bluuebunny/crossref_metadata_2025 huggingface dataset:
From sequence data to patient result: a solution for HIV drug resistance genotyping with Exatype, end to end software for Pol-HIV-1 Sequence analysis and patient HIV drug resistance result generation
Authors: King’wara Leonard , Karanja Muthoni , Ngugi Catherine , Kangogo Geoffrey , Bera Kipkerich , Kimani Maureen , Bowen Nancy , Abuya Dorcas , Oramisi Violet , Mukui Irene
Published: February 2020

Introduction

With the rapid scale-up of antiretroviral therapy (ART) to treat HIV infection, there are ongoing concerns regarding probable emergence and transmission of HIV drug resistance (HIVDR) mutations. This scale-up has to lead to an increased need for routine HIVDR testing to inform the clinical decision on a regimen switch. Although the majority of wet laboratory processes are standardized, slow, labor-intensive data transfer and subjective manual sequence interpretation steps are still required to finalize and release patient results. We thus set out to validate the applicability of a software package to generate HIVDR patient results from raw sequence data independently.

Methods

We assessed the performance characteristics of Hyrax Bioscience’s Exatype (a sequence data to patient result, fully automated sequence analysis software, which consolidates RECall, MEGA X and the Stanford HIV database) against the standard method (RECall and Stanford database). Exatype is a web-based HIV Drug resistance bioinformatic pipeline available atsanger.exatype.com. To validate the exatype, we used a test set of 135 remnant HIV viral load samples at the National HIV Reference Laboratory (NHRL).

Result

We analyzed, and successfully generated results of 126 sequences out of 135 specimens by both standard and Exatype software. Result production using Exatype required minimal hands-on time in comparison to the standard (6 computation-hours using the standard method versus 1.5 Exatype computation-hours). Concordance between the two systems was 99.8% for 311,227 bases compared. 99.7 % of the 0.2% discordant bases, were attributed to nucleotide mixtures as a result of the sequence editing in Recall. Both methods identified similar (99.1%) critical antiretroviral resistance-associated mutations resulting in a 99.2% concordance of resistance susceptibility interpretations. Base calling comparison between the two methods had Cohen’s kappa (0.97 to 0.99) implying an almost perfect agreement with minimal base calling variation. On a predefined dataset, RECall editing displayed the highest probability to score mixtures accurately one vs. 0.71 and the lowest chance to inaccurately assign mixtures to pure nucleotides (0.002–0.0008). This advantage is attributable to the manual sequence editing in RECall.

Conclusion

The reduction in hands-on time needed is a benefit when using the Exatype HIV DR sequence analysis platform and result generation tool. There is a minimal difference in base calling between Exatype and standard methods. Although the discrepancy has minimal impact on drug resistance interpretation, allowance of sequence editing in Exatype as RECall can significantly improve its performance.
A genetic model of ivabradine recapitulates results from randomized clinical trials
Authors: Legault Marc-André , Sandoval Johanna , Provost Sylvie , Barhdadi Amina , Perreault Louis-Philippe Lemieux , Shah Sonia , Lumbers R.Thomas , de Denus Simon , Tyl Benoit , Tardif Jean-Claude , Dubé Marie-Pierre
Published: February 2020

Background

Naturally occurring human genetic variants provide a valuable tool to identify drug targets and guide drug prioritization and clinical trial design. Ivabradine is a heart rate lowering drug with protective effects on heart failure despite increasing the risk of atrial fibrillation. In patients with coronary artery disease without heart failure, the drug does not protect against major cardiovascular adverse events prompting questions about the ability of genetics to have predicted those effects. This study evaluates the effect of a mutation in HCN4, ivabradine’s drug target, on safety and efficacy endpoints.

Methods

We used genetic association testing and Mendelian randomization to predict the effect of ivabradine and heart rate lowering on cardiovascular outcomes.

Results

Using data from the UK Biobank and large GWAS consortia, we evaluated the effect of a heart rate-reducing genetic variant at the HCN4 locus encoding ivabradine’s drug target. These genetic association analyses showed increases in risk for atrial fibrillation (OR 1.09, 95% CI: 1.06-1.13, P=9.3 ×10−9) in the UK Biobank. In a cause-specific competing risk model to account for the increased risk of atrial fibrillation, the HCN4 variant reduced incident heart failure in participants that did not develop atrial fibrillation (HR 0.90, 95% CI: 0.83-0.98, P=0.013). In contrast, the same heart rate reducing HCN4 variant did not prevent a composite endpoint of myocardial infarction or cardiovascular death (OR 0.99, 95% CI: 0.93-1.04, P=0.61).

Conclusion

Genetic modelling of ivabradine recapitulates its benefits in heart failure, promotion of atrial fibrillation, and neutral effect on myocardial infarction.

CONDENSED ABSTRACT

The effects of drugs can sometimes be predicted from the effects of mutations in genes encoding drug targets. We tested the effect of a heart rate reducing allele at the HCN4 locus encoding ivabradine’s drug target and found results coherent with the SHIFT and SIGNIFY clinical trials of ivabradine. The genetic variant increased the risk of atrial fibrillation and cardioembolic stroke and protected against heart failure in a competing risk model accounting for the increased risk of atrial fibrillation. The variant had a neutral effect on a composite of myocardial infarction and cardiovascular death.
Collapsing the list of myocardial infarction-related differential expressed genes into a diagnostic signature
Authors: Osmak German , Baulina Natalia , Koshkin Philipp , Favorova Olga
Published: February 2020

Myocardial infarction (MI) is one of the most severe manifestations of coronary artery disease (CAD) and the leading cause of death from non-infectious diseases worldwide. It is known that the central component of CAD pathogenesis is a chronic vascular inflammation. However, the mechanisms underlying the changes that occur in T, B and NK lymphocytes, monocytes and other immune cells during CAD and MI are still poorly understood. One of those pathogenic mechanisms might be the dysregulation of intracellular signaling pathways in the immune cells.

In the present study we performed a transcriptome profiling in peripheral blood mononuclear cells of MI patients and controls. The machine learning algorithm was then used to search for MI-associated signatures, that could reflect the dysregulation of intracellular signaling pathways.

The genes ADAP2, KLRC1, MIR21, PDGFD and CD14 were identified as the most important signatures for the classification model with L1-norm penalty function. The classifier output quality was equal to 0.911 by Receiver Operating Characteristic metric on test data. These results were validated on two independent open GEO datasets. Identified MI-associated signatures can be further assisted in MI diagnosis and/or prognosis.

Thus, our study presents a pipeline for collapsing the list of differential expressed genes, identified by high-throughput techniques, in order to define disease-associated diagnostic signatures.
Apolipoprotein E genotype, lifestyle and coronary artery disease: gene-environment interaction analyses in the UK Biobank population
Authors: Bos Maxime M , de Vries Lina , Rensen Patrick CN , van Dijk Ko Willems , Blauw Gerard Jan , van Heemst Diana , Noordam Raymond
Published: February 2020

Background

Carriers of theAPOE ε4genotype have an increased risk for developing coronary artery disease (CAD), but there is preliminary evidence that lifestyle factors interact withAPOEgenotype on CAD risk. Here, we assessed the interactions of physical activity, oily fish intake and polyunsaturated fatty acid (PUFA) intake withAPOEgenotype on risk of incident cardiovascular disease in a large population of middle-aged individuals.

Methods and Results

The present study was embedded in the UK Biobank population and comprised 344,092 European participants (mean age: 56.5 years, 45.7% men) without a history of CAD. Information regarding physical activity, oily fish intake and PUFA intake was collected through questionnaires, and information on incident CAD through linkage with hospital admission records. Analyses were performed using Cox proportional hazard models adjusted for age and sex. From these analyses, higher physical activity level and a higher intake of oily fish were associated with a lower incidence of CAD. These associations were similar across all APOE isoform groups (p-values for interaction > 0.05). A higher PUFA intake was only associated with a lower CAD risk inAPOE ε4carriers (hazard ratio: 0.76, 95% confidence interval: 0.62,0.90), however, no statistically significant interaction was observed (p-valueinteraction= 0.137).

Conclusion

While higher physical activity, fish intake and PUFA intake all decreased the risk of CAD, no evidence for interaction of these lifestyle factors withAPOEgenotype was observed in UK Biobank participants. Interventions intended to reduce cardiovascular risk might therefore be similarly effective across the APOE isoform carriers.
Functional abnormalities in the cerebello-thalamic pathways in an animal model of dystonia
Authors: Margarint Elena Laura , Aïssa Hind Baba , Varani Andrés Pablo , Sala Romain , Menardy Fabien , Pelosi Assunta , Hervé Denis , Léna Clément , Popa Daniela
Published: February 2020

Dystonia is often associated with functional alterations in the cerebello-thalamic pathways, which have been proposed to contribute to the disorder by propagating pathological firing patterns to the forebrain. Here, we examined the function of the cerebello-thalamic pathways in a model of DYT25 dystonia, mice carrying a heterozygous invalidation ofGnalgene which notably disrupts striatal function, exhibiting dystonic movements and postures following systemic or striatal administration of oxotremorine. Theta-burst optogenetic stimulations of the cerebellar nuclei evoked a potentiation of the responses to cerebellar stimulations in the thalamus and motor cortex in WT mice, without evident motor function disruption. In contrast, theta burst stimulations evoked a depression of these responses only in dystonia-manifestingGnal+/− mice after oxotremorine administration, decreased the disabling dystonia attacks, and increased normal active wake behaviour inGnal+/− mice. The cerebellum could thus offer a gateway for a corrective treatment of motor impairments in dystonia including striatal dysfunction.

One sentence summary

A mouse model of DYT25 dystonia, carrying aGnalmutation disrupting striatal neurotransmission, exhibits anomalous cerebello-thalamic plasticity in the non-manifesting state, but theta-burst cerebellar stimulations during cholinergic-induced dystonia depress the cerebello-thalamic transmission and reduce the severity of the motor symptoms.
Improving esophageal protection during AF ablation: The IMPACT study
Authors: Leung Lisa WM , Bajpai Abhay , Zuberi Zia , Li Anthony , Norman Mark , Kaba Riyaz , Akhtar Zaki , Evranos Banu , Gonna Hanney , Harding Idris , Sohal Manav , Al-Subaie Nawaf , Louis-Auguste John , Hayat Jamal , Gallagher Mark M
Published: February 2020

Background

Thermal injury to the esophagus is a known complication of ablation for atrial fibrillation (AF) and accounts for most procedure-related mortality. Thermal protection of the esophageal lumen by infusing cold liquid can reduce thermal injury to a limited extent. A method to control the local luminal esophageal temperature is investigated by this study.

Objective

To investigate the ability of a powerful temperature control device to protect the esophagus from ablation-related thermal injury.

Methods

A single-center, prospective, double-blinded randomized controlled trial was used to investigate the ability of the ensoETM device to protect the esophagus from thermal injury. This method was compared in a 1:1 randomization to a control group of standard practice utilizing a single-point temperature probe. In the study group, the device was used to keep the luminal temperature at 4°C during radiofrequency (RF) ablation for AF. Endoscopic examination was performed at 7 days post-ablation and esophageal injury was scored. The patient and the endoscopist were blinded to the randomization.

Results

We recruited 188 patients, of whom 120 underwent endoscopy. Thermal injury to the mucosa was significantly more common in the control group than in those receiving esophageal protection (12/60 versus 2/60; P=0.008), with a trend toward reduction in gastroparesis (6/60 Vs 2/60, p=0.27). There was no difference between groups in RF duration, force, power and combined ablation index (P value range= 0.2-0.9). Procedure duration and fluoroscopy duration were similar (P=0.97, P=0.91 respectively).

Conclusion

Thermal protection of the esophageal lumen significantly reduces ablation-related thermal injury compared to standard care. This method of esophageal protection is safe and does not compromise the efficacy of the ablation procedure.

CONDENSED ABSTRACT

Thermal injury to the esophagus causes most ablation-related deaths. We investigated the ability of a powerful method of esophageal temperature control to protect from thermal lesions during ablation, using a double-blinded randomized clinical trial to compare this to standard care. Patients randomised to receive thermal protection experienced significantly fewer lesions to the esophageal mucosa and a trend towards reduction in gastroparesis. Procedure efficacy and efficiency were not compromised.
Is mammography screening beneficial: An individual-based stochastic model for breast cancer incidence and mortality
Authors: Le Thuy T. T. , Adler Frederick R.
Published: February 2020

Abstract

BACKGROUND

The benefits of mammography screening have been controversial, with conflicting findings from various studies.

METHODS

We hypothesize that unmeasured heterogeneity in tumor aggressiveness underlies these conflicting results. Based on published data from the Canadian National Breast Screening Study (CNBSS), we develop and parameterize an individual-based mechanistic model for breast cancer incidence and mortality that tracks five stages of breast cancer progression and incorporates the effects of age on breast cancer incidence and all-cause mortality.

RESULTS

The model accurately reproduces the reported outcomes of the CNBSS. By varying parameters, we predict that the benefits of mammography depend on the effectiveness of cancer treatment and tumor.

CONCLUSIONS

In particular, patients with the most rapidly growing or potentially largest tumors have the highest benefit and least harm from the screening, with only a relatively small effect of age. However, the model predicts that confining mammography populations with a high risk of acquiring breast cancer increases the screening benefit only slightly compared with the full population.
Circulating lipids associate with future weight gain in individuals with an at-risk mental state and in first-episode psychosis
Authors: Lamichhane Santosh , Dickens Alex M. , Sen Partho , Laurikainen Heikki , Suvisaari Jaana , Hyötyläinen Tuulia , Howes Oliver , Hietala Jarmo , Orešič Matej
Published: February 2020

Patients with schizophrenia have a lower than average life span, largely due to the increased prevalence of cardiometabolic co-morbidities. Identification of individuals with psychotic disorders with a high risk of rapid weight gain, and the associated development of metabolic complications, is an unmet need as regards public health. Here, we applied mass spectrometry-based lipidomics in a prospective study comprising 48 controls (CTR), 44 first-episode psychosis (FEP) patients and 22 individuals at clinical-high-risk (CHR) for psychosis, from two study centers (Turku/Finland and London/UK). Baseline serum samples were analyzed by lipidomics, while body mass index (BMI) was assessed at baseline and after 12 months. We found that baseline triacylglycerols with low double bond counts and carbon numbers were positively associated with the change in BMI at follow-up. In addition, a molecular signature comprised of two triacylglycerols (TG(48:0) and TG(45:0)), was predictive of weight gain in individuals with a psychotic disorder, with an area under the receiver operating characteristic curve (AUROC) of 0.74 (95% CI: 0.60–0.85). When independently tested in the CHR group, this molecular signature predicted said weight change with AUROC = 0.73 (95% CI: 0.61–0.83). We conclude that molecular lipids may serve as a predictor of weight gain in psychotic disorders in at-risk individuals, and may thus provide a useful marker for identifying individuals who are most prone to developing cardiometabolic co-morbidities.
Association of the use of hearing aids with the conversion from mild cognitive impairment to dementia and progression of dementia: a longitudinal retrospective study
Authors: Bucholc Magda , McClean Paula L. , Bauermeister Sarah , Todd Stephen , Ding Xuemei , Ye Qinyong , Wang Desheng , Huang Wei , Maguire Liam P.
Published: February 2020

INTRODUCTION

Hearing aid usage has been linked to improvements in cognition, communication, and socialization, but the extent to which it can affect the incidence and progression of dementia is unknown. Such research is vital given the high prevalence of dementia and hearing impairment in older adults, and the fact that both conditions often coexist. In this study, we examined for the first time the effect of the use of hearing aids on the conversion from mild cognitive impairment (MCI) to dementia and progression of dementia.

METHODS

We used a large referral-based cohort of 2114 hearing-impaired patients obtained from the National Alzheimer’s Coordinating Center. Survival analyses using multivariable Cox proportional hazards regression model and weighted Cox regression model with censored data were performed to assess the effect of hearing aid use on the risk of conversion from MCI to dementia and risk of death in hearing-impaired participants. Disease progression was assessed with CDR® Dementia Staging Instrument Sum of Boxes (CDRSB) scores. Three types of sensitivity analyses were performed to validate the robustness of the results.

RESULTS

MCI participants that used hearing aids were at significantly lower risk of developing all-cause dementia compared to those not using hearing aids (hazard ratio [HR] 0.73, 95%CI, 0.61-0.89; false discovery rate [FDR]P=0.004). The mean annual rate of change (standard deviation) in CDRSB scores for hearing aid users with MCI was 1.3 (1.45) points and significantly lower than for individuals not wearing hearing aids with a 1.7 (1.95) point increase in CDRSB per year (P=0.02). No association between hearing aid use and risk of death was observed. Our findings were robust subject to sensitivity analyses.

DISCUSSION

Among hearing-impaired adults, hearing aid use was independently associated with reduced dementia risk. The causality between hearing aid use and incident dementia should be further tested.

Highlights

High prevalence of dementia and hearing impairment in older adults

Hearing aid (HA) use associated with a lower risk of incident dementia

Slower cognitive decline in users than non-users of HA with mild cognitive impairment

The relationship between hearing impairment and dementia should be further tested
Exploring the potential for collaborative use of an app-based platform for n-of-1 trials among healthcare professionals that treat patients with insomnia
Authors: Bobe Jason R. , De Freitas Jessica K. , Glicksberg Benjamin S.
Published: February 2020

Background

N-of-1 trials are single patient, multiple crossover, comparative effectiveness experiments. Despite their rating as “level 1” evidence, they are not routinely used in clinical medicine to evaluate the effectiveness of treatments.

Objective

We explored the potential for implementing a mobile app-based n-of-1 trial platform for collaborative use by clinicians and patients to support data-driven decisions around the treatment of insomnia.

Methods

A survey assessing awareness and utilization of n-of-1 trials was administered to healthcare professionals that frequently treat patients with insomnia at the Icahn School of Medicine at Mount Sinai in New York City. 1M electronic health records were analyzed to evaluate evidence for a comorbid relationship between insomnia and dementia or Alzheimer’s disease among a patient population that may benefit from n-of-1 trials for the selection of optimal sleep treatments.

Results

A total of 45 healthcare professionals completed the survey and were included in the analysis. We found that 64% of healthcare professionals surveyed had not heard of n-of-1 trials. After a brief description of these methods, 75% of healthcare professionals reported that they are likely or highly likely to use an app-based n-of-1 trial at least once in the next year if the service were free and easy to offer to their patients.

Conclusions

An app-based n-of-1 trials platform might be a valuable tool for clinicians and patients to identify the best treatments for insomnia. Educational interventions that raise awareness and provide training are also likely necessary. The electronic health record (EHR) may help identify eligible patients.
Loss of COX4i1 leads to combined respiratory chain deficiency and impaired mitochondrial proteosynthesis
Authors: Kristýna Čunátová , David Pajuelo Reguera , Marek Vrbacký , Erika Fernández-Vizarra , Shujing Ding , Ian Fearnley , Massimo Zeviani , Josef Houštěk , Tomáš Mráček , Petr Pecina
Published: February 2020

Oxidative phosphorylation (OXPHOS) system localized in the inner mitochondrial membrane secures production of the majority of ATP in mammalian organisms. Individual OXPHOS complexes were shown to form supramolecular assemblies termed supercomplexes. It has been repeatedly shown that complexes are not linked only by their function but also by interdependence of individual complex biogenesis or maintenance. For instance, cytochromecoxidase (cIV, COX) or cytochromebc1complex (cIII) deficiencies affect the level of fully assembled NADH dehydrogenase (cI) in monomer as well as within supercomplexes. It was hypothesized that cI is affected at the level of enzyme assembly as well as at the level of cI stability and maintenance. However, the true nature of interdependency between cI and cIV is not fully understood yet. We used HEK293 cellular model with complete knockout of COX4 subunit, which serves as an ideal system to study interdependency of cI and cIV, as early phases of cIV assembly process are disrupted. Total absence of cIV was accompanied by profound deficiency of cI, documented by selective decrease in cI subunits amount and significantly reduced amount of assembled cI. Supercomplexes assembled from cI, cIII and cIV were missing in COX4dKO due to loss of cIV and decrease in cI amount. Pulse-chase metabolic labelling of mtDNA-encoded proteins uncovered decrease of cIV and cI subunits translation. Moreover, partial impairment of mitochondrial proteosynthesis correlated with decreased level of mitochondrial ribosomal proteins. In addition, complexome profiling approach uncovered accumulation of cI assembly intermediates indicating that cI biogenesis was affected rather than stability. We propose that impairment of mitochondrial proteosynthesis caused by cIV deficiency represents one of the mechanisms which may couple biogenesis of cI and cIV.
Harmine enhances the activity of the HIV-1 latency-reversing agents ingenol A and SAHA
Authors: Taylor Jared P. , Armitage Lucas H. , Aldridge Daniel L. , Cash Melanie N. , Wallet Mark A.
Published: February 2020

Infection of HIV-1 remains incurable because long-lived, latently-infected cells persist during prolonged antiretroviral therapy. Attempts to pharmacologically reactivate and purge the latent reservoir with latency reactivating agents (LRAs) such as protein kinase C (PKC) agonists (e.g. ingenol A) or histone deacetylase (HDAC) inhibitors (e.g. SAHA) have shown promising but incomplete efficacy. Using the J-Lat T cell model of HIV latency, we found that the plant-derived compound harmine enhanced the efficacy of existing PKC agonist LRAs in reactivating latently-infected cells. Treatment with harmine increased not only the number of reactivated cells but also increased HIV transcription and protein expression on a per-cell basis. Importantly, we observed an additive effect when harmine was used in combination with ingenol A and the HDAC inhibitor SAHA. An investigation into the mechanism revealed that harmine, when used with LRAs, increased the availability of transcription factors needed for viral reactivation such as NFκB, MAPK p38, and ERK1/2. We also found that harmine treatment resulted in reduced expression of HEXIM1, a negative regulator of transcriptional elongation. Despite harmine’s reported inhibitory effects on DYRK1A and consequent enhancement of NFAT signaling, the HIV reactivating effects of harmine occurred independent of DYRK1A and NFAT. Harmine increases the efficacy of LRAs by increasing the availability of HIV-1 transcription factors and decreasing expression of HEXIM1. Combination therapies with harmine and LRAs could benefit patients by achieving deeper reactivation of the latent pool of HIV provirus.
Spatial transcriptomics of tumor microenvironment in formalin-fixed paraffin-embedded breast cancer
Authors: Romanens Lou , Chaskar Prasad , Tille Jean-Christophe , Ryser Stephan , Liaudet Nicolas , Hu-Heimgartner Ketty , Heimgartner Killian , Kaya Gurkan , Tsantoulis Petros , Labidi-Galy S. Intidhar
Published: February 2020

Tumor samples are conserved in clinical practice in formalin-fixed paraffin-embedded (FFPE) blocks. Formalin fixation chemically alters nucleic acids, rendering transcriptomic analysis challenging. RNA-sequencing is usually performed on tumor bulk, without distinction of cell subtypes or location. Here we describe the development of a robust method for RNA extraction and exome-capture RNA-sequencing of laser-capture microdissected tumor cells (TC) and stromal immune cells (TIL) based on their morphology. We applied this method on 7 tumor samples (surgical or core needle biopsy) of triple-negative breast cancer (TNBC) stored in FFPE blocks over 3-10 years. Unsupervised clustering and principal component analysis showed a clear separation between gene-expression profile of TIL and TC. TIL were enriched in markers of B cells (CD79B, PAX5 and BLNK) and T cells (CD2, CD3D and CD8B) whereas tumor cells expressed epithelial markers (EPCAM, MUC1andKRT8). Microenvironment cell populations-counter (MCP)-counter deconvolution showed an enrichment in adaptive immune cell signatures in microdissected TIL. Transcripts of immune checkpoints were differentially expressed in TIL and TC. We further validated our results by qRT-PCR and multispectral immunohistochemistry. In conclusion, we showed that combining laser-capture microdissection and RNA-sequencing on archived FFPE blocks is feasible and allows spatial transcriptional characterization of tumor microenvironment.
Single-molecule imaging of telomerase RNA reveals a Recruitment – Retention model for telomere elongation
Authors: Laprade Hadrien , Querido Emmanuelle , Smith Michael J. , Guérit David , Crimmins Hannah , Conomos Dimitri , Pourret Emilie , Chartrand Pascal , Sfeir Agnel
Published: February 2020

Extension of telomeres is a critical step in the immortalization of cancer cells. This complex reaction requires proper spatio-temporal coordination of telomerase and telomeres, and remains poorly understood at the cellular level. To understand how cancer cells execute this process, we combined CRISPR genome editing and MS2 RNA-tagging to image single-molecules of telomerase RNA (hTR). Real-time dynamics and photoactivation experiments of hTR in Cajal bodies (CBs) reveal that hTERT controls the exit of hTR from CBs. Single-molecule tracking of hTR at telomeres shows that TPP1-mediated recruitment results in short telomere-telomerase scanning interactions, then base-pairing between hTR and telomere ssDNA promotes long interactions required for stable telomerase retention. Interestingly, POT1 OB-fold mutations that result in abnormally long telomeres in cancers act by enhancing this retention step. In summary, single-molecule imaging unveils the life-cycle of telomerase RNA and provides a framework to understand how cancer-associated mutations mechanistically drive defects in telomere homeostasis.
TheE. coliNudL enzyme is a Nudix hydrolase that cleaves CoA and its derivatives
Authors: Spangler Joseph Rankin , Huang Faqing
Published: February 2020

The process of bacterial coenzyme A (CoA) degradation has remained unknown despite the otherwise detailed characterization of the CoA synthesis pathway over 30 years ago. Numerous enzymes capable of CoA degradation have been identified in other domains of life that belong to the Nudix superfamily of hydrolases, but the molecule responsible for this process in the model bacterial system ofE. coli remains a mystery. We report here thatE. coli contains two such Nudix enzymes capable of CoA degradation into 4’-phosphopantetheine and 3’,5’-adenosine monophosphate. TheE. coli enzymes NudC and NudL were cloned in various promoter-fusion constructs in order to purify them as soluble active enzymes and characterize their ability to catalyze the phosphohydrolysis of CoA. NudC, an enzyme known to hydrolyze NADH as its principal substrate, demonstrated the ability to hydrolyze CoA, among other coenzymes, at comparable rates to eukaryotic Nudix hydrolases. NudL, a previously uncharacterized enzyme, demonstrated the ability to cleave only CoA and CoA-related molecules at a rate orders of magnitude slower than its eukaryotic orthologs. NudC and NudL therefore represent a previously uncharacterized pathway of CoA degradation in the highly studiedE. coli system. While the two enzymes display some substrate overlap, their respective activities imply that NudC may play a role as a general coenzyme hydrolase, while NudL specifically targets CoA. These data further suggest a role for these enzymes in the regulation of bacterial CoA-RNA.
Phosphorylation of Elovl5 changes its substrate preference to synthesize Mead acid in response to essential fatty acid deficiency
Authors: Hayashi Yuri , Yamano Misato , Kono Nozomu , Arai Hiroyuki , Fujiwara Yoko , Ichi Ikuyo
Published: February 2020

Polyunsaturated fatty acids (PUFAs) of the n-6 and n-3 series cannot be synthesized in mammals and therefore are called essential fatty acids (EFAs). Mead acid (20:3n-9) is an unusual n-9 PUFA, endogenously synthesized from oleic acid (18:1n-9) in an EFA-deficient state. Although Elovl5, a fatty acid elongase, has long been known to selectively elongate C18 and C20 PUFAs, it can use 18:1n-9 as a substrate for the synthesis of Mead acid under C20 PUFA-deficient, but not-sufficient, conditions. We found, by an in vitro enzyme assay, that the microsomal fraction obtained from PUFA-deficient, but not -sufficient, cells showed significant Elovl5 activity toward 18:1n-9, with no effect on its constitutive activity toward 18:3n-6, implying that Elovl5 acquires the activity toward 18:1n-9 under the PUFA-deficient conditions at the enzyme level. Further biochemical analysis revealed that Elovl5 was phosphorylated in the C20 PUFA-supplemented cells, and that treatment with an inhibitor of glycogen synthase kinase 3 (GSK3) completely abolished the phosphorylation of Elovl5 and retained the Elovl5 activity toward 18:1n-9, even in the presence of C20 PUFA. Finally, mutation of putative phosphorylation sites (T281A/S283A/S285A) on Elovl5 did not decrease the activity of Elovl5 toward 18:1n-9 by supplementation with C20 PUFA, suggesting that the phosphorylation of Elovl5 contributed to a change in substrate preference. Thus, by changing its substrate specificity in an EFA-deficient state, Elovl5 is able to regulate the synthesis of Mead acid to maintain levels of long-chain PUFAs.
Unification of Environmental Metabolomics with Metacommunity Ecology
Authors: Danczak Robert E. , Chu Rosalie K. , Fansler Sarah J. , Goldman Amy E. , Graham Emily B. , Tfaily Malak M. , Toyoda Jason , Stegen James C.
Published: February 2020

Environmental metabolomics, enabled by high-resolution mass spectrometric techniques, have demonstrated the biogeochemical importance of the metabolites which comprise natural organic matter (NOM). However, significant gaps exist in our understanding of the spatiotemporal organization of NOM composition. We suggest that the underlying mechanisms governing NOM can be revealed by applying tools and concepts from metacommunity ecology to environmental metabolomics. After illustrating the similarities between metabolomes and ecological communities, we call this conceptual synthesis ‘meta-metabolome ecology’ and demonstrate its potential utility using a freshwater mass spectrometry dataset. Specifically, we developed three relational metabolite dendrograms using combinations of molecular properties (i.e., aromaticity index, double-bond equivalents, etc.) and putative biochemical transformations. Using these dendrograms, which are similar to phylogenetic or functional trait trees in ecological communities, we illustrate potential analytical techniques by investigating relationally-informed α-diversity and β-diversity metrics (e.g., MPD, MNTD, UniFrac), and null model analyses (e.g., NRI, NTI, and βNTI). Furthermore, we demonstrate that this synthesis allows ecological communities (e.g., microbes) and the metabolites they produce and consume using the same framework. We propose that applying this framework to a broad range of ecosystems will reveal generalizable principles that can advance our predictive capabilities regarding NOM dynamics.
Myeloid cell mPGES-1 mediates inflammatory pain hypersensitivity in mice
Authors: Chen Lihong , Yang Guangrui , Cormode David P. , Saigal Ashmita , Madhavan Shravanthi , Mazaleuskaya Liudmila L. , Grant Gregory R. , FitzGerald Garret A. , Grosser Tilo
Published: February 2020

Nonsteroidal anti-inflammatory drugs (NSAIDs) relieve inflammatory pain by predominant suppression of cyclooxygenase-2 derived prostaglandin (PG) E2. Innate immune cells contribute to inflammatory pain hypersensitivity and may be an attractive target for novel non-addictive approaches to pain management. We studied the contribution of PGE2produced by myeloid cell microsomal prostaglandin E synthase -1 (mPGES-1) to peripheral inflammation and hyperalgesia in mice. Selective deletion of mPGES-1 in myeloid cells by crossing LysM-Cre mice with mPGES-1flox/flox mice (Mac-mPGES-1-KO) resulted in significantly reduced mechanical and thermal hyperalgesia in complete Freund’s adjuvant (CFA)-evoked hind paw inflammation, zymosan-induced peri-articular inflammation and collagen II antibody-induced arthritis models. Systemic COX-2 inhibition or myeloid cell specific COX-2 deletion (by crossing LysM-Cre with COX-2 flox/flox mice) recapitulated reduction of CFA-induced inflammation and hyperalgesia. In contrast, deletion of mPGES-1 in neurons and glial cells by crossing mPGES-1flox/flox mice with Nestin-Cre mice had no detectable effect on inflammatory pain hypersensitivity. While macrophage recruitment was unaltered, tissue concentrations of PGE2, IL-1β and TNFα were significantly reduced in Mac-mPGES-1-KO paw tissues following CFA induction. Our results demonstrate that myeloid cell mPGES-1 is the dominant source of PGE2in inflammatory pain hypersensitivity. Targeting myeloid cell mPGES-1 may afford a novel approach to inflammatory pain therapy.
Predicting commercially available antiviral drugs that may act on the novel coronavirus (2019-nCoV), Wuhan, China through a drug-target interaction deep learning model
Authors: Beck Bo Ram , Shin Bonggun , Choi Yoonjung , Park Sungsoo , Kang Keunsoo
Published: February 2020

The infection of a novel coronavirus found in Wuhan of China (2019-nCoV) is rapidly spreading, and the incidence rate is increasing worldwide. Due to the lack of effective treatment options for 2019-nCoV, various strategies are being tested in China, including drug repurposing. In this study, we used our pretrained deep learning-based drug-target interaction model called Molecule Transformer-Drug Target Interaction (MT-DTI) to identify commercially available drugs that could act on viral proteins of 2019-nCoV. The result showed that atazanavir, an antiretroviral medication used to treat and prevent the human immunodeficiency virus (HIV), is the best chemical compound, showing a inhibitory potency withKdof 94.94 nM against the 2019-nCoV 3C-like proteinase, followed by efavirenz (199.17 nM), ritonavir (204.05 nM), and dolutegravir (336.91 nM). Interestingly, lopinavir, ritonavir, and darunavir are all designed to target viral proteinases. However, in our prediction, they may also bind to the replication complex components of 2019-nCoV with an inhibitory potency withKd< 1000 nM. In addition, we also found that several antiviral agents, such as Kaletra, could be used for the treatment of 2019-nCoV, although there is no real-world evidence supporting the prediction. Overall, we suggest that the list of antiviral drugs identified by the MT-DTI model should be considered, when establishing effective treatment strategies for 2019-nCoV.
Selective augmentation of intestinal immunity by CD22-dependent SHP-1 control of β7integrin expression
Authors: Ballet Romain , Brandl Carolin , Feng Ningguo , Berri Jeremy , Cheng Julian , Ocón Borja , Sheikh Amin Alborzian Deh , Marki Alex , Abram Clare L. , Lowell Clifford A. , Tsubata Takeshi , Greenberg Harry B. , Macauley Matthew S. , Ley Klaus , Nitschke Lars , Butcher Eugene C.
Published: February 2020

The regulation of integrin expression and function controls interactions of immune cells and targets their trafficking locally and systemically. We show here that the tyrosine phosphatase SHP-1 is required for lymphocyte surface expression of the intestinal immune response-associated integrin β7, but not for β1or β2integrins.Viable motheatenmice deficient for SHP-1 have less β7on T cells and lack β7on B cells. SHP-1 function is targeted in B cells by the B cell specific lectin CD22 (Siglec-2), suggesting a potential role for CD22 in β7expression. CD22-deficiency on B cells phenocopies the effects of SHP-1 haplodeficiency. Mechanistically, we show that SHP-1 suppresses β7endocytosis: internalization of β7but not β1integrin is accelerated in SHP-1+/−and CD22−/−B cells. Moreover, mutations in CD22 cytoplasmic SHP1-binding ITIM sequences reduce α4β7comparably, and loss of CD22 lectin activity has an intermediate effect suggesting a model in which the CD22 ITIM sequences recruit SHP-1 to control β7expression. Integrin α4β7selectively contributes to cell interactions in intestinal immunity. Consistent with this, CD22 deficient and SHP-1+/−B cells display reduced β7-dependent homing to gut associated Peyer’s patches (PP); and CD22-deficiency impairs intestinal but not systemic antibody responses and delays clearance of the gut pathogen rotavirus. The results define a novel role for SHP-1 in the differential control of leukocyte integrins and an unexpected integrin β7-specific role for CD22-SHP-1 interplay in mucosal immunity.
The ECF sigma factor PvdS regulates the type I-F CRISPR-Cas system inPseudomonas aeruginosa
Authors: Ahator Stephen Dela , Jianhe Wang , Zhang Lian-Hui
Published: February 2020

During infection, successful colonization of bacteria requires a fine-tuned supply of iron acquired via iron transport systems. However, the transport systems serve as phage attachment sites and entry portals for foreign nucleic acid. Most bacteria possess the CRISPR-Cas system, which targets and destroys foreign nucleic acids and prevents deleterious effects of horizontal gene transfer. To understand the regulation of the CRISPR-Cas system, we performed genome-wide random transposon mutagenesis which led to the identification of the Extracytoplasmic Function (ECF) Sigma factor, PvdS as a regulator of the Type I-F CRISPR-Cas system inP. aeruginosa. We show that under iron-depleted conditions PvdS induces the expression of the type I-F CRISPR-Cas system. This regulatory mechanism involves direct interaction of PvdS with specific binding sites in the promoter region ofcas1. Furthermore, activation of the CRISPR-Cas system under iron-depleted conditions increases horizontal gene transfer (HGT) interference and adaptation. The PvdS activation of the CRISPR-Cas system under iron limitation highlights the versatility of theP. aeruginosain multitasking its regulatory machinery to integrate multiple stress factors.

Importance

P. aeruginosainfects a wide range of host organisms and adapts to various environmental stress factors such as iron limitation due to its elaborate regulatory system.P aeruginosapossesses the type I-F CRISPR-Cas system as a defense mechanism against phages infection and HGT. This work highlights the ability ofP. aeruginosato multitask its iron regulatory system to control the CRISPR-Cas system under a physiologically relevant stress factor such as iron limitation where the bacteria are vulnerable to phage infection. It also adds to the knowledge of the regulation of the CRISPR-Cas system in bacteria and presents a possible target that could prevent the emergence of phage resistance via the CRISPR-Cas system during the development of phage therapy.
IL4-driven microglia modulate stress resilience through BDNF-dependent neurogenesis
Authors: Zhang Jinqiang , Rong Peijing , Zhang Lijuan , He Hui , Zhou Tao , Fan Yonghua , Mo Li , Zhao Qiuying , Han Yue , Li Shaoyuan , Wang Yifei , Yan Wan , Chen Huafu , You Zili
Published: February 2020

Adult neurogenesis in the dentate gyrus of the hippocampus is regulated by specific groups of microglia and is functionally implicated in behavioral responses to stress. However, the role of microglia in modulating hippocampal neurogenesis in stress responses remains poorly understood. Here we investigated the effects of IL4-driven Arg1+microglia in the restoration of hippocampal neurogenesis and conferment of stress resilience. We found that low IL4 levels in the hippocampus of mice was associated with greater stress vulnerability and, conversely, overexpression of IL4 in the hippocampus induced a large number of Arg1+microglia and ameliorated stress-induced depressive-like behaviors. Knockdown of microglial IL4 receptors in the hippocampus of mice exacerbated the stress-induced inflammatory response and abolished the antidepressant effects of IL4 overexpression. Enhancement or inhibition of IL4 signaling in hippocampal microglia modulated neurogenesis, and blockade of neurogenesis abolished the resilience to stress-induced depression. We further show that IL4-activated microglia is associated with upregulation of BDNF levels and neurogenesis. Taken together, our findings suggest that IL4-driven microglia in the hippocampus trigger BDNF-dependent neurogenesis in response to chronic stress, helping protect against depressive-like symptoms. These findings identify the modulation of a specific microglial phenotype as a treatment strategy for mood disorders.

In Brief

Zhang et al. show that IL4-induced Arg1+microglia restore hippocampal neurogenesis and promote resilience against stress in mice by increasing BDNF levels. Targeting microglia with immunomodulatory factors may be a strategy for treating mood disorders.

Highlights

Vulnerability to stress in mice is associated with reduced IL4 signaling in the hippocampus

Brain-derived IL4 promotes adult hippocampal neurogenesis and stress resistance by driving Arg1+microglia

IL4-driven Arg1+microglia enhance hippocampal neurogenesis via a BDNF-dependent pathway
G-baToN: a versatile reporter system for cancer cell-stromal cell interactions
Authors: Tang Rui , Murray Christopher W. , Linde Ian , Kramer Nicholas J. , Lyu Zhonglin , Tsai Min K. , Chen Leo , Cai Hongchen , Gitler Aaron D. , Engleman Edgar , Lee Wonjae , Winslow Monte M.
Published: February 2020

Cell-cell interactions influence all aspects of development, homeostasis, and disease. In cancer, interactions between cancer cells and stromal cells play a major role in nearly every step of carcinogenesis. Thus, the ability to record cell-cell interactions would facilitate mechanistic delineation of the role of cancer microenvironment. Here, we describe GFP-based Touching Nexus (G-baToN) which relies upon nanobody-directed fluorescent protein transfer to enable sensitive and specific labeling of cells after cell-cell interactions. G-baToN is a generalizable system that enables physical contact-based labeling between various cell types, including diverse cancer-stromal cell pairs. A suite of orthogonal baToN tools enables reciprocal cell-cell labeling, interaction-dependent cargo transfer, and the identification of higher-order cell-cell interactions across a wide range of cell types. The ability to track physically interacting cells with these simple and sensitive systems will greatly accelerate our understanding of the outputs of cell-cell interactions in cancer as well as across many biological processes.
Large-scale Dynamics of Perceptual Decision Information across Human Cortex
Authors: Wilming Niklas , Murphy Peter R , Meyniel Florent , Donner Tobias H
Published: February 2020

Perceptual decisions entail the accumulation of sensory evidence for a particular choice towards an action plan. An influential framework holds that sensory cortical areas encode the instantaneous sensory evidence and downstream, action-related regions accumulate this evidence. The large-scale distribution of this computation across the cerebral cortex has remained largely elusive. We developed a regionally-specific magnetoencephalography decoding approach to exhaustively map the dynamics of stimulus- and choice-specific signals across the human cortical surface during a visual decision. Comparison with the evidence accumulation dynamics inferred from behavior enabled us to disentangle stimulus-dependent and endogenous components of choice-predictive activity across the visual cortical hierarchy. The endogenous component was present in primary visual cortex, expressed in a low (< 20 Hz) frequency-band, and its time course tracked, with delay, the build-up of choice-predictive activity in (pre-)motor regions. Our results are consistent with choice-specific cortical feedback signaling in a specific frequency channel during decision formation.
Aquatic microbial community is partially functionally redundant: insights from anin situreciprocal transplant experiment
Authors: Tandon Kshitij , Wan Min-Tao , Yang Chia-Chin , Yang Shan-Hua , Baatar Bayanmunkh , Chiu Chih-Yu , Tsai Jeng-Wei , Liu Wen-Cheng , Ng Chen Siang , Tang Sen-Lin
Published: February 2020

Microbial communities are considered to be functionally redundant, but few studies have tested this hypothesis empirically. In this study, we performed anin situreciprocal transplant experiment on the surface and bottom waters of two lakes with disparate trophic states and tracked changes in their microbial community and functional attributes for 6 weeks using high-throughput sequencing and functional approaches. The communities from both lakes were resistant to changes in composition after the reciprocal transplant, but their functions tended to become similar to the incubating lakes’ functional profiles. A significant linear positive relationship was observed between the microbial community and functional attributes, though with varying scales of similarity, suggesting partial functional redundancy. Furthermore, the entropy-basedL-divergence measure quantified the scale of partial functional redundancy in the lakes’ surface and bottom waters. This study establishes and quantifies the scale of partial functional redundancy in the freshwater ecosystem through empirical investigation.