Prediction of tumor-reactive T cell receptors from scRNA-seq data for personalized T cell therapy

The identification of patient-derived, tumor-reactive T cell receptors (TCRs) as a basis for personalized transgenic T cell therapies remains a time- and cost-intensive endeavor. Current approaches to identify tumor-reactive TCRs analyze tumor mutations to predict T cell activating (neo)antigens and use these to either enrich tumor infiltrating lymphocyte (TIL) cultures or validate individual TCRs for transgenic autologous therapies. Here we combined high-throughput TCR cloning and reactivity validation to train predicTCR, a machine learning classifier that identifies individual tumor-reactive TILs in an antigen-agnostic manner based on single-TIL RNA sequencing. PredicTCR identifies tumor-reactive TCRs in TILs from diverse cancers better than previous gene set enrichment-based approaches, increasing specificity and sensitivity (geometric mean) from 0.38 to 0.74. By predicting tumor-reactive TCRs in a matter of days, TCR clonotypes can be prioritized to accelerate the manufacture of personalized T cell therapies.

H3K27M neoepitope vaccination in diffuse midline glioma induces B and T cell responses across diverse HLA loci of a recovered patient

H3K27M, a driver mutation with T and B cell neoepitope characteristics, defines an aggressive subtype of diffuse glioma with poor survival. We functionally dissect the immune response of one patient treated with an H3K27M peptide vaccine who subsequently entered complete remission. The vaccine robustly expanded class II human leukocyte antigen (HLA)-restricted peripheral H3K27M-specific T cells. Using functional assays, we characterized 34 clonally unique H3K27M-reactive T cell receptors and identified critical, conserved motifs in their complementarity-determining region 3 regions. Using detailed HLA mapping, we further demonstrate that diverse HLA-DQ and HLA-DR alleles present immunogenic H3K27M epitopes. Furthermore, we identified and profiled H3K27M-reactive B cell receptors from activated B cells in the cerebrospinal fluid. Our results uncover the breadth of the adaptive immune response against a shared clonal neoantigen across multiple HLA allelotypes and support the use of class II-restricted peptide vaccines to stimulate tumor-specific T and B cells harboring receptors with therapeutic potential.

NLGN4X TCR transgenic T cells to treat gliomas

BACKGROUND

Neuroligin 4 X-linked (NLGN4X) harbors a human leukocyte antigen (HLA)-A*02-restricted tumor-associated antigen, overexpressed in human gliomas, that was found to induce specific cytotoxic T cell responses following multi-peptide vaccination in patients with newly diagnosed glioblastoma.

METHODS

T cell receptor (TCR) discovery was performed using droplet-based single-cell TCR sequencing of NLGN4X-tetramer-sorted T cells postvaccination. The identified TCR was delivered to Jurkat T cells and primary human T cells (NLGN4X-TCR-T). Functional profiling of NLGN4X-TCR-T was performed by flow cytometry and cytotoxicity assays. Therapeutic efficacy of intracerebroventricular NLGN4X-TCR-T was assessed in NOD scid gamma (NSG) major histocompatibility complex (MHC) I/II knockout (KO) (NSG MHC I/II KO) mice bearing NLGN4X-expressing experimental gliomas.

RESULTS

An HLA-A*02-restricted vaccine-induced T cell receptor specifically binding NLGN4X131-139 was applied for preclinical therapeutic use. Reactivity, cytotoxicity, and polyfunctionality of this NLGN4X-specific TCR are demonstrated in various cellular models. Intracerebroventricular administration of NLGN4X-TCR-T prolongs survival and leads to an objective response rate of 44.4% in experimental glioma-bearing NSG MHC I/II KO mice compared to 0.0% in control groups.

CONCLUSION

NLGN4X-TCR-T demonstrate efficacy in a preclinical glioblastoma model. On a global scale, we provide the first evidence for the therapeutic retrieval of vaccine-induced human TCRs for the off-the-shelf treatment of glioblastoma patients.Keywords cell therapy | glioblastoma | T cell receptor | tumor antigen.

T-FINDER: A highly sensitive, pan-HLA platform for functional T cell receptor and ligand discovery

Effective, unbiased, high-throughput methods to functionally identify both class II and class I HLA-presented T cell epitopes and their cognate T cell receptors (TCRs) are essential for and prerequisite to diagnostic and therapeutic applications, yet remain underdeveloped. Here, we present T-FINDER [T cell Functional Identification and (Neo)-antigen Discovery of Epitopes and Receptors], a system to rapidly deconvolute CD4 and CD8 TCRs and targets physiologically processed and presented by an individual's unmanipulated, complete human leukocyte antigen (HLA) haplotype. Combining a highly sensitive TCR signaling reporter with an antigen processing system to overcome previously undescribed limitations to target expression, T-FINDER both robustly identifies unknown peptide:HLA ligands from antigen libraries and rapidly screens and functionally validates the specificity of large TCR libraries against known or predicted targets. To demonstrate its capabilities, we apply the platform to multiple TCR-based applications, including diffuse midline glioma, celiac disease, and rheumatoid arthritis, providing unique biological insights and showcasing T-FINDER's potency and versatility.

Correction: The circadian clock gene bmal1 is necessary for co-ordinated circatidal rhythms in the marine isopod Eurydice pulchra (Leach)

[This corrects the article DOI: 10.1371/journal.pgen.1011011.].

A H3K27M-targeted vaccine in adults with diffuse midline glioma

Substitution of lysine 27 to methionine in histone H3 (H3K27M) defines an aggressive subtype of diffuse glioma. Previous studies have shown that a H3K27M-specific long peptide vaccine (H3K27M-vac) induces mutation-specific immune responses that control H3K27M+ tumors in major histocompatibility complex-humanized mice. Here we describe a first-in-human treatment with H3K27M-vac of eight adult patients with progressive H3K27M+ diffuse midline glioma on a compassionate use basis. Five patients received H3K27M-vac combined with anti-PD-1 treatment based on physician's discretion. Repeat vaccinations with H3K27M-vac were safe and induced CD4+ T cell-dominated, mutation-specific immune responses in five of eight patients across multiple human leukocyte antigen types. Median progression-free survival after vaccination was 6.2 months and median overall survival was 12.8 months. One patient with a strong mutation-specific T cell response after H3K27M-vac showed pseudoprogression followed by sustained complete remission for >31 months. Our data demonstrate safety and immunogenicity of H3K27M-vac in patients with progressive H3K27M+ diffuse midline glioma.

The circadian clock gene bmal1 is necessary for co-ordinated circatidal rhythms in the marine isopod Eurydice pulchra (Leach)

Circadian clocks in terrestrial animals are encoded by molecular feedback loops involving the negative regulators PERIOD, TIMELESS or CRYPTOCHROME2 and positive transcription factors CLOCK and BMAL1/CYCLE. The molecular basis of circatidal (~12.4 hour) or other lunar-mediated cycles (~15 day, ~29 day), widely expressed in coastal organisms, is unknown. Disrupting circadian clockworks does not appear to affect lunar-based rhythms in several organisms that inhabit the shoreline suggesting a molecular independence of the two cycles. Nevertheless, pharmacological inhibition of casein kinase 1 (CK1) that targets PERIOD stability in mammals and flies, affects both circadian and circatidal phenotypes in Eurydice pulchra (Ep), the speckled sea-louse. Here we show that these drug inhibitors of CK1 also affect the phosphorylation of EpCLK and EpBMAL1 and disrupt EpCLK-BMAL1-mediated transcription in Drosophila S2 cells, revealing a potential link between these two positive circadian regulators and circatidal behaviour. We therefore performed dsRNAi knockdown of Epbmal1 as well as the major negative regulator in Eurydice, Epcry2 in animals taken from the wild. Epcry2 and Epbmal1 knockdown disrupted Eurydice's circadian phenotypes of chromatophore dispersion, tim mRNA cycling and the circadian modulation of circatidal swimming, as expected. However, circatidal behaviour was particularly sensitive to Epbmal1 knockdown with consistent effects on the power, amplitude and rhythmicity of the circatidal swimming cycle. Thus, three Eurydice negative circadian regulators, EpCRY2, in addition to EpPER and EpTIM (from a previous study), do not appear to be required for the expression of robust circatidal behaviour, in contrast to the positive regulator EpBMAL1. We suggest a neurogenetic model whereby the positive circadian regulators EpBMAL1-CLK are shared between circadian and circatidal mechanisms in Eurydice but circatidal rhythms require a novel, as yet unknown negative regulator.

Pneumonia, Meningitis, and Septicemia in Adults and Older Children in Rural Gambia: 8 Years of Population-Based Surveillance

BACKGROUND

Representative data describing serious infections in children aged ≥5 years and adults in Africa are limited.

METHODS

We conducted population-based surveillance for pneumonia, meningitis, and septicemia in a demographic surveillance area in The Gambia between 12 May 2008 and 31 December 2015. We used standardized criteria to identify, diagnose, and investigate patients aged ≥5 years using conventional microbiology and radiology.

RESULTS

We enrolled 1638 of 1657 eligible patients and investigated 1618. Suspected pneumonia, septicemia, or meningitis was diagnosed in 1392, 135, and 111 patients, respectively. Bacterial pathogens from sterile sites were isolated from 105 (7.5%) patients with suspected pneumonia, 11 (8.1%) with suspected septicemia, and 28 (25.2%) with suspected meningitis. Streptococcus pneumoniae (n = 84), Neisseria meningitidis (n = 16), and Staphylococcus aureus (n = 15) were the most common pathogens. Twenty-eight (1.7%) patients died in hospital and 40 (4.1%) died during the 4 months after discharge. Thirty postdischarge deaths occurred in patients aged ≥10 years with suspected pneumonia. The minimum annual incidence was 133 cases per 100 000 person-years for suspected pneumonia, 13 for meningitis, 11 for septicemia, 14 for culture-positive disease, and 46 for radiological pneumonia. At least 2.7% of all deaths in the surveillance area were due to suspected pneumonia, meningitis, or septicemia.

CONCLUSIONS

Pneumonia, meningitis, and septicemia in children aged ≥5 years and adults in The Gambia are responsible for significant morbidity and mortality. Many deaths occur after hospital discharge and most cases are culture negative. Improvements in prevention, diagnosis, inpatient, and follow-up management are urgently needed.

T cell receptor dynamic and transcriptional determinants of T cell expansion in glioma-infiltrating T cells

Background

Glioblastoma (GBM) is characterized by low numbers of glioma-infiltrating lymphocytes (GIL) with a dysfunctional phenotype. Whether this dysfunctional phenotype is fixed or can be reversed upon ex vivo culturing is poorly understood. The aim of this study was to assess T cell receptor (TCR)-dynamics and -specificities as well as determinants of in vitro GIL expansion by sequencing-based technologies and functional assays to explore the use of GIL for cell therapy.

Methods

By means of flow cytometry, T cell functionality in GIL cultures was assessed from 9 GBM patients. TCR beta sequencing (TCRB-seq) was used for TCR repertoire profiling before and after in vitro expansion. Microarrays or RNA sequencing (RNA-seq) were performed from 6 micro-dissected GBM tissues and healthy brain RNA to assess the individual expression of GBM-associated antigens (GAA). GIL reactivity against in silico predicted tumor-associated antigens (TAA) and patient-individual GAA was assessed by ELISpot assay. Combined ex vivo single cell (sc)TCR-/RNA-seq and post-expansion TCRB-seq were used to evaluate transcriptional signatures that determine GIL expansion.

Results

Human GIL regains cellular fitness upon in vitro expansion. Profound TCR dynamics were observed during in vitro expansion and only in one of six GIL cultures, reactivity against GAA was observed. Paired ex vivo scTCR/RNA-seq and TCRB-seq revealed predictive transcriptional signatures that determine GIL expansion.

Conclusions

Profound TCR repertoire dynamics occur during GIL expansion. Ex vivo transcriptional T cell states determine expansion capacity in gliomas. Our observation has important implications for the use of GIL for cell therapy including genetic manipulation to maintain both antigen specificity and expansion capacity.

Visualization of Mutant Aggregates from Clock Neurons by Agarose Gel Electrophoresis (AGERA) in Drosophila melanogaster

The clock neurons of the fruit fly Drosophila melanogaster have become a useful model for expressing misfolded protein aggregates that accumulate in several human neurodegenerative diseases. One advantage of such an approach is that the behavioral effects can be readily quantified on circadian locomotor rhythms, sleep or activity levels via automated, highly reliable and objective procedures. Therefore, a rapid assay is required to visualize whether these neurons develop aggregates. Here we describe a modified immunoblot method, agarose gel electrophoresis (AGERA) that has been optimized for resolving aggregates from fly clock neurons.

Characterising cancer-associated fibroblast heterogeneity in non-small cell lung cancer: a systematic review and meta-analysis

Cancer-associated fibroblasts (CAFs) are a key component of the tumour microenvironment with evidence suggesting they represent a heterogeneous population. This study summarises the prognostic role of all proteins characterised in CAFs with immunohistochemistry in non-small cell lung cancer thus far. The functions of these proteins in cellular processes crucial to CAFs are also analysed. Five databases were searched to extract survival outcomes from published studies and statistical techniques, including a novel method, used to capture missing values from the literature. A total of 26 proteins were identified, 21 of which were combined into 7 common cellular processes key to CAFs. Quality assessments for sensitivity analyses were carried out for each study using the REMARK criteria whilst publication bias was assessed using funnel plots. Random effects models consistently identified the expression of podoplanin (Overall Survival (OS)/Disease-specific Survival (DSS), univariate analysis HR 2.25, 95% CIs 1.80-2.82) and α-SMA (OS/DSS, univariate analysis HR 2.11, 95% CIs 1.18-3.77) in CAFs as highly prognostic regardless of outcome measure or analysis method. Moreover, proteins involved in maintaining and generating the CAF phenotype (α-SMA, TGF-β and p-Smad2) proved highly significant after sensitivity analysis (HR 2.74, 95% CIs 1.74-4.33) supporting attempts at targeting this pathway for therapeutic benefit.

IMMU-41. HIGH-THROUGHPUT RETRIEVAL OF THERAPEUTIC T CELL RECEPTORS FROM GLIOMA

Gliomas are tumors with low mutational burden with the majority of them being resistant to checkpoint inhibition due to few immunogenic antigens. Multicenter vaccine trials targeting personalized neoantigens in gliomas demonstrated feasibility and illustrated the challenges of retrieving neoepitope-specific T cells based on the prediction of immunogenic neoepitopes. Here we took an entirely different T cell-centric approach and established a single cell sequencing-based high-throughput T cell receptor (TCR) retrieval platform, exploiting the therapeutic potential of spontaneous intratumoral T cell clonotypes for the development of adoptive cell therapy. We conducted direct ex vivo TCR single cell sequencing from freshly sorted human glioma-infiltrating T cell samples. High fidelity PCR was established to clone TCRs from single cell libraries directly into episomal expression vectors further optimized for T cell therapy. In parallel to standard therapy, patient-derived xenografts were developed and characterized. Tumor-reactivity of retrieved TCRs was demonstrated against patient-derived cell lines. Collectively, we provide a novel sequencing-based platform for high-throughput identification and validation of endogenous glioma-targeting TCRs and demonstrate their therapeutic applicability.

A non-linear optimisation method to extract summary statistics from Kaplan-Meier survival plots using the published P value

Background

Meta-analyses of studies evaluating survival (time-to-event) outcomes are a powerful technique to assess the strength of evidence for a given disease or treatment. However, these studies rely on the adequate reporting of summary statistics in the source articles to facilitate further analysis. Unfortunately, many studies, especially within the field of prognostic research do not report such statistics, making secondary analyses challenging. Consequently, methods have been developed to infer missing statistics from the commonly published Kaplan-Meier (KM) plots but are liable to error especially when the published number at risk is not included.

Methods

We therefore developed a method using non-linear optimisation (nlopt) that only requires the KM plot and the commonly published P value to better estimate the underlying censoring pattern. We use this information to then calculate the natural logarithm of the hazard ratio (ln (HR)) and its variance (var) ln (HR), statistics important for meta-analyses.

Results

We compared this method to the Parmar method which also does not require the number at risk to be published. In a validation set consisting of 13 KM studies, a statistically significant improvement in calculating ln (HR) when using an exact P value was obtained (mean absolute error 0.014 vs 0.077, P = 0.003). Thus, when the true HR has a value of 1.5, inference of the HR using the proposed method would set limits between 1.49/1.52, an improvement of the 1.39/1.62 limits obtained using the Parmar method. We also used Monte Carlo simulations to establish recommendations for the number and positioning of points required for the method.

Conclusion

The proposed non-linear optimisation method is an improvement on the existing method when only a KM plot and P value are included and as such will enhance the accuracy of meta-analyses performed for studies analysing time-to-event outcomes. The nlopt source code is available, as is a simple-to-use web implementation of the method.

Constitutive Expression of the Immunosuppressive Tryptophan Dioxygenase TDO2 in Glioblastoma Is Driven by the Transcription Factor C/EBPβ

Catabolism of the essential amino acid tryptophan is a key metabolic pathway contributing to the immunosuppressive tumor microenvironment and therefore a viable drug target for cancer immunotherapy. In addition to the rate-limiting enzyme indoleamine-2,3-dioxygenase-1 (IDO1), tryptophan catabolism via tryptophan-2,3-dioxygenase (TDO2) is a feature of many tumors, particularly malignant gliomas. The pathways regulating TDO2 in tumors are poorly understood; using unbiased promoter and gene expression analyses, we identify a distinct CCAAT/enhancer-binding protein β (C/EBPβ) binding site in the promoter of TDO2 essential for driving constitutive TDO2 expression in glioblastoma cells. Using The Cancer Genome Atlas (TCGA) data, we find that C/EBPβ expression is correlated with TDO2, and both are enriched in malignant glioma of the mesenchymal subtype and associated with poor patient outcome. We determine that TDO2 expression is sustained mainly by the LAP isoform of CEBPB and interleukin-1β, which activates TDO2 via C/EBPβ in a mitogen-activated protein kinase (MAPK) kinase-dependent fashion. In summary, we provide evidence for a novel regulatory and therapeutically targetable pathway of immunosuppressive tryptophan degradation in a subtype of glioblastoma with a particularly poor prognosis.

Novel Non-integrating DNA Nano-S/MAR Vectors Restore Gene Function in Isogenic Patient-Derived Pancreatic Tumor Models

We describe herein non-integrating minimally sized nano-S/MAR DNA vectors, which can be used to genetically modify dividing cells in place of integrating vectors. They represent a unique genetic tool, which avoids vector-mediated damage. Previous work has shown that DNA vectors comprising a mammalian S/MAR element can provide persistent mitotic stability over hundreds of cell divisions, resisting epigenetic silencing and thereby allowing sustained transgene expression. The composition of the original S/MAR vectors does present some inherent limitations that can provoke cellular toxicity. Herein, we present a new system, the nano-S/MAR, which drives higher transgene expression and has improved efficiency of establishment, due to the minimal impact on cellular processes and perturbation of the endogenous transcriptome. We show that these features enable the hitherto challenging genetic modification of patient-derived cells to stably restore the tumor suppressor gene SMAD4 to a patient-derived SMAD4 knockout pancreatic cancer line. Nano-S/MAR modification does not alter the molecular or phenotypic integrity of the patient-derived cells in cell culture and xenograft mouse models. In conclusion, we show that these DNA vectors can be used to persistently modify a range of cells, providing sustained transgene expression while avoiding the risks of insertional mutagenesis and other vector-mediated toxicity.

A Computational Error and Restricted Use of Time-series Analyses Underlie the Failure to Replicate period-Dependent Song Rhythms in Drosophila

From 1980 to 1991, Kyriacou, Hall, and collaborators (K&H) reported that the Drosophila melanogaster courtship song has a 1-min cycle in the length of mean interpulse intervals (IPIs) that is modulated by circadian rhythm period mutations. In 2014, Stern failed to replicate these results using a fully automated method for detecting song pulses. Manual annotation of Stern’s song records exposed a ~50% error rate in detection of IPIs, but the corrected data revealed period-dependent IPI cycles using a variety of statistical methods. In 2017, Stern et al. dismissed the sine/cosine method originally used by K&H to detect significant cycles, claiming that randomized songs showed as many significant values as real data using cosinor analysis. We first identify a simple mathematical error in Stern et al.’s cosinor implementation that invalidates their critique of the method. Stern et al. also concluded that although the manually corrected wild-type and perL mutant songs show similar periods to those observed by K&H, each song is usually not significantly rhythmic by the Lomb-Scargle (L-S) periodogram, so any genotypic effect simply reflects “noise.” Here, we observe that L-S is extremely conservative compared with 3 other time-series analyses in assessing the significance of rhythmicity, both for conventional locomotor activity data collected in equally spaced time bins and for unequally spaced song records. Using randomization of locomotor and song data to generate confidence limits for L-S instead of the theoretically derived values, we find that L-S is now consistent with the other methods in determining significant rhythmicity in locomotor and song records and that it confirms period-dependent song cycles. We conclude that Stern and colleagues’ failure to identify song cycles stems from the limitations of automated methods in accurately reflecting song parameters, combined with the use of an overly stringent method to discriminate rhythmicity in courtship songs.

TCR validation toward gene therapy for cancer

The speed of T cell receptor (TCR) discovery has been revolutionized by barcode-based TCR sequencing approaches that allow the reconstitution of a T cell's paired alpha and beta TCR chain, and the process of TCR discovery promises to become ever faster and cheaper with the continuing development single cell analysis techniques. This technological progress has generated an urgent need to develop efficient TCR validation platforms for the rapid and safe clinical translation of TCRs into therapeutic agents. Whereas much attention has in the past focused on CD8-positive cytotoxic T cells recognizing MHC class I presented epitopes, the increasing demand to validate TCRs expressed on neoepitope-reactive CD4 T cells requires the implementation of large-scale T cell activation-based readout assays to complement existing multimer and cytotoxicity-based assays. Here, we present commonly used TCR validation assays, and include detailed guidance on TCR synthesis, delivery, and appropriate experimental control TCRs. We also comment on upcoming methods that hold promise for further speeding the process of TCR validation, hastening the translation of TCRs from the laboratory into the clinic.

Publisher Correction: Deubiquitinase Usp12 functions noncatalytically to induce autophagy and confer neuroprotection in models of Huntington's disease

The original version of this Article incorrectly gave a publication date of 8 October 2018; this should have been 28 September 2018. This has now been corrected in the PDF and HTML versions of the Article.

Omics Approaches in Sleep-Wake Regulation

Although sleep seems an obvious and simple behaviour, it is extremely complex involving numerous interactions both at the neuronal and the molecular levels. While we have gained detailed insight into the molecules and neuronal networks responsible for the circadian organization of sleep and wakefulness, the molecular underpinnings of the homeostatic aspect of sleep regulation are still unknown and the focus of a considerable research effort. In the last 20 years, the development of techniques allowing the simultaneous measurement of hundreds to thousands of molecular targets (i.e. 'omics' approaches) has enabled the unbiased study of the molecular pathways regulated by and regulating sleep. In this chapter, we will review how the different omics approaches, including transcriptomics, epigenomics, proteomics, and metabolomics, have advanced sleep research. We present relevant data in the framework of the two-process model in which circadian and homeostatic processes interact to regulate sleep. The integration of the different omics levels, known as 'systems genetics', will eventually lead to a better understanding of how information flows from the genome, to molecules, to networks, and finally to sleep both in health and disease.

period and timeless mRNA Splicing Profiles under Natural Conditions in Drosophila melanogaster

Previous analysis of Drosophila circadian behavior under natural conditions has revealed a number of novel and unexpected features. Here we focus on the oscillations of per and tim mRNAs and their posttranscriptional regulation and observe significant differences in molecular cycling under laboratory and natural conditions. In particular, robust per mRNA cycling from fly heads is limited to the summers, whereas tim RNA cycling is observed throughout the year. When both transcripts do cycle, their phases are similar, except for the very warmest summer months. We also study the natural splicing profiles of per and tim transcripts and observe a clear relationship between temperature and splicing. In natural conditions, we confirm the relationship between accumulation of the per(spliced) variant, low temperature, and the onset of the evening component of locomotor activity, first described in laboratory conditions. Intriguingly, in the case of tim splicing, we detect the opposite relationship, with tim(spliced) expression increasing at higher temperatures. A first characterization of the 4 different TIM protein isoforms (resulting from the combination of the natural N-terminus length polymorphism and the C-terminus alternative splicing) using the 2-hybrid assay showed that the TIM(unspliced) isoforms have a stronger affinity for CRY, but not for PER, suggesting that the tim 3' splicing could have physiological significance, possibly in temperature entrainment and/or adaptation to seasonal environments.

Genetic analysis of circadian responses to low frequency electromagnetic fields in Drosophila melanogaster

The blue-light sensitive photoreceptor cryptochrome (CRY) may act as a magneto-receptor through formation of radical pairs involving a triad of tryptophans. Previous genetic analyses of behavioral responses of Drosophila to electromagnetic fields using conditioning, circadian and geotaxis assays have lent some support to the radical pair model (RPM). Here, we describe a new method that generates consistent and reliable circadian responses to electromagnetic fields that differ substantially from those already reported. We used the Schuderer apparatus to isolate Drosophila from local environmental variables, and observe extremely low frequency (3 to 50 Hz) field-induced changes in two locomotor phenotypes, circadian period and activity levels. These field-induced phenotypes are CRY- and blue-light dependent, and are correlated with enhanced CRY stability. Mutational analysis of the terminal tryptophan of the triad hypothesised to be indispensable to the electron transfer required by the RPM reveals that this residue is not necessary for field responses. We observe that deletion of the CRY C-terminus dramatically attenuates the EMF-induced period changes, whereas the N-terminus underlies the hyperactivity. Most strikingly, an isolated CRY C-terminus that does not encode the Tryptophan triad nor the FAD binding domain is nevertheless able to mediate a modest EMF-induced period change. Finally, we observe that hCRY2, but not hCRY1, transformants can detect EMFs, suggesting that hCRY2 is blue light-responsive. In contrast, when we examined circadian molecular cycles in wild-type mouse suprachiasmatic nuclei slices under blue light, there was no field effect. Our results are therefore not consistent with the classical Trp triad-mediated RPM and suggest that CRYs act as blue-light/EMF sensors depending on trans-acting factors that are present in particular cellular environments.

Genetic analysis of Drosophila circadian behavior in seminatural conditions

The study of circadian behavior in model organisms is almost exclusively confined to the laboratory, where rhythmic phenotypes are studied under highly simplified conditions such as constant darkness or rectangular light-dark cycles. Environmental cycles in nature are far more complex, and recent work in rodents and flies has revealed that when placed in natural/seminatural situations, circadian behavior shows unexpected features that are not consistent with laboratory observations. In addition, the recent observations of clockless mutants, both in terms of their circadian behavior and their Darwinian fitness, challenge some of the traditional beliefs derived from laboratory studies about what constitutes an adaptive circadian phenotype. Here, we briefly summarize the results of these newer studies and then describe how Drosophila behavior can be studied in the wild, pointing out solutions to some of the technical problems associated with extending locomotor monitoring to this unpredictable environment. We also briefly describe how to generate sophisticated simulations of natural light and temperature cycles that can be used to successfully mimic the fly's natural circadian behavior. We further clarify some misconceptions that have been raised in recent studies of natural fly behavior and show how these can be overcome with appropriate methodology. Finally, we describe some recent technical developments that will enhance the naturalistic study of fly circadian behavior.

An electromagnetic field disrupts negative geotaxis in Drosophila via a CRY-dependent pathway

Many higher animals have evolved the ability to use the Earth’s magnetic field, particularly for orientation. Drosophila melanogaster also respond to electromagnetic fields (EMFs), although the reported effects are quite modest. Here we report that negative geotaxis in flies, scored as climbing, is disrupted by a static EMF, and this is mediated by cryptochrome (CRY), the blue-light circadian photoreceptor. CRYs may sense EMFs via formation of radical pairs of electrons requiring photoactivation of flavin adenine dinucleotide (FAD) bound near a triad of Trp residues, but mutation of the terminal Trp in the triad maintains EMF responsiveness in climbing. In contrast, deletion of the CRY C terminus disrupts EMF responses, indicating that it plays an important signalling role. CRY expression in a subset of clock neurons, or the photoreceptors, or the antennae, is sufficient to mediate negative geotaxis and EMF sensitivity. Climbing therefore provides a robust and reliable phenotype for studying EMF responses in Drosophila.

The earth’s electromagnetic field has a modest effect on the behaviour of Drosophila melanogaster. Here, Fedele et al. use an assessment of climbing behaviour to describe how the blue-light circadian photoreceptor cryptochrome mediates a negative movement response to gravity in flies.

DJ-1 modulates aggregation and pathogenesis in models of Huntington's disease

The oxidation-sensitive chaperone protein DJ-1 has been implicated in several human disorders including cancer and neurodegenerative diseases. During neurodegeneration associated with protein misfolding, such as that observed in Alzheimer's disease and Huntington's disease (HD), both oxidative stress and protein chaperones have been shown to modulate disease pathways. Therefore, we set out to investigate whether DJ-1 plays a role in HD. We found that DJ-1 expression and its oxidation state are abnormally increased in the human HD brain, as well as in mouse and cell models of HD. Furthermore, overexpression of DJ-1 conferred protection in vivo against neurodegeneration in yeast and Drosophila. Importantly, the DJ-1 protein directly interacted with an expanded fragment of huntingtin Exon 1 (httEx1) in test tube experiments and in cell models and accelerated polyglutamine aggregation and toxicity in an oxidation-sensitive manner. Our findings clearly establish DJ-1 as a potential therapeutic target for HD and provide the basis for further studies into the role of DJ-1 in protein misfolding diseases.

Glutathione peroxidase activity is neuroprotective in models of Huntington's disease

Huntington's disease is a fatal neurodegenerative disorder caused by a CAG repeat expansion encoding a polyglutamine tract in the huntingtin (Htt) protein. Here we report a genome-wide overexpression suppressor screen in which we identified 317 ORFs that ameliorate the toxicity of a mutant Htt fragment in yeast and that have roles in diverse cellular processes, including mitochondrial import and copper metabolism. Two of these suppressors encode glutathione peroxidases (GPxs), which are conserved antioxidant enzymes that catalyze the reduction of hydrogen peroxide and lipid hydroperoxides. Using genetic and pharmacological approaches in yeast, mammalian cells and Drosophila, we found that GPx activity robustly ameliorates Huntington's disease-relevant metrics and is more protective than other antioxidant approaches tested here. Notably, we found that GPx activity, unlike many antioxidant treatments, does not inhibit autophagy, which is an important mechanism for clearing mutant Htt. Because previous clinical trials have indicated that GPx mimetics are well tolerated in humans, this study may have important implications for treating Huntington's disease.

A K(ATP) channel gene effect on sleep duration: from genome-wide association studies to function in Drosophila

Humans sleep approximately a third of their lifetime. The observation that individuals with either long or short sleep duration show associations with metabolic syndrome and psychiatric disorders suggests that the length of sleep is adaptive. Although sleep duration can be influenced by photoperiod (season) and phase of entrainment (chronotype), human familial sleep disorders indicate that there is a strong genetic modulation of sleep. Therefore, we conducted high-density genome-wide association studies for sleep duration in seven European populations (N=4251). We identified an intronic variant (rs11046205; P=3.99 × 10(-8)) in the ABCC9 gene that explains ≈5% of the variation in sleep duration. An influence of season and chronotype on sleep duration was solely observed in the replication sample (N=5949). Meta-analysis of the associations found in a subgroup of the replication sample, chosen for season of entry and chronotype, together with the discovery results showed genome-wide significance. RNA interference knockdown experiments of the conserved ABCC9 homologue in Drosophila neurons renders flies sleepless during the first 3 h of the night. ABCC9 encodes an ATP-sensitive potassium channel subunit (SUR2), serving as a sensor of intracellular energy metabolism.

Reliability and variability of sleep and activity as biomarkers of ageing in Drosophila

There are currently no reliable biomarkers of ageing. A biomarker should indicate biological age, that is, the amount of an animal's total lifespan it has lived and, therefore, the amount of time it has remaining. Some potential biomarkers cannot be validated as their measurement involves harm or death of the animal, such that its ultimate lifespan cannot be determined. A non-destructive biomarker would allow us to test molecular markers potentially involved directly in the ageing process, to monitor the effectiveness of therapeutic interventions to delay ageing, and provide a useful measure of general health of the organism. In the model organism Drosophila, various behavioural phenotypes change directionally with age, but we do not know whether they predict lifespan. Here we measure activity and sleep parameters in 64 wild type male flies from two recently wild-caught populations over the course of their natural lives, and determine whether such measures may predict biological age and ultimate lifespan. Indices of sleep fragmentation and circadian rhythm were the best predictors of lifespan, though population differences were evident. However, when used to predict a biological age of 50 % lifespan elapsed our best behavioural measure was slightly less accurate and less precise compared with using chronological age as predictor.

Peroxiredoxins are conserved markers of circadian rhythms

Cellular life emerged ∼3.7 billion years ago. With scant exception, terrestrial organisms have evolved under predictable daily cycles owing to the Earth's rotation. The advantage conferred on organisms that anticipate such environmental cycles has driven the evolution of endogenous circadian rhythms that tune internal physiology to external conditions. The molecular phylogeny of mechanisms driving these rhythms has been difficult to dissect because identified clock genes and proteins are not conserved across the domains of life: Bacteria, Archaea and Eukaryota. Here we show that oxidation-reduction cycles of peroxiredoxin proteins constitute a universal marker for circadian rhythms in all domains of life, by characterizing their oscillations in a variety of model organisms. Furthermore, we explore the interconnectivity between these metabolic cycles and transcription-translation feedback loops of the clockwork in each system. Our results suggest an intimate co-evolution of cellular timekeeping with redox homeostatic mechanisms after the Great Oxidation Event ∼2.5 billion years ago.

The kynurenine pathway modulates neurodegeneration in a Drosophila model of Huntington's disease

Neuroactive metabolites of the kynurenine pathway (KP) of tryptophan degradation have been implicated in the pathophysiology of neurodegenerative disorders, including Huntington's disease (HD) [1]. A central hallmark of HD is neurodegeneration caused by a polyglutamine expansion in the huntingtin (htt) protein [2]. Here we exploit a transgenic Drosophila melanogaster model of HD to interrogate the therapeutic potential of KP manipulation. We observe that genetic and pharmacological inhibition of kynurenine 3-monooxygenase (KMO) increases levels of the neuroprotective metabolite kynurenic acid (KYNA) relative to the neurotoxic metabolite 3-hydroxykynurenine (3-HK) and ameliorates neurodegeneration. We also find that genetic inhibition of tryptophan 2,3-dioxygenase (TDO), the first and rate-limiting step in the pathway, leads to a similar neuroprotective shift toward KYNA synthesis. Importantly, we demonstrate that the feeding of KYNA and 3-HK to HD model flies directly modulates neurodegeneration, underscoring the causative nature of these metabolites. This study provides the first genetic evidence that inhibition of KMO and TDO activity protects against neurodegenerative disease in an animal model, indicating that strategies targeted at two key points within the KP may have therapeutic relevance in HD, and possibly other neurodegenerative disorders.

Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock

The central circadian pacemaker of the suprachiasmatic nucleus (SCN) is characterized as a series of transcriptional/posttranslational feedback loops. How this molecular mechanism coordinates daily rhythms in the SCN and hence the organism is poorly understood. We conducted the first systematic exploration of the "circadian intracellular proteome" of the SCN and revealed that approximately 13% of soluble proteins are subject to circadian regulation. Many of these proteins have underlying nonrhythmic mRNAs, so they have not previously been noted as circadian. Circadian proteins of the SCN include rate-limiting factors in metabolism, protein trafficking, and, intriguingly, synaptic vesicle recycling. We investigated the role of this clock-regulated pathway by treating organotypic cultures of SCN with botulinum toxin A or dynasore to block exocytosis and endocytosis. These manipulations of synaptic vesicle recycling compromised circadian gene expression, both across the SCN as a circuit and within individual SCN neurons. These findings reveal how basic cellular processes within the SCN are subject to circadian regulation and how disruption of these processes interferes with SCN cellular pacemaking. Specifically, we highlight synaptic vesicle cycling as a novel point of clock cell regulation in mammals.

Down's syndrome, complete atrioventricular canal, and pulmonary vascular obstructive disease

We reviewed our experience over a 10-year period to determine whether children with Down's syndrome and complete atrioventricular canal develop pulmonary vascular obstructive disease earlier than children with normal chromosomes and this defect. Comparisons were made between Down's syndrome and normal chromosome children regarding (1) pulmonary blood flow and pulmonary vascular resistance at initial catheterization, (2) operability as related to elevation in pulmonary vascular resistance, and (3) age at diagnosis of fixed pulmonary vascular obstructive disease. The 45 patients with Down's syndrome catheterized under 1 year of age had a lower mean pulmonary blood flow (3.2 versus 5.7; p = 0.0001) and higher mean pulmonary vascular resistance (8.3 versus 4.6 Wood units.m2; p = 0.0003) than their 34 normal chromosome counterparts. When all ages were included, 38 of 81 (47%) of the children with Down's syndrome and 32 of 40 (80%) of the normal children were considered operable. Non-Down's syndrome patients who had operations had a higher pulmonary blood flow (5.8 versus 3.3; p = 0.004) and lower pulmonary vascular resistance (3.6 versus 6.0 Wood units.m2; p = 0.005) than Down's syndrome patients. Of the 34 patients who did not have operations because of pulmonary vascular obstructive disease, 31 had Down's syndrome. In 10 of 81 children with Down's syndrome, fixed pulmonary vascular obstructive disease was diagnosed before the age of 1 year, while this was found in none of 40 normal children. Our data demonstrate that Down's syndrome patients with complete atrioventricular canal have a greater degree of elevation of pulmonary vascular resistance in the first year of life and more rapid progression to fixed pulmonary vascular obstructive disease than children with normal chromosomes.

GRATEFUL MED searching: a hospital library perspective

The Health Sciences Information Center of Cedars-Sinai Medical Center implemented an end user search service utilizing NLM's GRATEFUL MED software. A librarian-taught seminar is required of all end users. The course's teaching strategies are described. A survey of users was conducted and results are shared.

Surgical and medical results of complete atrioventricular canal: a ten year review

The files of 121 patients who presented to Children's Hospital of Michigan over the last 10 years with complete atrioventricular (AV) canal were reviewed to evaluate long-term management and overall outcome. Of 121 patients, 70 underwent corrective surgery, 21 (30%) of whom died perioperatively. The surgical mortality rate was 13% when patients with hypoplastic left or right ventricle (n = 6), double-orifice mitral valve or extreme deficiency of mitral tissue (n = 5), and pulmonary vascular obstructive disease (n = 5) were excluded. Of the 49 patients who survived operation, 36 are in New York Heart Association class I, 1 patient requires a pacemaker and 3 died late. In 34 of the 51 patients (28%) who did not undergo operation, pulmonary vascular obstructive disease developed; it occurred within 12 months in 10 patients (8%). Eight other patients who did not undergo operation died before planned surgery (age 1 to 9 months). Although surgical prognosis in good candidates is acceptable, the overall prognosis for children with complete AV canal is guarded because of the risk of early death or early pulmonary vascular obstructive disease and frequently unfavorable anatomy.

Pacing in children and young adults with nonsurgical atrioventricular block: comparison of single-rate ventricular and dual-chamber modes

A prospective comparison of physiologic response to single-rate ventricular and dual-chamber atrioventricular pacing was conducted in 14 pediatric patients (age 1 to 24 years, median 14) with symptomatic nonsurgical second- or third-degree atrioventricular block. All patients were studied acutely during cardiac catheterization before and after 1 hour of both pacing modes. Following pacemaker implant, eight patients were reevaluated after 1 month of each mode with symptom questionnaire, resting ECG, resting echocardiogram, and Doppler cardiac output measurement at rest and at peak treadmill exercise. Cardiac outputs (mean +/- standard error) increased acutely (n = 14) with both ventricular (32 +/- 12%) and dual-chamber (39 +/- 10%) pacing over intrinsic rhythm values (p less than 0.01 in both). During chronic pacing (n = 8), symptoms were reported only with the ventricular mode. Dual-chamber synchronous pacing was associated with improved mean resting shortening fraction and cardiac output, slower mean resting sinus rate (89 +/- 5 compared to 73 +/- 4 bpm (p less than 0.02), and a 23% increase in mean excerise cardiac output (4.2 +/- 0.4 compared to 3.4 +/- 0.3 L/min/m2) compared to single-rate ventricular pacing. Exercise-induced dysrhythmias occurred only with ventricular pacing. This study demonstrates that pediatric patients with nonsurgical atrioventricular block can compensate for loss of atrioventricular synchrony at rest but exhibit improved cardiac function with chronic dual-chamber atrioventricular compared to single-rate ventricular pacing.

Myocardial dysfunction in hypothyroid children

Eleven children with primary hypothyroidism were studied by echocardiography. Eight patients had pericardial effusion. Systolic time intervals (preejection period-ejection time ratio and left ventricular isovolumic contraction time) were suggestive of abnormal myocardial function. Asymmetric septal hypertrophy without left ventricular out-flow obstruction (ventricular septal-left ventricular posterior wall diastolic thickness ratio, greater than 1.3) was present in two hypothyroid children. After full replacement therapy, these cardiac abnormalities reversed to normal. Our data suggest that the myopericardial response to hypothyroidism in children is similar to that seen in adults.

Classic shunting operations for congenital cyanotic heart defects

A total of 297 consecutive classic systemic artery-pulmonary artery shunts were performed in 281 patients over the past 9 years. This experience includes 200 Blalock-Taussig shunts (67.3%), 84 Waterston shunts (28.2%), and 13 Potts shunts (4.3%). The overall early mortality after the Blalock-Taussig shunt (5.5%) was significantly lower (p less than 0.02) than for the Waterston shunt (13%). The early mortality after either the Blalock-Taussig or Waterston shunt was not statistically related to the age of the patient at operation. Both the Blalock-Taussig and Waterston shunts demonstrated a higher mortality (p less than 0.02) among patients in Group II (complex defects) than in patients in Group I (tetralogy of Fallot and pulmonary atresia with ventricular septal defect [VSD]). However, the Blalock-Taussig shunt had a significantly lower (p less than 0.04) probability of early postoperative death than the Waterston shunt among patients with complex lesions. The Blalock-Taussig shunt also revealed a lower incidence of important late postoperative complications and did not affect adversely the hemodynamic result after intracardiac correction, as evidenced by late postoperative cardiac catheterization. This study also confirms the feasibility of the Blalock-Taussig shunt during the neonatal period without significantly increased age-related risk of postoperative death (p = 0.13) and with good early and late long-term patency rates.

Surgical treatment of cor triatriatum

Six patients with cor triatriatum underwent surgical correction. They ranged for 1.5 to 93 months old (mean, 22 months). Congestive heart failure was present in 3 patients. Cardiomegaly and increased pulmonary vascularity were evident roentgenographically in all patients. Cardiac cineangiography demonstrated the subdividing left atrial membrane in 5 patients and suggested the correct diagnosis by revealing an abnormal configuration of the left atrium in the other patient. The opening in the anomalous left atrial membrane was stenotic in every instance. The proximal left atrial chamber communicated with the right atrium through an atrial septal defect in 5 patients and with the systemic venous circuit through a persistent left superior vena cava in the other patient, in whom the atrial septum was intact. A right atrial-transseptal approach provided ample exposure for complete excision of the obstructing membrane and repair of the atrial septum in all patients. One patient died of low cardiac output during the early postoperative period. The other 5 are alive and well at an average of 48 months after operation.