bluuebunny/crossref_metadata_2025 huggingface dataset:
Cocaine regulation of Nr4a1 chromatin bivalency and mRNA in male and female mice
Authors: Fischer Delaney K. , Krick Keegan S. , Han Chloe , Woolf Morgan , Heller Elizabeth A.
Published: May 2022

BACKGROUND

Cocaine epigenetically regulates gene expression via changes in histone post-translational modifications (HPTMs). We previously found that the immediate early gene Nr4a1 is epigenetically activated by cocaine in mouse brain reward regions. HPTMs act combinatorically, yet few studies examine multiple HPTMs at a single gene. Bivalent gene promoters are simultaneously enriched in both activating (H3K4me3 (K4)) and repressive (H3K27me3 (K27)) HPTMs. As such, bivalent genes are lowly expressed but poised for activity-dependent gene regulation. In the current study, we defined regulation of K4&K27 bivalency at Nr4a1 following cocaine treatment in male and female mice. The inclusion of female mice can shed light on the epidemiological relevance of sex to cocaine use disorder.

METHODS

Male and female mice were injected with saline or cocaine (i.p. 20mg/kg). We applied sequential chromatin immunoprecipitation and qPCR to define Nr4a1 bivalency and expression in striatum (STR), prefrontal cortex (PFC), and hippocampus (HPC). Pearson’s correlation matrices quantified relationships within each brain region across treatment conditions for each sex.

RESULTS

We defined K4&K27 bivalency at the Nr4a1 promoter in all three brain regions, in both sexes. In female STR, cocaine increased Nr4a1 mRNA, coupled to maintenance of Nr4a1 K4&K27 bivalency. In male STR, cocaine enriched repressive H3K27me3 and K4&K27 bivalency at Nr4a1 and failed to increase Nr4a1 mRNA. Furthermore, cocaine epigenetically regulated a putative NR4A1 target, Cartpt, in male PFC.

CONCLUSION

This study defined the epigenetic regulation of Nr4a1 in reward brain regions in male and female mice. Cocaine treatment in female mice increased Nr4a1 mRNA in STR, but there was no change in Nr4a1 H3K27me3 or K4&K27 promoter bivalency. Following cocaine treatment in male mice, Nr4a1 mRNA did not change in STR, HPC, or PFC, and Nr4a1 H3K27me3 and K4&K27 promoter bivalency increased in the STR.
Genetic dissection of the pluripotent proteome through multi-omics data integration
Authors: Aydin Selcan , Pham Duy T. , Zhang Tian , Keele Gregory R. , Skelly Daniel A. , Pankratz Matthew , Choi Ted , Gygi Steven P. , Reinholdt Laura G. , Baker Christopher L. , Churchill Gary A. , Munger Steven C.
Published: May 2022

Genetic background is a major driver of phenotypic variability in pluripotent stem cells (PSCs). Most studies of variation in PSCs have relied on transcript abundance as the primary molecular readout of cell state. However, little is known about how proteins, the primary functional units in the cell, vary across genetically diverse PSCs, how protein abundance relates to variation in other cell characteristics, and how genetic background confers these effects. Here we present a comprehensive genetic study characterizing the pluripotent proteome of 190 unique mouse embryonic stem cell lines (mESCs) derived from genetically heterogeneous Diversity Outbred (DO) mice. The quantitative proteome is highly variable across DO mESCs, and we identified differentially activated pluripotency-associated pathways in the proteomics data that were not evident in transcriptome data from the same cell lines. Comparisons of protein abundance to transcript levels and chromatin accessibility show broad co-variation across molecular layers and variable correlation across samples, with some lines showing high and others low correlation between these multi-omics datasets. Integration of these three molecular data types using multi-omics factor analysis revealed shared and unique drivers of quantitative variation in pluripotency-associated pathways. QTL mapping localized the genetic drivers of this quantitative variation to a number of genomic hotspots, and demonstrated that multi-omics data integration consolidates the influence of genetic signals shared across molecular traits to increase QTL detection power and overcome the limitations inherent in mapping individual molecular features. This study reveals transcriptional and post-transcriptional mechanisms and genetic interactions that underlie quantitative variability in the pluripotent proteome, and in so doing provides a regulatory map for mouse ESCs that can provide a rational basis for future mechanistic studies, including studies of human PSCs.
Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade and the role of insertions and extensions in diversification
Authors: Burnim Audrey A. , Spence Matthew A. , Xu Da , Jackson Colin , Ando Nozomi
Published: May 2022

Ribonucleotide reductases (RNRs) are used by all organisms and many viruses to catalyze an essential step in the de novo biosynthesis of DNA precursors. RNRs are remarkably diverse by primary sequence and cofactor requirement, while sharing a conserved fold and radical-based mechanism for nucleotide reduction. Here, we structurally aligned the diverse RNR family by the conserved catalytic barrel to reconstruct the first large-scale phylogeny consisting of 6,779 sequences that unites all extant classes of the RNR family and performed evo-velocity analysis to independently validate our evolutionary model. With a robust phylogeny in-hand, we uncovered a novel, phylogenetically distinct clade that is placed as ancestral to the classes I and II RNRs, which we have termed clade Ø. We employed small-angle X-ray scattering (SAXS), cryogenic-electron microscopy (cryo-EM), and AlphaFold2 to investigate a member of this clade from Synechococcus phage S-CBP4 and report the most minimal RNR architecture to-date. Using the catalytic barrel as a starting point for diversification, we traced the evolutionarily relatedness of insertions and extensions that confer the diversity observed in the RNR family. Based on our analyses, we propose an evolutionary model of diversification in the RNR family and delineate how our phylogeny can be used as a roadmap for targeted future study.
Placental mammal derived microRNAs alter pathways in the endometrial epithelia important for endometrial function
Authors: Hume Laura , Edge Jessica C. , Tinning Haidee , Wang Dapeng , Taylor Alysha S. , Ovchinnikov Vladimir , Geijer-Simpson Annika , Vrljicak Pavle , Brosens Jan J. , Lucas Emma S. , Simson Nigel A.B. , Shillito Jane , Forbes Karen , O’Connell Mary J. , Forde Niamh
Published: May 2022

We tested the hypothesis that a panel of placental mammal-specific miRNAs and their targets play important to establish receptivity to implantation and their dysregulated expression may be a feature in women with early pregnancy loss. Relative expression levels of miR-340-5p, −542-3p, and −671-5p all increased following treatment of Ishikawa cells with progesterone (10 μg/ml) for 24 hrs (p < 0.05). RNA sequencing of these P4-treated cells identified co-ordinate changes to 6,367 transcripts of which 1713 were predicted targets of miR-340-5p, 670 of miR-542-3p, and 618 of miR-671-5p. Quantitative proteomic analysis of Ishikawa cells transfected with mimic or inhibitor (48 hrs: n=3 biological replicates) for each of the P4-regulated miRNAs was carried out to identify targets of these miRNAs. Excluding off target effects, mir-340-5p mimic altered 1,369 proteins while inhibition changed expression of 376 proteins (p < 0.05) of which, 72 were common to both treatments. A total of 280 proteins were identified between predicted (mirDB) and confirmed (in vitro) targets. In total, 171 proteins predicted to be targets by mirDB were altered in vitro by treatment with miR-340-5p mimic or inhibitor and were also altered by treatment of endometrial epithelial cells with P4. In vitro targets of miR-542-3p identified 1,378 proteins altered by mimic while inhibition altered 975 a core of 200 proteins were changed by both. 100 protein targets were predicted and only 46 proteins were P4 regulated. miR-671-mimic altered 1,252 proteins with inhibition changing 492 proteins of which 97 were common to both, 95 were miDB predicted targets and 46 were also P4-regulated. All miRNAs were detected in endometrial biopsies taken from patients during the luteal phase of their cycle, irrespective of prior or future pregnancy outcomes Expression of mir-340-5p showed an overall increase in patients who had previously suffered a miscarriage and had a subsequent miscarriage, as compared to those who had infertility or previous miscarriage and subsequently went on to have a life birth outcome. The regulation of these miRNAs and their protein targets regulate the function of transport and secretion, and adhesion of the endometrial epithelia required for successful implantation in humans. Dysfunction of these miRNAs (and therefore the targets they regulate) may contribute to endometrial-derived recurrent pregnancy loss in women.
The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus)
Authors: Fuentes-Pardo Angela P. , Farrell Edward D. , Pettersson Mats E. , Sprehn C. Grace , Andersson Leif
Published: May 2022

Understanding how populations adapt to local environments is increasingly important to prevent biodiversity loss due to climate change. Here we examined whole-genome variation of twelve Atlantic horse mackerel samples from the North Sea to North Africa, and the western Mediterranean Sea. This marine migratory benthopelagic fish is one of the most widely distributed and commercially important species in the eastern Atlantic. We found low population structure at neutral loci, but high differentiation at adaptive loci distinguishing the western Mediterranean and the North Sea populations from other Atlantic locations. Candidate genes distinctive of the Mediterranean include a green-sensitive-opsin harbouring two missense mutations that might fine-tune the spectral sensitivity to blue-green light conditions. Candidate genes characteristic of the North Sea could play a critical role in cold tolerance (energy metabolism and cell membrane structure) and increased sensitivity to odours, presumably to compensate reduced visibility in turbid waters. We also discovered a putative chromosomal inversion (9.9 Mb) that follows a climate-related latitudinal cline with a break near mid Portugal. Genome-environment association analysis indicated that seawater-dissolved oxygen concentration and temperature are likely the main environmental drivers of local adaptation. Our genomic data broadly supports the current stock divisions, but recommends revision of the western and southern stock boundaries. We developed a reduced SNP panel that genetically discriminate the North Sea and North Africa from neighbouring populations. Our study highlights the importance of life history and chromosomal inversions in adaptation with gene flow, and the complexity of evolutionary and ecological processes involved in local adaptation.
Loss of Myosin-1e biases MMTV-PyMT induced breast cancer towards a differentiated and secretory state
Authors: Plante Eric L. , Chase Sharon E. , de Jong Ebbing P. , Curtis Theresa M. , Garone Michael E. , Krendel Mira
Published: May 2022

Expression of the unconventional myosin, Myosin-1e (Myo1e), has been shown to contribute to tumor progression in the MMTV-PyMT mouse model of mammary tumorigenesis and is associated with poor outcome in breast cancer patients. However, the specific effects of Myo1e expression on the mammary tumor cells remain unidentified. Here, we used Myo1e-KO and wild-type (WT) MMTV-PyMT mice on a pure genetic background to further investigate the molecular and cellular effects of Myo1e expression. Myo1e-WT tumors were characterized by an increased abundance of intra-epithelial macrophages and lower amounts of the extracellular matrix. Transcriptomic profiling of WT and Myo1e-KO tumors identified a pattern of differential expression of tumor suppressor and tumor-promoting genes that was consistent with the observed differences in tumor progression and morphology between the genotypes, and also revealed differential expression of genes associated with secretion and cell-cell adhesion. In agreement with the RNA-seq findings, Myo1e-expressing tumor cells exhibited increased proliferation and elevated nuclear enrichment of YAP1 transcriptional activator compared to Myo1e-KO tumor cells. To investigate tumor cell-autonomous effects of Myo1e expression, we used the epithelial cell line PY-230 derived from the MMTV-PyMT-induced mouse tumor to create Myo1e-depleted cells by Crispr-mediated genome editing. Cells deficient in Myo1e had increased expression of genes encoding milk components compared to the wild-type cells. Electric cell-substrate impedance sensing (ECIS) measurements showed that depletion of Myo1e in PY-230 cells resulted in increased resistance to electrical current indicating enhanced epithelial barrier function. Overall, we find that Myo1e expression biases tumors towards a less-differentiated, pro-tumorigenic state, and that depletion of Myo1e is associated with a pro-secretory, more differentiated state.
Fic-mediated AMPylation tempers the Unfolded Protein Response during physiological stress
Authors: Casey Amanda K. , Gray Hillery F. , Chimalapati Suneeta , Hernandez Genaro , Moehlman Andrew , Stewart Nathan , Fields Hazel A. , Gulen Burak , Servage Kelly A. , Stefanius Karoliina , Blevins Aubrie , Daoud Elena , Evers Bret , Krämer Helmut , Orth Kim
Published: May 2022

The proper balance of synthesis, folding, modification and degradation of proteins, also known as protein homeostasis, is vital to cellular health and function. The unfolded protein response (UPR) is activated when the mechanisms maintaining protein homeostasis in the endoplasmic reticulum (ER) become overwhelmed. However, prolonged or strong UPR responses can result in elevated inflammation and cellular damage. Previously, we discovered that the bifunctional enzyme Fic can modulate the UPR response via post-translational modification of BiP by AMPylation and deAMPylation. Loss of fic in Drosophila leads to vision defects and altered UPR activation in the fly eye. To investigate the importance of Fic-mediated AMPylation in a mammalian system, we generated a conditional null allele of Fic in mice and characterized the effect of Fic loss on the exocrine pancreas. Compared to controls, Fic-/- mice exhibit elevated serum markers for pancreatic dysfunction and display enhanced UPR signaling in the exocrine pancreas in response to physiologic and pharmacological stress. In addition, both fic-/- flies and Fic-/- mice show reduced capacity to recover from damage by stress that triggers the UPR. These findings show that Fic- mediated AMPylation acts as a molecular rheostat that is required to temper the UPR response in the mammalian pancreas during physiological stress.
Mediator-RNA Polymerase II Interactions Critical for Transcriptional Activation Are Mediated by the N-terminal Half of MED14 and C-terminal Domain of RPB1
Authors: Baris Yasemin , Jabbar Javaid , Yozgat Yasemin , Cigirgan Ege , Bay Sadik , Tucer Merve Erden , Aslan Volkan , Dinccelik-Aslan Melike , Cevher Murat Alper
Published: May 2022

Mediator is a large and evolutionarily conserved coactivator complex essential for RNA polymerase II (Pol II)-mediated gene regulation at multiple steps of the transcription process, including preinitiation complex (PIC) assembly and function. Here, we used the MultiBac baculovirus expression system to generate recombinant human core Mediator subcomplexes and subsequent biochemical approaches to dissect the mechanism by which Mediator facilitates direct recruitment of Pol II to core promoters. Our results highlight a pivotal role in this process for the N-terminal half (NTD) of the MED14 subunit. We show that a reconstituted 15-subunit human core Mediator complex that contains only the MED14-NTD is fully functional in facilitating both basal and activated (p53) transcription. This complex directly interacts with the C-terminal domain (CTD) of the RPB1 subunit of Pol II (RPB1 CTD) and is required for recruiting Pol II to core promoters. Moreover, recombinant RPB1 can completely reverse the human core Mediator-Pol II interaction. Notably, the human MED14-NTD region has secondary structure conservation with Schizosaccharomyces pombe. In addition, reanalysis of published cryo-EM structures of yeast Mediator-Pol II complexes strongly supports our conclusion. Thus, our analyses provide critical new insights into how Mediator binds to Pol II and recruits it to the promoters to facilitate transcription.
Neurite outgrowth deficits caused by rare PLXNB1 mutation in pediatric bipolar disorder
Authors: Yang Guang , Parker Ethan , Gorsi Bushra , Liebowitz Mark , Maguire Colin , King Jace B. , Coon Hilary , Lopez-Larson Melissa , Anderson Jeffrey , Yandell Mark , Shcheglovitov Alex
Published: May 2022

Pediatric Bipolar Disorder (PBD) is a severe mood dysregulation condition that affects 0.5–1% of children and teens in the United States. It is associated with recurrent episodes of psychosis and depression and an increased risk of suicidality. However, the genetics and neuropathology of PBD are largely unknown. Here, we used a combinatorial family-based approach to characterize the cellular, molecular, genetic, and network-level deficits associated with PBD. We recruited a PBD patient and three unaffected family members from a family with a history of psychiatric illnesses. Using resting-state functional magnetic resonance imaging (rs-fMRI), we detected altered resting-state functional connectivity in the patient as compared to the unaffected sibling. Using transcriptomic profiling of patient and control induced pluripotent stem cell (iPSC) derived telencephalic organoids, we found aberrant signaling in the molecular pathways related to neurite outgrowth. We corroborated the presence of neurite outgrowth deficits in patient iPSC-derived cortical neurons and identified a rare homozygous loss-of-functionPLXNB1variant (c.1360C>C; p.Ser454Arg) in the patient. Expression of wild-typePLXNB1, but not the variant, rescued neurite outgrowth deficit in patient neurons, and expression of the variant caused neurite outgrowth deficit in cortical neurons fromPlxnB1knock-out mice. These results indicate that dysregulated PLXNB1 signaling may contribute to an increased risk of PBD and other mood dysregulation-related disorders by disrupting neurite outgrowth and functional brain connectivity. Overall, the study established and validated a novel family-based combinatorial approach for studying cellular and molecular deficits in psychiatric disorders.
10.4 Million Children Affected by COVID-19-associated Orphanhood and Caregiver Death: An Imperative for Action
Authors: Hillis Susan , Ntwali N’konzi Joel-Pascal , Msemburi William , Cluver Lucie , Villaveces Andrés , Flaxman Seth , Unwin H. Juliette T.
Published: May 2022

The new WHO estimates for COVID-19 excess deaths allow us to generate supdated and more accurate models of COVID-19 associated orphanhood and caregiver loss. Using methodology established in prior studies, we combine age-specific fertility and excess death estimates from January 2020 to May 2022. We find 10.4 million children have lost a parent or caregiver due to COVID-associated excess deaths, and 7.5 million children have experienced COVID-associated orphanhood. Without supportive intervention, caregiver loss can bring severe risks of poverty, school dropout, sexual exploitation, and mental health distress. It is essential that evidence-based care for these children is integrated into all national response plans as a caring action to protect children from immediate and long-term harms of COVID-19.
Risk factors associated with Ahmed valve implant dysfunction in patients with neovascular glaucoma during the first postoperative year
Authors: Ureña-Wong K. , Jimenez-Román J. , Rivas-Ruiz R. , Morales-Gonzalez J A.
Published: May 2022

Background

The current surgical management of Neovascular Glaucoma (NVG) is with the placement of the Ahmed Valve. However, up to 70% fail and the factors associated with this failure are unknown. Recognizing the factors associated with dysfunction will help to identify patients prone to failure promptly to establish prompt management and improve visual and functional prognosis.

Objective

To determine the risk factors associated with Ahmed valve dysfunction in patients with NVG during the first year after surgery.

Population

Patients diagnosed with VNG who have undergone Ahmed valve implantation in the Glaucoma - APEC service, during the 2013 to 2019 period.

Methods

ambispective cohort. Patients with NVG defined as the Presence of neovessels in the iris or angle of the anterior chamber were included, those who had a history of implantation of a drainage device, and patients with a diagnosis of glaucoma in the terminal phase, worse visual acuity of perception were excluded. of light. The research unit was eyes subjected to Ahmed valve implantation. The demographic characteristics of the patients were evaluated, as well as the characteristics of the eyes.

The primary outcome and the secondary outcomes were adverse events, visual acuity, and final intraocular pressure. An unadjusted Cox proportional hazards model was used to determine risk factors such as Hazzard ratios (HR). Those significant factors were included in a Cox proportional hazards model to adjust for the main confounding variables.

Results

174 eyes were included. Baseline intraocular pressure (IOP) was 46.03 (±11.8) mmHG. Baseline VA in LogMAR was 1.52(0.89-2.3). Risk factors were: Age <50 years with HR 1.54(95% CI 1.04-2.30); HB1Ac >8% HR 1.71 (95% CI 1.12-2.60) and presence hypertensive phase HR 3.13 (95% CI 1.57-6.23). The multivariate model was adjusted for the following variables, baseline IOP less than 40mmHg HR 1.60 (95% CI 1.04-2.47); HB1Ac >8% HR 1.80 (95% CI 1.16-2.78); FP7 valve type HR 1.75(95% CI 1.04-2.94) and presence of hypertensive phase HR 3.24 (95% CI 1.60-6.59).

Conclusion

Basal IOP less than 40mmHg, HB1Ac >8%, type of FP7 valve, surgery performed by a resident, lack of photocoagulation after implantation, and the presence of a hypertensive phase are the independent risk factors for implant valvular dysfunction.
Low serum levels of magnesium, phosphate, and zinc in ICU patients – prevalence, management, characteristics, and outcomes Protocol and statistical analysis plan for The WhyTrace cohort study
Authors: Vesterlund Gitte Kingo , Thorsen-Meyer Hans-Christian , Kaas-Hansen Benjamin Skov , Møller Morten Hylander , Perner Anders
Published: May 2022

Background

Patients admitted to the intensive care unit often have low serum levels of magnesium, phosphate, and zinc. We aim to describe the prevalence, management, characteristics, and outcomes of patients with low levels of these minerals in a large cohort of Danish ICU patients.

Methods

In this multicenter cohort, we will include all adult ICU patients admitted to one of 10 ICUs during a six years period. Patients will be excluded if the ICU admission is post-operative after planned surgery, length of stay is <24 hours, they are transferred from ICUs not participating in the study, or are without measurements of neither magnesium, phosphate nor zinc. First, we will do a descriptive assessment of the prevalence of low serum levels and management of supplementation according to different patient characteristics. Second, we will conduct a cohort study using prospectively registered outcome data, to assess associations between serum levels of magnesium, phosphate, and zinc respectively, and each of two principal outcomes: time to successful extubation and incident tachyarrhythmia. We will use a joint modelling approach for estimating the strengths of associations, combining time to event data and longitudinal data from repeated measurements of serum levels.

Discussion

This study will provide information from a very large cohort of Danish ICU patients. Strengths of the study will be the large number of patients, the interconnection of data from several registers, and for the association analysis the use of a statistical approach making the optimal use of the repeated measures of serum levels. Limitations will be the risk of bias from unmeasured or unregistered confounding factors, and the lack of randomization in the observational design, which will prevent us from interpreting possible associations between serum levels and outcomes as definite effects on the outcome.
UDCA and INT-777 suppress cardiac fibrosis triggered by IL-11 through involvement of TGR5
Authors: Reilly-O’Donnell B. , Ferraro E. , Tikhomirov R. , Nunez-Toldra R. , Shchendrygina A. , Patel L. , Wu Y. , Mitchell A. L. , Endo A. , Adorini L. , Chowdhury R. A. , Srivastava P. K. , Ng F. S. , Terracciano C. M. , Williamson C. , Gorelik J.
Published: May 2022

Cardiac fibrosis occurs in a wide range of cardiac diseases and is characterised by the transdifferentiation of cardiac fibroblasts (FB) into myofibroblasts (MFB). Myofibroblasts produce large quantities of extracellular matrix proteins, resulting in myocardial scar. The antifibrotic effect of the bile acid ursodeoxycholic acid (UDCA) is established in cases of liver fibrosis but not the adult myocardium.

Our hypothesis is: UDCA is antifibrotic in the adult heart, mediated by the membrane bile acid receptor Takeda G protein-coupled receptor 5 (TGR5).

We constructed a predictive network of fibrosis using RNA-seq datasets. We found that UDCA and it’s analogue INT-777, both reduced MFB markers in rat and human FBs and living myocardial slices (LMS). Utilising a knock-out mouse model, we show that the antifibrotic effect of UDCA is mediated by TGR5. Finally, we performed RNA-seq upon UDCA-treated human FB and integrated with our network of fibrosis, establishing the mechanism of TGR5 agonists.
Multi-omics Mendelian randomisation using expression, splicing and protein quantitative trait loci: identification of novel drug targets for gliomagenesis
Authors: Thornton Zak A , Andrews Lily J , Zhao Huiling , Zheng Jie , Paternoster Lavinia , Robinson Jamie W , Kurian Kathreena M
Published: May 2022

Background

Genetic variants associated with molecular traits that are also associated with liability to glioma can provide causal evidence for the prioritisation of these traits as candidate drug targets.

Methods

We performed two-sample Mendelian randomisation and genetic colocalisation of a large panel of molecular traits on glioma. Molecular data were taken from studies of expression quantitative trait loci (QTL) [11,985 genes]; splicing QTL [13,285 genes] and protein QTL [7,376 proteins] derived from 15 brain tissues. Glioma summary-level data was extracted from a genome-wide association meta-analysis of 12,496 cases and 18,190 controls.

Results

Our MR analysis showed evidence for a causal effect of 85 molecular traits on glioma – 37 were robust according to colocalisation and Steiger filtering. We found causal evidence for 10 genes previously associated with glioma risk. We identified one novel genetic locus with strong causal evidence in the gene expression analysis:HBEGF(5q31.3) in all glioma [OR 1.36 (95%CI 1.19 to 1.55); P = 4.41 x 10-6]. We also identified three novel genetic loci with strong causal evidence in the splicing variation analysis:CEP192(18p11.21) in glioblastoma [OR 4.40 (95%CI 2.28 to 8.48); P = 9.78 x 10-4];FAIM(3q22.3) in all glioma [OR 2.72 to 3.43; P = 1.03 x 10-5to 1.09 x 10-5] andSLC8A1(2p22.1) in all glioma [OR 0.37 (95%CI 0.24 to 0.56; P = 5.72 x 10-6].

Conclusions

We provide robust causal evidence for genes previously associated with glioma risk in genome-wide association studies, as well as four novel genes.
Performance study of a point-of-care antigen test during the SARS-CoV-2 Delta to Omicron variant transition in the USA
Authors: Drain Paul K , Chiklis Gregory , Guest Poppy , Lindner Nigel M , Ellis Jayne E
Published: May 2022

Introduction

Concerns have been raised regarding the accuracy of diagnostic antigen testing for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant. We compared the performance of the LumiraDx SARS-CoV-2 Antigen Test between symptomatic participants recruited prospectively during the Delta to Omicron variant transition in the USA.

Methods

Two paired anterior nasal swabs were collected from each participant (adults and children) within 12 days of symptom onset between November 24th, 2021 and February 1st, 2022, during which time Omicron replaced Delta as the dominant variant in the sample population. Swabs were tested by the LumiraDx SARS-CoV-2 Antigen Test and compared using real-time polymerase chain reaction (RT-PCR) reference testing. Reference samples identified as positive were sequenced to identify the SARS-CoV-2 variant. Positive percent agreement (PPA) was calculated, with results stratified by RT-PCR cycle threshold (Ct).

Results

Of the 38 participants for whom LumiraDx SARS-CoV-2 Antigen Test results were available, 36 were confirmed positive by RT-PCR. Overall, PPA of the LumiraDx SARS-CoV-2 Antigen Test was 94.7% (95% confidence interval: 82.3%, 99.4%) and PPA was 100% for samples with a Ct <33. Sufficient viral load for sequencing was present in nine samples (six Delta, three Omicron), all of which returned a positive result using the LumiraDx SARS-CoV-2 Antigen Test. There were no performance differences observed between participants with the Delta and Omicron variants.

Conclusions

SARS-CoV-2 differences between Delta and Omicron variant mutations did not affect the performance of the LumiraDx SARS-CoV-2 Antigen Test which detects the nucleocapsid protein antigen. The LumiraDx SARS-CoV-2 Antigen Test can be a useful antigen test to diagnose emerging variants of coronavirus disease 2019.
The impact of trade and investment agreements on the implementation non-communicable disease policies, 2014-2019: protocol for a statistical study
Authors: Barlow P. , Allen L.
Published: May 2022

Introduction

Regulating tobacco, alcohol, and unhealthy foods and drinks is a cornerstone of global efforts to combat the Non-Communicable Disease (NCD) pandemic, but implementation of these policies remains slow. It has been suggested that producers of these unhealthy commodities use rules in Trade and Investment Agreements (TIAs) to delay and undermine NCD policy implementation. Yet, there is no systematic empirical evidence linking TIA participation to reduced implementation. Here we present a study protocol for a statistical analysis of the relationship between TIA participation and the implementation of regulations on tobacco, alcohol, and unhealthy food and drink in 154 countries, 2014-2019.

Methods and analysis

We aim to examine whether participation in TIAs with the EU and US is associated with implementation of regulations targeting tobacco, alcohol, and unhealthy food and drink. We focus on TIAs with these countries as their TIAs create multiple opportunities to contest health regulations, and a majority of the major unhealthy commodity producers are registered in these jurisdictions. Partial and full implementation is captured in a recently published dataset which systematically coded implementation of 11 NCD policies in 2014, 2016 and 2019. We will combine these outcome data with TIA membership and covariate data from multiple sources. We will calculate descriptive statistics and use both regression adjustment and matching to conduct covariate-adjusted, quasi-experimental comparisons of implementation levels and progress according to whether or not countries have a TIA with the EU or US. Further analyses and robustness checks will examine additional TIA participation arrangements and test the sensitivity of our results to our model specifications.

Ethics and dissemination

Ethics approval will not be required as the study uses anonymised and pre-aggregated data. Findings will be disseminated to policymakers via personal contacts and press releases in parallel with scientific papers and conference presentations.

Funding

This research received no specific grant from any funding agency in the public, commercial or not-for-profit sectors.
Humoral immune responses against SARS-CoV-2 Spike variants after mRNA vaccination in solid organ transplant recipients
Authors: Tauzin Alexandra , Beaudoin-Bussières Guillaume , Gong Shang Yu , Chatterjee Debashree , Gendron-Lepage Gabrielle , Bourassa Catherine , Goyette Guillaume , Racine Normand , Khrifi Zineb , Turgeon Julie , Tremblay Cécile , Martel-Laferrière Valérie , Kaufmann Daniel E. , Cloutier Marc , Bazin Renée , Duerr Ralf , Dieudé Mélanie , Hébert Marie-Josée , Finzi Andrés
Published: May 2022

While SARS-CoV-2 mRNA vaccination has been shown to be safe and effective in the general population, immunocompromised solid organ transplant recipients (SOTR) were reported to have impaired immune responses after one or two doses of vaccine. In this study, we examined humoral responses induced after the second and the third dose of mRNA vaccine in different SOTR (kidney, liver, lung and heart). Compared to a cohort of SARS-CoV-2 naïve immunocompetent health care workers (HCW), the second dose induced weak humoral responses in SOTR, except for the liver recipients. The third dose boosted these responses but they did not reach the same level as in HCW. Interestingly, while the neutralizing activity against Delta and Omicron variants remained very low after the third dose, Fc-mediated effector functions in SOTR reached similar levels as in the HCW cohort. Whether these responses will suffice to protect SOTR from severe outcome remains to be determined.
Neuroinflammation in neuronopathic Gaucher disease: Role of microglia and NK cells
Authors: Boddupalli Chandra Sekhar , Nair Shiny , Belinsky Glenn , Gans Joseph , Teeple Erin , Nguyen Tri-Hung , Mehta Sameet , Guo Lilu , Kramer Martin L , Ruan Jiapeng , Wang Hongge , Davison Matthew , Vidyadhara D.J , Bailin Zhang , Klinger Katherine , Mistry Pramod K.
Published: May 2022

Background

Neuronopathic Gaucher Disease (nGD) is a rare neurodegenerative disorder caused by biallelic mutations in Gba, and buildup of glycosphingolipids in lysosomes. Neuronal injury and cell death are prominent pathological features, however the role of Gba in individual cell types and involvement of microglia, blood derived macrophages and immune infiltrates in nGD pathology remains enigmatic.

Methods

Here, using single cell resolution of mouse nGD brains, we found induction of neuroinflammation pathways involving microglia, NK cells, astrocytes, and neurons.

Results

Targeted rescue of Gba in microglia and in neurons, respectively in Gba deficient, nGD mice reversed the buildup of glucosylceramide (GlcCer) and glucosylsphingosine (GlcSph), concomitant with amelioration of neuroinflammation, reduced level of serum neurofilament light chain (Nf-L) and improved survival. The levels of bioactive lipid, GlcSph was strongly correlated with serum Nf-L and ApoE in nGD mouse models as well as GD patients. Gba rescue in microglia/macrophage compartment prolonged survival, that was further enhanced upon treatment with brain permeant inhibitor of glucosylceramide synthase, effects mediated via improved glycosphingolipid homeostasis and reversal of neuroinflammation involving activation of microglia, brain macrophages and NK cells.

Conclusions

Together, our study delineates individual cellular effects of Gba deficiency in nGD brains, highlighting the central role of neuroinflammation driven by microglia activation and the role of brain permeant small molecule glucosylceramide inhibitor in reversing complex multidimensional pathophysiology of nGD. Our findings advance disease biology whilst identifying compelling biomarkers of nGD to improve patient management, enrich clinical trials and illuminate therapeutic targets.

Funding:

Research grant from Sanofi Genzyme; other support includes R01NS110354.Yale Liver Center P30DK034989, pilot project grant.
Shedding Light on functional Near Infrared Spectroscopy and Open Science Practices
Authors: Kelsey Caroline M. , Taylor Jebediah , Pirazzoli Laura , Lorenzo Renata Di , Sullivan Eileen F. , Nelson Charles A.
Published: May 2022

Open science practices work to increase methodological rigor, transparency, and replicability of published findings. This review aims to reflect and commemorate what the functional Near Infrared Spectroscopy (fNIRS) community has done to promote open science practices in fNIRS research and set goals to accomplish over the next ten years.
Novel sterol binding domains in bacteria
Authors: Zhai Liting , Bonds Amber C. , Smith Clyde A. , Oo Hannah , Chou Jonathan Chiu-Chun , Welander Paula V. , Dassama Laura M. K.
Published: May 2022

Sterol lipids are widely present in eukaryotes and play essential roles in signaling and modulating membrane fluidity. Although rare, some bacteria also produce sterols, but their function in bacteria is not known. Moreover, many more species, including pathogens and commensal microbes, acquire or modify sterols from eukaryotic hosts through poorly understood molecular mechanisms. The aerobic methanotrophMethylococcus capsulatuswas the first bacterium shown to synthesize sterols, producing a mixture of C-4 methylated sterols that are distinct from those observed in eukaryotes. C-4 methylated sterols are synthesized in the cytosol and localized to the outer membrane, suggesting that a bacterial sterol transport machinery exists. Until now, the identity of such machinery remained a mystery. In this study, we identified three novel proteins that may be the first examples of transporters for bacterial sterol lipids. The proteins, which all belong to well-studied families of bacterial metabolite transporters, are predicted to reside in the inner membrane, periplasm, and outer membrane ofM. capsulatus,and may work as a conduit to move modified sterols to the outer membrane. Quantitative analysis of ligand binding revealed their remarkable specificity for 4-methylsterols, and crystallographic structures coupled with docking and molecular dynamics simulations revealed the structural bases for substrate binding by two of the putative transporters. Their striking structural divergence from eukaryotic sterol transporters signals that they form a distinct sterol transport system within the bacterial domain. Finally, bioinformatics revealed the widespread presence of similar transporters in bacterial genomes, including in some pathogens that use host sterol lipids to construct their cell envelopes. The unique folds of these bacterial sterol binding proteins should now guide the discovery of other proteins that handle this essential metabolite.
Comprehensive machine-learning survival framework develop a consensus model in large scale multi-center cohorts for pancreatic cancer
Authors: Wang Libo , Liu Zaoqu , Liang Ruopeng , Wang Weijie , Zhu Rongtao , Li Jian , Xing Zhe , Weng Siyuan , Han Xinwei , Sun Yuling
Published: May 2022

Background

As the most aggressive tumor, the outcome of pancreatic cancer (PACA) has not improved observably over the last decade. Anatomy-based TNM staging does not exactly identify treatment-sensitive patients, and an ideal biomarker is urgently needed for precision medicine.

Methods

A total of 1280 patients from 10 multi-center cohorts were enrolled. 10 machine-learning algorithms were transformed into 76 combinations, which were performed to construct an artificial intelligence-derived prognostic signature (AIDPS). The predictive performance, multi-omic alterations, immune landscape, and clinical significance of AIDPS were further explored.

Results

Based on 10 independent cohorts, we screened 32 consensus prognostic genes via univariate Cox regression. According to the criterion with the largest average C-index in the nine validation sets, we selected the optimal algorithm to construct the AIDPS. After incorporating several vital clinicopathological features and 86 published signatures, AIDPS exhibited robust and dramatically superior predictive capability. Moreover, in other prevalent digestive system tumors, the 9-gene AIDPS could still accurately stratify the prognosis. Of note, our AIDPS had important clinical implications for PACA, and patients with low AIDPS owned a dismal prognosis, relatively high frequency of mutations and copy number alterations, and denser immune cell infiltrates as well as were more sensitive to immunotherapy. Correspondingly, the high AIDPS group possessed dramatically prolonged survival, and panobinostat might be a potential agent for patients with high AIDPS.

Conclusions

The AIDPS could accurately predict the prognosis and immunotherapy efficacy of PACA, which might become an attractive tool to further guide the stratified management and individualized treatment.

Funding

This study was supported by the National Natural Science Foundation of China (No. 81870457, 82172944).
Studying protein-protein interaction through side-chain modeling method OPUS-Mut
Authors: Xu Gang , Wang Yilin , Wang Qinghua , Ma Jianpeng
Published: May 2022

Protein side chains are vitally important to many biological processes such as protein-protein interaction. In this study, we evaluate the performance of our previous released side-chain modeling method OPUS-Mut, together with some other methods, on three oligomer datasets, CASP14 (11), CAMEO-Homo (65), and CAMEO-Hetero (21). The results show that OPUS-Mut outperforms other methods measured by all residues or by the interfacial residues. We also demonstrate our method on evaluating protein-protein docking pose on a dataset Oligomer-Dock (75) created using the top 10 predictions from ZDOCK 3.0.2. Our scoring function correctly identifies the native pose as the top-1 in 45 out of 75 targets. Different from traditional scoring functions, our method is based on the overall side-chain packing favorableness in accordance with the local packing environment. It emphasizes the significance of side chains and provides a new and effective scoring term for studying protein-protein interaction.
Feature Importance Network reveals novel functional relationships between biological features inArabidopsis thaliana
Authors: Ng Jonathan Wei Xiong , Chua Swee Kwang , Mutwil Marek
Published: May 2022

Understanding how the different cellular components are working together to form a living cell requires multidisciplinary approaches combining molecular and computational biology. Machine learning shows great potential in life sciences, as it has the ability to find novel relationships between biological features. Here, we constructed a dataset of 11,801 gene features for 31,522Arabidopsis thalianagenes, and developed a machine learning workflow to identify linked features. The detected linked features are visualised as a Feature Important Network (FIN), which can be mined to reveal a variety of novel biological insights pertaining to gene function. We demonstrate how FIN can be used to generate novel insights into gene function. To make this network easily accessible to the scientific community, we present the FINder database, available at finder.plant.tools (http://finder.plant.tools/).
Allosteric inactivation of an engineered optogenetic GTPase
Authors: Jain Abha , Dokholyan Nikolay V. , Lee Andrew L.
Published: May 2022

Optogenetics is a technique for establishing direct spatiotemporal control over molecular function within living cells using light. Light application induces conformational changes within targeted proteins that produce changes in function. One of the applications of optogenetic tools is an allosteric control of proteins via light-sensitive LOV2 domain, which allows direct and robust control of protein function. Computational studies supported by cellular imaging demonstrated that application of light allosterically controlled signaling proteins Vav2, ITSN, and Rac1, but the structural and dynamic basis of such control has yet to be elucidated by experiment. Here, using NMR spectroscopy, we discover principles of action of allosteric control of cell division control protein 42 (CDC42), a small GTPase involved in cell signaling. Both LOV2 and Cdc42 employ flexibility in their function to switch between “dark”/ “lit” or active/inactive states, respectively. By conjoining Cdc42 and LOV2 domains into the bi-switchable fusion Cdc42Lov, application of light – or alternatively, mutation in LOV2 to mimic light absorption – allosterically inhibits Cdc42 downstream signaling. The flow and patterning of allosteric transduction in this flexible system is well-suited to observation by NMR. Close monitoring of the structural and dynamic properties of dark versus lit states of Cdc42Lov revealed lit-induced allosteric perturbations. Chemical shift perturbations for lit mimic, I539E, have distinct regions of sensitivity and both the domains are coupled together leading to bi-directional interdomain signaling. Insights gained from this optoallosteric design will increase our ability to control response sensitivity in future designs.

Significance Statement

Control of cell signaling activity in proteins by light is one of the primary goals of optogenetics. The hybrid light-receptor/cell-signaling protein Cdc42Lov was engineered recently as an optogenetic tool, employing a novel allosteric strategy that results in photoinhibition. In contrast to previous activation designs, the mechanism of inhibition of GTPase signaling activity in Cdc42 is only apparent at a detailed structural and dynamic level. NMR characterization of dark and mutationally “lit” forms reveals the allosteric interdomain perturbations, knowledge of which will enhance future applications of this design strategy.
Optimal balancing of xylem efficiency and safety explains plant vulnerability to drought
Authors: Franklin Oskar , Fransson Peter , Hofhansl Florian , Joshi Jaideep
Published: May 2022

In vast areas of the world, the growth of forests and vegetation is water-limited and plant survival depends on the ability to avoid catastrophic hydraulic failure. Therefore, it is remarkable that plants take high hydraulic risks by operating at water potentials (ψ) that induce partial failure of the water conduits (xylem). Here we present an eco-evolutionary optimality principle for xylem conduit design that explains this phenomenon.

Based on the hypothesis that conductive efficiency and safety are optimally co-adapted to the environment, we derive a simple relationship between the intrinsic tolerance to negative water potential (ψ50) and the environmentally dependent minimum xylem ψ.

This relationship is constrained by a physiological tradeoff between xylem conductivity and safety, which is relatively strong at the level of individual conduits although it may be weak at the whole sapwood level. The model explains observed variation in ψ50 both across a large number of species, and along the xylem path in two species. The larger hydraulic safety margin in gymnosperms compared to angiosperms is explained as an adaptation to the gymnosperms’ lower capacity to recover from conductivity loss.

The constant xylem safety factor provides a powerful principle for simplifying and improving plant and vegetation models.