm of this prospective study, high serum retinol and α-carotene concentrations were associated with increased risk of total and high-grade prostate cancers.
Impact: Men with higher levels of serum retinol and α-carotene may be at increased risk for prostate cancer. Cancer Epidemiol Biomarkers Prev; 24(10); 1507–15. ©2015 AACR.
Activation of EZH2 and SUZ12 Regulated by E2F1 Predicts the Disease Progression and Aggressive Characteristics of Bladder Cancer
Authors: Lee Se-Ra , Roh Yun-Gil , Kim Seon-Kyu , Lee Ju-Seog , Seol So-Young , Lee Hyun-Hee , Kim Won-Tae , Kim Wun-Jae , Heo Jeonghoon , Cha Hee-Jae , Kang Tae-Hong , Chung Jin Woong , Chu In-Sun , Leem Sun-Hee 
Published: August 2015

Abstract
Purpose: Previous study identified E2F1 as a key mediator of non–muscle-invasive bladder cancer (NMIBC) progression. The aim of this study was to identify the E2F1-related genes associated with poor prognosis and aggressive characteristics of bladder cancer.
Experimental Design: Microarray analysis was performed to find E2F1-related genes associated with tumor progression and aggressiveness in the gene expression data from 165 primary patients with bladder cancer. The biologic activity of E2F1-related genes in tumor progression and aggressiveness was confirmed with experimental assays using bladder cancer cells and tumor xenograft assay.
Results: The expression of E2F1 was significantly associated with EZH2 and SUZ12. The overexpression of E2F1, EZH2, and SUZ12 enhanced cancer progression including cell colony formation, migration, and invasiveness. Knockdown of these genes reduced motility, blocked invasion, and decreased tumor size in vivo. E2F1 bound the proximal EZH2 and SUZ12 promoter to activate transcription, suggesting that E2F1 and its downstream effectors, EZH2 and SUZ12, could be important mediators for the cancer progression. In addition, we confirmed an association between these genes and aggressive characteristics. Interestingly, the treatment of anticancer drugs to the cells overexpressing E2F1, EZH2, and SUZ12 induced the expression of CD44, KLF4, OCT4, and ABCG2 known as cancer stem cell (CSC)–related genes.
Conclusions: The link between E2F1, EZH2, and/or SUZ12 revealed that E2f1 directly regulates transcription of the EZH2 and SUZ12 genes. The signature of E2F1–EZH2–SUZ12 shows a predictive value for prognosis in bladder tumors and the E2F1–EZH2–SUZ12–driven transcriptional events may regulate the cancer aggressiveness and chemo-resistance, which may provide opportunity for development of new treatment modalities. Clin Cancer Res; 21(23); 5391–403. ©2015 AACR.
Redesigning a Monospecific Anti-FGFR3 Antibody to Add Selectivity for FGFR2 and Expand Antitumor Activity
Authors: Yin Yiyuan , Djakovic Stevan , Marsters Scot , Tien Janet , Peng Jing , Tremayne Jarrod , Lee Genee , Neve Richard M. , Wu Yan , Merchant Mark , Ashkenazi Avi , Carter Paul J. 
Published: August 2015

AbstractFGF receptors (FGFR) are attractive candidate targets for cancer therapy because they are dysregulated in several human malignancies. FGFR2 and FGFR3 can be inhibited potentially without disrupting adult tissue homeostasis. In contrast, blocking the closely related FGFR1 and FGFR4, which regulate specific metabolic functions, carries a greater safety risk. An anti-FGFR3 antibody was redesigned here to create function-blocking antibodies that bind with dual specificity to FGFR3 and FGFR2 but spare FGFR1 and FGFR4. R3Mab, a previously developed monospecific anti-FGFR3 antibody, was modified via structure-guided phage display and acquired additional binding to FGFR2. The initial variant was trispecific, binding tightly to FGFR3 and FGFR2 and moderately to FGFR4, while sparing FGFR1. The X-ray crystallographic structure indicated that the antibody variant was bound to a similar epitope on FGFR2 as R3Mab on FGFR3. The antibody was further engineered to decrease FGFR4-binding affinity while retaining affinity for FGFR3 and FGFR2. The resulting dual-specific antibodies blocked FGF binding to FGFR3 and FGFR2 and inhibited downstream signaling. Moreover, they displayed efficacy in mice against human tumor xenografts overexpressing FGFR3 or FGFR2. Thus, a monospecific antibody can be exquisitely tailored to confer or remove binding to closely related targets to expand and refine therapeutic potential. Mol Cancer Ther; 14(10); 2270–8. ©2015 AACR.