Stable Persistence Research Articles

Improved statistical methods enable greater sensitivity in rhythm detection for genome-wide data.

Robust methods for identifying patterns of expression in genome-wide data are important for generating hypotheses regarding gene function. To this end, several analytic methods have been developed for detecting periodic patterns. We improve one such method, JTK_CYCLE, by explicitly calculating the null distribution such that it accounts for multiple hypothesis testing and by including non-sinusoidal reference waveforms. We term this method empirical JTK_CYCLE with asymmetry search, and we compare its performance to JTK_CYCLE with Bonferroni and Benjamini-Hochberg multiple hypothesis testing correction, as well as to five other methods: cyclohedron test, address reduction, stable persistence, ANOVA, and F24. We find that ANOVA, F24, and JTK_CYCLE consistently outperform the other three methods when data are limited and noisy; empirical JTK_CYCLE with asymmetry search gives the greatest sensitivity while controlling for the false discovery rate. Our analysis also provides insight into experimental design and we find that, for a fixed number of samples, better sensitivity and specificity are achieved with higher numbers of replicates than with higher sampling density. Application of the methods to detecting circadian rhythms in a metadataset of microarrays that quantify time-dependent gene expression in whole heads of Drosophila melanogaster reveals annotations that are enriched among genes with highly asymmetric waveforms. These include a wide range of oxidation reduction and metabolic genes, as well as genes with transcripts that have multiple splice forms.

Differences in AMPA and GABAA/B receptor subunit expression between the chronically reorganized cortex and brainstem of adult squirrel monkeys

The primate somatosensory neuraxis provides a highly translational model system with which to investigate adult neural plasticity. Here, we report immunohistochemical staining data for AMPA and GABAA/B receptor subunits of area 3b cortex and cuneate nucleus of adult squirrel monkeys one to five years after median and ulnar nerve transection. In Area 3B cortex, the expression of GluR1 AMPAR subunits in reorganized regions are significantly increased, while the expression of GluR2/3 AMPAR subunits are not. GABAA α1 subunit expression in the reorganized region is not significantly different from control regions. Presynaptic GABABR1a subunit expression was also not significantly different between reorganized and control regions, while postsynaptic GABABR1b subunit expression was significantly decreased. In the cuneate nucleus of the brainstem, the expression of GluR1 AMPAR subunits in reorganized regions was not significantly different, while GluR2/3 AMPAR subunit expression was significantly elevated. GABAA α1 subunit expression in the reorganized region was significantly decreased. Presynaptic GABABR1a subunit expression was not significantly different, while postsynaptic GABABR1b subunit expression was significantly decreased. When subunit expression is compared, brainstem and cortical patterns diverge over longer periods of recovery. Persistent patterns of change in the cortex are stable by 1-year. Alternatively, subunit expression in the cuneate nucleus one to five years after nerve injury is similar to that seen 1-month after a reorganizing injury. This suggests that cortical plasticity continues to change over many months as receptive field reorganization occurs, while brainstem plasticity obtains a level of stable persistence by one month.

Stable persistence of the yeast plasmid by hitchhiking on chromosomes during vegetative and germ-line divisions of host cells.

The chromosome-like stability of the Saccharomyces cerevisiae plasmid 2 micron circle likely stems from its ability to tether to chromosomes and segregate by a hitchhiking mechanism. The plasmid partitioning system, responsible for chromosome-coupled segregation, is comprised of 2 plasmid coded proteins Rep1 and Rep2 and a partitioning locus STB. The evidence for the hitchhiking model for mitotic plasmid segregation, although compelling, is almost entirely circumstantial. Direct tests for plasmid-chromosome association are hampered by the limited resolving power of current cell biological tools for analyzing yeast chromosomes. Recent investigations, exploiting the improved resolution of yeast meiotic chromosomes, have revealed the plasmid's propensity to be present at or near chromosome tips. This localization is consistent with the rapid plasmid movements during meiosis I prophase, closely resembling telomere dynamics driven by a meiosis-specific nuclear envelope motor. Current evidence is consistent with the plasmid utilizing the motor as a platform for gaining access to telomeres. Episomes of viruses of the papilloma family and the gammaherpes subfamily persist in latently infected cells by tethering to chromosomes. Selfish genetic elements from fungi to mammals appear to have, by convergent evolution, arrived at the common strategy of chromosome association as a means for stable propagation.

Genetic analysis of plant endophytic Pseudomonas putida BP25 and chemo-profiling of its antimicrobial volatile organic compounds

Black pepper associated bacterium BP25 was isolated from root endosphere of apparently healthy cultivar Panniyur-5 that protected black pepper against Phytophthora capsici and Radopholus similis – the major production constraints. The bacterium was characterized and mechanisms of its antagonistic action against major pathogens are elucidated. The polyphasic phenotypic analysis revealed its identity as Pseudomonas putida. Multi locus sequence typing revealed that the bacterium shared gene sequences with several other isolates representing diverse habitats. Tissue localization assays exploiting green fluorescence protein expression clearly indicated that PpBP25 endophytically colonized not only its host plant – black pepper, but also other distantly related plants such as ginger and arabidopsis. PpBP25 colonies could be enumerated from internal tissues of plants four weeks post inoculation indicated its stable establishment and persistence in the plant system. The bacterium inhibited broad range of pathogens such as Phytophthora capsici, Pythium myriotylum, Giberella moniliformis, Rhizoctonia solani, Athelia rolfsii, Colletotrichum gloeosporioides and plant parasitic nematode, Radopholus similis by its volatile substances. GC/MS based chemical profiling revealed presence of Heneicosane; Tetratetracontane; Pyrrolo [1,2-a] pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl); Tetracosyl heptafluorobutyrate; 1-3-Eicosene, (E)-; 1-Heneicosanol; Octadecyl trifluoroacetate and 1-Pentadecene in PpBP25 metabolite. Dynamic head space GC/MS analysis of airborne volatiles indicated the presence of aromatic compounds such as 1-Undecene;Disulfide dimethyl; Pyrazine, methyl-Pyrazine, 2,5-dimethyl-; Isoamyl alcohol; Pyrazine, methyl-; Dimethyl trisulfide, etc. The work paved way for profiling of broad spectrum antimicrobial VOCs in endophytic PpBP25 for crop protection.

A recombination suppressor contributes to ecological speciation in OSTRINIA moths.

Despite unparalleled access to species' genomes in our post-genomic age, we often lack adequate biological explanations for a major hallmark of the speciation process-genetic divergence. In the presence of gene flow, chromosomal rearrangements such as inversions are thought to promote divergence and facilitate speciation by suppressing recombination. Using a combination of genetic crosses, phenotyping of a trait underlying ecological isolation, and population genetic analysis of wild populations, we set out to determine whether evidence supports a role for recombination suppressors during speciation between the Z and E strains of European corn borer moth (Ostrinia nubilalis). Our results are consistent with the presence of an inversion that has contributed to accumulation of ecologically adaptive alleles and genetic differentiation across roughly 20% of the Ostrinia sex chromosome (~4 Mb). Patterns in Ostrinia suggest that chromosomal divergence may involve two separate phases-one driving its transient origin through local adaptation and one determining its stable persistence through differential introgression. As the evolutionary rate of rearrangements in lepidopteran genomes appears to be one of the fastest among eukaryotes, structural mutations may have had a disproportionate role during adaptive divergence and speciation in Ostrinia and in other moths and butterflies.

EBNA1.

Epstein-Barr nuclear antigen 1 (EBNA1) plays multiple important roles in EBV latent infection and has also been shown to impact EBV lytic infection. EBNA1 is required for the stable persistence of the EBV genomes in latent infection and activates the expression of other EBV latency genes through interactions with specific DNA sequences in the viral episomes. EBNA1 also interacts with several cellular proteins to modulate the activities of multiple cellular pathways important for viral persistence and cell survival. These cellular effects are also implicated in oncogenesis, suggesting a direct role of EBNA1 in the development of EBV-associated tumors.

Immunogenicity and tolerability of an MF59-adjuvanted, egg-derived, A/H1N1 pandemic influenza vaccine in children 6-35 months of age.

Vaccines against pandemic A/H1N1 influenza should provide protective immunity in children, because they are at greater risk of disease than adults. This study was conducted to identify the optimal dose of an MF59®-adjuvanted, egg-derived, A/H1N1 influenza vaccine for young children. Children 6-11 months (N = 144) and 12-35 months (N = 186) of age received vaccine formulations containing either 3.75 μg antigen with half the standard dose of MF59 or 7.5 μg antigen with a standard dose of MF59, or a nonadjuvanted formulation containing 15 μg antigen (children 12-35 months only). Participants were given 2 primary vaccine doses 3 weeks apart, followed by 1 booster dose of MF59-adjuvanted seasonal influenza vaccine 1 year later. Immunogenicity was assessed by hemagglutination inhibition and microneutralization assays. All vaccine formulations were highly immunogenic and met all 3 European licensure criteria after 2 doses. MF59-adjuvanted vaccines met all licensure criteria after 1 dose in both age cohorts, while nonadjuvanted vaccine did not meet all criteria after 1 dose in children 12-35 months. A single booster dose was highly immunogenic, and stable antibody persistence was observed in response to all vaccines. All vaccines were well tolerated. In this study, a single dose of 3.75 μg antigen with half the standard dose of MF59 was shown to be optimal, providing adequate levels of immediate and long-term antibodies in pediatric subjects 6-35 months of age. These data demonstrated that MF59 adjuvant allowed for reduced antigen content and promoted significant long-term antibody persistence in children, with a satisfactory safety profile.

The partitioning and copy number control systems of the selfish yeast plasmid: an optimized molecular design for stable persistence in host cells.

The multi-copy 2 micron plasmid of Saccharomyces cerevisiae, a resident of the nucleus, is remarkable for its high chromosome-like stability. The plasmid does not appear to contribute to the fitness of the host, nor does it impose a significant metabolic burden on the host at its steady state copy number. The plasmid may be viewed as a highly optimized selfish DNA element whose genome design is devoted entirely towards efficient replication, equal segregation and copy number maintenance. A partitioning system comprised of two plasmid coded proteins, Rep1 and Rep2, and a partitioning locus STB is responsible for equal or nearly equal segregation of plasmid molecules to mother and daughter cells. Current evidence supports a model in which the Rep-STB system promotes the physical association of the plasmid with chromosomes and thus plasmid segregation by a hitchhiking mechanism. The Flp site-specific recombination system housed by the plasmid plays a critical role in maintaining steady state plasmid copy number. A decrease in plasmid population due to rare missegregation events is rectified by plasmid amplification via a recombination induced rolling circle replication mechanism. Appropriate plasmid amplification, without runaway increase in copy number, is ensured by positive and negative regulation of FLP gene expression by plasmid coded proteins and by the control of Flp level/activity through host mediated post-translational modification(s) of Flp. The Flp system has been successfully utilized to understand mechanisms of site-specific recombination, to bring about directed genetic alterations for addressing fundamental problems in biology, and as a tool in biotechnological applications.

Endoscopic Endonasal Transpterygoid Transmaxillary Approach to the Infratemporal and Upper Parapharyngeal Tumors

To describe the endoscopic transnasal approach to the infratemporal fossa (ITF) and upper parapharyngeal space (UPS) and to analyze the indications and outcomes of this surgical technique in the management of the tumors localized in this critical area. Case series with chart review. Tertiary-care referral center. Retrospective review of patients with benign and malignant tumors arising in or extending to the ITF and UPS, treated from 2002 to 2012 at a single institute. The tumors were surgically resected using an endoscopic endonasal transpterygoid transmaxillary approach. Thirty-seven consecutive patients with benign tumors (20 juvenile nasopharyngeal angiofibromas, 2 extracranial trigeminal Schwannomas, 2 meningiomas, 1 cavernous hemangioma) and nonmetastatic malignant tumors (2 adenoid-cystic carcinoma, 1 mucoepidermoid carcinoma, 1 squamous cell carcinoma, 1 adenocarcinoma, 1 recurrence of chondrosarcoma, and 6 recurrences of undifferentiated carcinoma of nasopharyngeal type) were treated with curative intent. A gross-total resection was achieved in 35 of 37 patients. Major complications were observed in 1 case (intraoperative internal carotid artery blowout). Postoperatively, 8 patients received some form of adjuvant treatment. Mean follow-up was 30 months for malignancies and 60 months for benign tumors. All patients are now alive without recurrences. Stable intracranial persistence of disease was reported in 2 cases (1 meningioma and 1 adenoid-cystic carcinoma). The purely endoscopic endonasal technique may provide a minimally invasive and safe approach to radically resect selected tumors involving the ITF and UPS. Larger case series and longer follow-up are needed to validate the reproducibility and efficacy of this technique.

Natural history of small radioiodine-avid bone metastases that have no structural correlate on imaging studies

Bone metastases from differentiated thyroid cancer are generally resistant to radioiodine (RAI) therapy and are associated with poor prognosis. However, in a recent study from our group we noted a small subgroup of patients with RAI-avid bone metastases who had no structural correlate on imaging studies, and had no skeletal complications during follow-up. The purpose of this study was to better define the natural history and outcome of these patients. In a retrospective review of medical records at Memorial Sloan-Kettering Cancer Center, 288 patients were identified with bone metastases from thyroid cancer between 1960 and 2011. Out of this group, 14 patients who had a RAI-avid bone metastasis without structural correlate on CT or MRI were included in the study. After a median follow-up period of 5 years (range 2-14 years) all patients were alive, none had evidence of structural bone metastases, and none had experienced skeletal-related events. The final disease status was: no evidence of disease in 6 patients (43 %), stable biochemical persistence in 2 patients (14 %), stable structural disease in 5 patients (36 %), and one patient with slowly progressive disease. To conclude, RAI-avid bone metastases with no structural correlate on high-resolution imaging studies often resolve following RAI treatment, do not cause skeletal-related complications, and do not have a major prognostic significance. Recognition of this unique type of bone metastases is important as it is not associated with the same poor prognosis and resistance to RAI therapy that is associated with structurally identifiable bone metastases.

Long-Term Functional Persistence, B Cell Aplasia and Anti-Leukemia Efficacy In Refractory B Cell Malignancies Following T Cell Immunotherapy Using CAR-Redirected T Cells Targeting CD19

▪ BackgroundRecent advances in T cell engineering have enabled clinical trials to evaluate the potential for adoptive transfer of T cells to target malignancy. A single treatment with engineered gene-modified T cells has the potential to generate potent and long-lasting anti-tumor immunity. We have reported initial clinical data on the use of T cells engineered to express a Chimeric Antigen Receptor (CAR) that targets CD19 (CTL019) in patients with advanced treatment-refractory CLL and pediatric ALL (Porter, et al NEJM 2011; Kalos et al. Sci Trans Med 2011, Grupp et al. NEJM 2013). The initial cohort of patients is now disease free between 1 and 3 years post-infusion. In this report we present data on the functional persistence, trafficking, and bioactivity of CTL019 cells from the initial cohort of CLL patients, a larger and more recently treated cohort of CLL patients, a cohort of pediatric ALL patients, as well as an initial cohort of adult ALL patients. MethodsCAR engineering of patient T cells was accomplished by lentivirus transduction followed by in-vitro expansion using anti-CD3 and anti-CD28 antibody-coated beads. Persistence of gene-modified T cells was assessed by quantitative PCR. CAR19 surface expression was detected by flow. B cell aplasia was evaluated by multiparametric flow cytometry. Multiplex cytokine analyses were performed using LuminexTMtechnology. ResultsDetailed clinical outcomes for each patient cohort will be reported separately at this meeting (Porter, D.L.et al, Grupp S. et al). In summary, as of July 15, 2013: For CLL: A total of 24 adult patients with advanced relapsed and/or treatment-refractory CLL have been treated under two separate protocols. To date 5 patients have achieved ongoing CR, 7 patients PR and 12 patients were NR at the primary endpoint (within 3 months post infusion). For ALL (pediatric): A total of 14 pediatric patients with treatment refractory ALL have been treated and were evaluable under a single protocol. To date 8 patients have ongoing CR, 4 patients have relapsed including 2 with CD19-negative disease and 2 patients were NR. For ALL (Adult): A total of 3 adult patients with advanced relapsed and/or treatment-refractory ALL have been treated under a single protocol. All 3 patients have ongoing CR; one patient went into an allogeneic transplant while in CTL019-induced CR.In all patients with CR, robust in vivo expansion of CTL019 cells was observed, as assessed by both molecular and flow cytometric analysis, followed by contraction and in all but one patient ongoing stable persistence of engineered cells, elimination of tumor B cells and ongoing B cell aplasia in blood and marrow at all evaluated time points (minimum 3 months, maximum ongoing at 35 months). In CR patients, peak marking exceeded 5% of total CD3+. Patients with PR demonstrated less robust in-vivo expansion accompanied by transient B cell elimination, while NR patients demonstrated minimal in-vivo expansion.Clinical MRD analysis in patients was supplemented with Illumina-HiSeq/MiSeq-deep sequencing based molecular MRD analysis. These analyses demonstrate that CRs were accompanied with deep and sustained molecular remissions as assessed by the absence of the tumor specific clonotype defined in the enrollment samples.All patients in CR experienced on-target cytokine release syndrome (CRS) and macrophage activation syndrome (MAS). Multiplex-cytokine analysis of serum samples from patients in CR demonstrated a broad pro-inflammatory signature with significant elevation in a subset of soluble immune modulators including IFN-g, IL-6, and IL2ra. In contrast, patients with NR did not have elevated serum cytokines. Elevation of cytokines coincided with expansion of CTL019 cells, elimination of B cells, and toxicity suggesting the potential for a cytokine-based diagnostic signature to monitor CTL019 treatment efficacy. ConclusionsAdoptive transfer of CTL019 cells engineered to express CD137 and TCR-zeta signaling domains can result in in-vivo expansion, homing to marrow, and long-term functional persistence of engineered cells, accompanied by ongoing complete clinical responses and long-term B cell aplasia in a substantial fraction of patients with advanced, refractory and high risk CLL and relapsed refractory pre- B cell ALL. These results highlight the potential of CTL019 therapy to effectively target CD19-positive malignancy. Disclosures:Kalos:Novartis corporation: CART19 technology, CART19 technology Patents & Royalties; Adaptive biotechnologies: Member scientific advisory board , Member scientific advisory board Other. Zheng:Novartis: Patents & Royalties. Levine:Novartis: cell and gene therapy IP, cell and gene therapy IP Patents & Royalties. Grupp:Novartis: Research Funding. June:Novartis: Patents & Royalties, Research Funding.

Carrot or Stick? Modelling How Landowner Behavioural Responses Can Cause Incentive-Based Forest Governance to Backfire

Mitigating the negative impacts of declining worldwide forest cover remains a significant socio-ecological challenge, due to the dominant role of human decision-making. Here we use a Markov chain model of land-use dynamics to examine the impact of governance on forest cover in a region. Each land parcel can be either forested or barren (deforested), and landowners decide whether to deforest their parcel according to perceived value (utility). We focus on three governance strategies: yearly incentive for conservation, one-time penalty for deforestation and one-time incentive for reforestation. The incentive and penalty are incorporated into the expected utility of forested land, which decreases the net gain of deforestation. By analyzing the equilibrium and stability of the landscape dynamics, we observe four possible outcomes: a stationary-forested landscape, a stationary-deforested landscape, an unstable landscape fluctuating near the equilibrium, and a cyclic-forested landscape induced by synchronized deforestation. We find that the two incentive-based strategies often result in highly fluctuating forest cover over decadal time scales or longer, and in a few cases, reforestation incentives actually decrease the average forest cover. In contrast, a penalty for deforestation results in the stable persistence of forest cover (generally >30%). The idea that larger conservation incentives will always yield higher and more stable forest cover is not supported in our findings. The decision to deforest is influenced by more than a simple, “rational” cost-benefit analysis: social learning and myopic, stochastic decision-making also have important effects. We conclude that design of incentive programs may need to account for potential counter-productive long-term effects due to behavioural feedbacks.

Endoscopic Transnasal Approach to the Infratemporal and Upper Parapharyngeal Tumors: Indications and Outcomes

Objectives: Describe the endoscopic transnasal approach to the infratemporal fossa (ITF) and upper parapharyngeal region (UPR), and analyze the indications and outcomes of this surgical technique in the management of the tumors localized in this critical area. Methods: Retrospective review of patients with benign and malignant tumors arising in or extending to the ITF and UPR, treated from 2002 to 2012 at a single institute. The tumors were surgically resected using an endoscopic transnasal transmaxillary transpterygoid approach, combined with a posterior septotomy to improve the controlateral maneuverability of surgical instruments. Results: Thirty-one consecutive patients with benign tumors (20 juvenile nasopharyngeal angiofibromas, 2 extracranial trigeminal schwannomas, 2 meningiomas, and 1 cavernous hemangioma) and malignancies (2 adenoid-cystic carcinoma, 1 mucoepidermoid carcinoma, 1 squamous-cell carcinoma, 1 adenocarcinoma, and 1 recurrence of chondrosarcoma after chemo-radiation therapy) were treated with curative intent. A gross-total resection was achieved in 28/30 patients. Major complications were observed in 1 case (intra-operative internal carotid artery blowout), and minor complications (postoperative palate and/or cheek numbness) were observed in 4 cases. Postoperatively, the 5 primitive malignancies received intensity-modulated radiotherapy. Mean follow-up was 30 months for malignancies and 54 months for benign tumors. All patients are now alive without recurrences, with stable intracranial persistence of disease in 2 cases (1 meningioma and 1 adenoid-cystic carcinoma). Conclusions: The purely endoscopic transnasal technique may provide a minimally-invasive and safe approach to resect selected tumors involving the ITF and UPR. Larger case series and longer follow-up are needed to validate the reproducibility and efficacy of this technique.

Abstract 2189: Inhibition of PIN1 suppresses tumorigenicity of EBV-associated NPC.

Abstract Nasopharyngeal carcinoma (NPC) is an EBV-associated epithelial malignancy which is prevalent in southern China and south-east Asia. EBV-encoded EBNA1 is consistently expressed in NPC cells and implicates the replication and stable persistence of latent viral genome. As a phosphorylated protein, the function of EBV is believed to be affected by phosphorylation.In this study, we aimed to investigate whether the phospho-Ser/Thr-Pro specific prolyl-isomerase PIN1 alters EBNA1 function and plays a role in the tumorigenesis of EBV-associated NPC.By western blotting and immunohistochemical staining, we have found that PIN1 was highly expressed in almost all 6 NPC tumor lines and 70 primary tumors. In the EBV-positive C666-1 cells, co-localization and interaction of EBNA1 and PIN1 was detected by immunofluorence staining and co-immunoprecipitation assay respectively. The interaction between PIN1 and EBNA1 at the specific serine-proline motif (Ser383 and Ser393 in EBNA1;WW domain in Pin1) was also demonstrated. To investigate potential role of PIN1 in NPC tumorigenesis, we established a stable nasopharyngeal epitheliacell line NP69 overexpressing PIN1. In this model, we found that overexpression of PIN1 up-regulated cyclin D1 and activated MAPK/JNK pathway. Increased anchorage-independent growth of NP69 overexpressing PIN was shown in soft agar assay.To further validate the oncogencity of PIN1, we knocked down its expression in the NPC cell line C666-1 by RNA interference (siRNA). The study confirmed the PIN1-mediated cyclin D1 suppression. Importantly, knocking down of PIN1 significantly inhibited the cell proliferation, DNA synthesis and migration of NPC cells.Similar findings were also detected in the NPC cells treated with PIN1 inhibitor, Juglone. Treating EBV-positive C666-1cell with Juglone,we found it can significantly induce apoptosisand suppress the cyclinD1expression in C666-1cells. The anti-tumor effect of PIN inhibitor was demonstrated in the in vitro NPC model. To elucidate the anti-tumor potential of PIN1 inhibitorin vivo, the mice implanted with NPC cells were subjected to treatment with different doses of Juglone. A dose-dependent inhibition of tumor growth was observed in the mice treated with PIN1 inhibitor. In conclusion, our findings imply that PIN1overexpression plays important role in the development of NPC. Targeting Pin1 may serve as a potential therapeutic approach for treating patients suffering from this EBV-associated cancer. Citation Format: Meng Xu, Chit Chow, Chartia Ching-Mei Cheung, Chi-Man Tsang, Samantha Wei-Man Lun, Jessie Wai-Fung Yuen, Grace Tin-Yun Chung, Sah-Wah Tsao, Ka Fai To, Kwok Wai Lo. Inhibition of PIN1 suppresses tumorigenicity of EBV-associated NPC. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2189. doi:10.1158/1538-7445.AM2013-2189

Characterization of the Two Intra-Individual Sequence Variants in the 18S rRNA Gene in the Plant Parasitic Nematode, Rotylenchulus reniformis

The 18S rRNA gene is fundamental to cellular and organismal protein synthesis and because of its stable persistence through generations it is also used in phylogenetic analysis among taxa. Sequence variation in this gene within a single species is rare, but it has been observed in few metazoan organisms. More frequently it has mostly been reported in the non-transcribed spacer region. Here, we have identified two sequence variants within the near full coding region of 18S rRNA gene from a single reniform nematode (RN) Rotylenchulus reniformis labeled as reniform nematode variant 1 (RN_VAR1) and variant 2 (RN_VAR2). All sequences from three of the four isolates had both RN variants in their sequences; however, isolate 13B had only RN variant 2 sequence. Specific variable base sites (96 or 5.5%) were found within the 18S rRNA gene that can clearly distinguish the two 18S rDNA variants of RN, in 11 (25.0%) and 33 (75.0%) of the 44 RN clones, for RN_VAR1 and RN_VAR2, respectively. Neighbor-joining trees show that the RN_VAR1 is very similar to the previously existing R. reniformis sequence in GenBank, while the RN_VAR2 sequence is more divergent. This is the first report of the identification of two major variants of the 18S rRNA gene in the same single RN, and documents the specific base variation between the two variants, and hypothesizes on simultaneous co-existence of these two variants for this gene.

Antiviral effects of autologous CD4 T cells genetically modified with a conditionally replicating lentiviral vector expressing long antisense to HIV

AbstractWe report the safety and tolerability of 87 infusions of lentiviral vector–modified autologous CD4 T cells (VRX496-T; trade name, Lexgenleucel-T) in 17 HIV patients with well-controlled viremia. Antiviral effects were studied during analytic treatment interruption in a subset of 13 patients. VRX496-T was associated with a decrease in viral load set points in 6 of 8 subjects (P = .08). In addition, A → G transitions were enriched in HIV sequences after infusion, which is consistent with a model in which transduced CD4 T cells exert antisense-mediated genetic pressure on HIV during infection. Engraftment of vector-modified CD4 T cells was measured in gut-associated lymphoid tissue and was correlated with engraftment in blood. The engraftment half-life in the blood was approximately 5 weeks, with stable persistence in some patients for up to 5 years. Conditional replication of VRX496 was detected periodically through 1 year after infusion. No evidence of clonal selection of lentiviral vector–transduced T cells or integration enrichment near oncogenes was detected. This is the first demonstration that gene-modified cells can exert genetic pressure on HIV. We conclude that gene-modified T cells have the potential to decrease the fitness of HIV-1 and conditionally replicative lentiviral vectors have a promising safety profile in T cells. This study is registered at www.clinicaltrials.gov as number NCT00295477.

Spatial aspects of prebiotic replicator coexistence and community stability in a surface-bound RNA world model

BackgroundThe coexistence of macromolecular replicators and thus the stability of presumed prebiotic replicator communities have been shown to critically depend on spatially constrained catalytic cooperation among RNA-like modular replicators. The necessary spatial constraints might have been supplied by mineral surfaces initially, preceding the more effective compartmentalization in membrane vesicles which must have been a later development of chemical evolution.ResultsUsing our surface-bound RNA world model – the Metabolic Replicator Model (MRM) platform – we show that the mobilities on the mineral substrate surface of both the macromolecular replicators and the small molecules of metabolites they produce catalytically are the key factors determining the stable persistence of an evolvable metabolic replicator community.ConclusionThe effects of replicator mobility and metabolite diffusion on different aspects of replicator coexistence in MRM are determined, including the maximum attainable size of the metabolic replicator system and its resistance to the invasion of parasitic replicators. We suggest a chemically plausible hypothetical scenario for the evolution of the first protocell starting from the surface-bound MRM system.

Proper design of silica nanoparticles combines high brightness, lack of cytotoxicity and efficient cell endocytosis

Silica-based luminescent nanoparticles (SiNPs) show promising prospects in nanomedicine in light of their chemical properties and versatility. In this study, we have characterized silica core-PEG shell SiNPs derivatized with PEG moieties (NP-PEG), with external amino- (NP-PEG-amino) or carboxy-groups (NP-PEG-carbo), both in cell cultures as well as in animal models. By using different techniques, we could demonstrate that these SiNPs were safe and did not exhibit appreciable cytotoxicity in different relevant cell models, of normal or cancer cell types, growing either in suspension (JVM-2 leukemic cell line and primary normal peripheral blood mononuclear cells) or in adherence (human hepatocarcinoma Huh7 and umbilical vein endothelial cells). Moreover, by multiparametric flow cytometry, we could demonstrate that the highest efficiency of cell uptake and entry was observed with NP-PEG-amino, with a stable persistence of the fluorescence signal associated with SiNPs in the loaded cell populations both in vitro and in vivo settings suggesting this as an innovative method for cell traceability and detection in whole organisms. Finally, experiments performed with the endocytosis inhibitor Genistein clearly suggested the involvement of a caveolae-mediated pathway in SiNP endocytosis. Overall, these data support the safe use of these SiNPs for diagnostic and therapeutic applications.

Sustained Functional T Cell Persistence and B Cell Aplasia Following CD19-Targeting Adoptive T Cell Immunotherapy for Relapsed, Refractory CD19+ Malignacy

Abstract 756 BackgroundAdvances in ex vivo T cell engineering have facilitated clinical trials to evaluate the potential for adoptive T cell transfer to target malignancy. Gene-modified T cells have the potential to expand, functionally persist and mediate long-term anti-tumor activity. Most clinical studies have shown only limited persistence of infused cells, with modest and often temporary anti-tumor activity. We reported initial clinical data on CAR T cells targeting CD19 expressed on normal and malignant B cells (CART19 cells) (Porter, et al NEJM 2011; Kalos et al Sci Trans Med 2011). The CAR included signaling domains from CD3zeta and CD137 (4-1BB) that mediated effector and proliferation/persistence signals. Here we report functional persistence of CART19 cells from the initial cohort at approximately 2 years post-infusion, and data from a more recently treated cohort of CLL patients and a pediatric patient with advanced, treatment refractory ALL. MethodsPersistence of gene-modified T cells was assessed by quantitative ABI-Taqman based PCR and a qualified assay that detects the CD137-TcR-zeta junction in the anti-CD19 CAR. CAR19 surface expression was detected by flow cytometry with an anti-CAR-19 idiotype specific antibody. B cell aplasia was evaluated by multiparametric flow cytometry. Multiplex cytokine analyses were performed using Luminex™assays. Results10 patients with relapsed, refractory disease have been treated to date: 9 adults w/CLL and one child w/pre- B cell ALL. Each had been extensively pre-treated and had active disease at the time of CART19 infusion. All CLL patients received lymphodepleting chemotherapy 4–6 days before infusions, while the ALL patient did not get further lymphodepletion. Patients were infused with an average total of 1.7–50 × 108 total T cells which corresponded to 0.14–5.9 x108CART-19 cells.9/10 treated patients were evaluable on 8.14.12. Detailed clinical outcomes will be reported separately at this meeting (Porter, D.L., Grupp S. et al). 4 pts (3 CLL, 1 ALL) had achieved CR at the primary endpoint (30 days post infusion) which is sustained and ongoing in all patients (range 1–24 months). Two CLL patients had a partial response (PR) lasting 3 and 5 months, while 3 patients did not respond (NR). In all patients with CR, robust in vivo expansion of CART19 cells was observed. By molecular analysis, CART19 cells demonstrated in vivo expansion, followed by contraction and an ongoing stable persistence at all evaluated timepoints. Expansion kinetics were unique for each patient; in all cases maximal expansion was observed by day +30 post CART-19 infusion. In patients with CR, observed peak marking for CART-19 ranged from 1 × 102-1 × 103 CART-19 cells/uL blood. Patients with PR demonstrated less robust in vivo expansion, with peak observed marking ∼1 × 101 CART-19 cells/uL blood. In NR patients, peak marking was <1 × 101CART-19 cells/uL blood. Long term peripheral blood persistence of CART19 cells and CAR19 surface expression was observed in all patients with CR in both CD3+/CD8+ and CD3+/CD4+ subsets. In patients with CR, elimination of peripheral B cells was observed at the time of CART19 in vivo expansion. Ongoing B cell aplasia has been documented in each CR patient in both peripheral blood and marrow by flow cytometry. Patients with PR showed transient elimination of malignant and normal B cells.Multiplex-cytokine analysis of serum samples from CR patients revealed a broad pro-inflammatory signature with significant elevation in a subset of soluble immune modulators including IL-6, IL-8, IFN-g, MIP1b, and IL2ra. In contrast, NR patients did not have elevated serum cytokines. In CR patients, elevation of cytokines tracked with expansion of CART19 cells and elimination of B cells, suggesting the potential for a cytokine-based diagnostic signature to monitor CART19 treatment efficacy. ConclusionsAdoptive transfer of CART19 cells engineered to express CD137 and TCR-zeta signaling domains can result in in vivo expansion, homing to disease sites, and long-term functional persistence of CART19 cells, accompanied by ongoing complete clinical responses and long-term B cell aplasia in a substantial fraction of patients with advanced, refractory and high risk CLL and relapsed refractory ALL. A detailed cytokine profile and persistent B cell aplasia has been identified that may correlate with treatment efficacy. Disclosures:Kalos:University of Pennsylvania: Patents & Royalties. Levine:TxCell: Consultancy, Membership on an entity’s Board of Directors or advisory committees; University of Pennsylvania: financial interest due to intellectual property and patents in the field of cell and gene therapy. Conflict of interest is managed in accordance with University of Pennsylvania policy and oversight, financial interest due to intellectual property and patents in the field of cell and gene therapy. Conflict of interest is managed in accordance with University of Pennsylvania policy and oversight Patents & Royalties. June:Novartis: Research Funding, institution owned patents have been licensed by Novartis, institution owned patents have been licensed by Novartis Patents & Royalties.

At low precursor frequencies, the T‐cell response to chronic self‐antigen results in anergy without deletion

The behavior of self-reactive T cells in the peripheral immune system has often been studied by following the fate of adoptively transferred antigen-specific T cells in antigen expressing mice. In most cases, after a period of expansion, such cells undergo a slow clonal deletion, accompanied by the onset of anergy and/or suppression in the remaining cells. Here, we demonstrate that at initial frequencies approaching those found in normal repertoires, it is possible to completely avoid deletion and still maintain peripheral tolerance. At starting numbers of <1000 T cells, stimulation by chronic self-antigens resulted in a period of robust clonal expansion, followed by a steady plateau phase extending beyond 4 months. Despite their stable persistence, the self-reactive T cells did not convert to a Foxp3⁺ fate. However, they displayed a considerable block in their ability to make IL-2, consistent with the onset of anergy - in a precursor frequency or deletion independent fashion.