bluuebunny/crossref_metadata_2025 huggingface dataset:
Moving from GWAS signals to rare functional variation in inflammatory bowel disease through application of GenePy2 as a potential DNA biomarker
Authors: Cheng Guo , Ashton James J , Collins Andrew , Beattie R Mark , Ennis Sarah
Published: April 2024

Objectives

We adopt a weighted variant burden score GenePy2.0 for the UK Biobank phase 2 cohort of inflammatory bowel disease (IBD), to explore potential genomic biomarkers underpinning IBD’s known associations.

Design

Nucleating from IBD GWAS signals, we identified 794 GWAS loci, including target genes/LD-blocks (LDBs) based on linkage-disequilibrium (LD) and functional mapping. We calculated GenePy2.0–a burden score of target regions integrating variants with CADDPhred>15 weighted by deleteriousness and zygosity. Collating with other burden-based test, GenePy-based Mann-Whitney-U tests on cases/controls with varying extreme scores were used. Significance-levels and effect sizes were used for tuning the optimal GenePy thresholds for discriminating patients from controls. Individual’s binarized GenePy status (above or below threshold) of candidate regions, was subject to itemset association test via the sparse Apriori algorithm.

Results

A tailored IBD cohort was curated (nCrohn’s_Disease(CD)=891, nUlcerative_Colitis(UC)=1409, nControls=60118). Analysing 885 unified target regions (794 GWAS loci and 104 monogenic genes with 13 overlaps), the GenePy approach detected statistical significance (permutationp<5.65×10-5) in 35 regions of CD and 25 of UC targets exerting risk and protective effects on the disease. Large effect sizes were observed,e.g. CYLD-AS1 (Mann-Whitney-□=0.89[CI:0.78-0.96]) in CD/controls with the top 1% highest scores of the gene. Itemset association learning further highlighted an intriguing signal whereby GenePy status ofIL23RandNOD2were mutually exclusive in CD but always co-occurring in controls.

Conclusion

GenePy score per IBD patient detected ‘deleterious’ variation of large effect underpinning known IBD associations and proved itself a promising tool for genomic biomarker discovery.

What is already known on this topic

Inflammatory bowel disease (IBD) is a genetically heterogeneous disease with both common polygenic, and rare monogenic, presentations. Previous studies have identified known genetic variants associated with disease.

What this study adds

A genomic biomarker tool, tailored for large cohort, GenePy2.0 is developed. It’s rank-based test is more powerful than mutation-burden based test in validating known associations and finding new associations of IBD. We identified large risk and protective effects of ‘pathogenic genes/loci’ in IBD, including expanding previous associations to wider genomic regions.

How this study might affect research, practice or policy

GenePy2.0 facilitates analysis of diseases with genetic heterogeneity and facilitates personalised genomic analysis on patients. The revealed genetic landscape of IBD captures both risk and protective effects of rare ‘pathogenic’ variants, alongside more common variation. This, could provide a fresh angle for future targeted therapies in specific groups of patients.
Comparison of the Sensitivity and Specificity of Commercial Anti-Dengue Virus IgG Tests to Identify Persons Eligible for Dengue Vaccination
Authors: Medina Freddy A. , Vila Frances , Adams Laura E. , Cardona Jaime , Carrion Jessica , Lamirande Elaine , Acosta Luz N. , De León-Rodríguez Carlos M. , Beltran Manuela , Grau Demian , Rivera-Amill Vanessa , Balmaseda Angel , Harris Eva , Madewell Zachary J. , Waterman Stephen H. , Paz-Bailey Gabriela , Whitehead Stephen , Muñoz-Jordán Jorge L.
Published: April 2024

The Advisory Committee on Immunization Practices (ACIP) recommended that dengue pre-vaccination screening tests for Dengvaxia administration have at least 98% specificity and 75% sensitivity. This study evaluates the performance of commercial anti-DENV IgG tests to identify tests that could be used for pre-vaccination screening. First, for 7 tests, we evaluated sensitivity and specificity in early convalescent dengue virus (DENV) infection, using 44 samples collected 7-30 days after symptom onset and confirmed by RT-PCR. Next, for the 5 best performing tests and two additional tests (with and without an external test reader) that became available later, we evaluated performance to detect past dengue infection among a panel of 44 specimens collected in 2018-2019 from healthy 9-16-year-old children from Puerto Rico. Finally, a full-scale evaluation was done with the 4 best performing tests using 400 specimens from the same population. We used virus focus reduction neutralization test and an in-house DENV IgG ELISA as reference standards.

Of seven tests, five showed ≥75% sensitivity detecting anti-DENV IgG in early convalescent specimens with low cross-reactivity to Zika virus. For the detection of previous DENV infections the tests with the highest performance were the Euroimmun NS1 IgG ELISA (sensitivity 84.5%, specificity 97.1%) and CTK Dengue IgG rapid test R0065C with the test reader (sensitivity 76.2% specificity 98.1%). There are IgG tests available that can be used to accurately classify individuals with previous DENV infection as eligible for dengue vaccination to support safe vaccine implementation.
A Biomarker-Centric Framework for the Prediction of Future Chronic Pain
Authors: Fillingim Matt , Tanguay-Sabourin Christophe , Parisien Marc , Zare Azin , Guglietti Gianluca V. , Norman Jax , Petre Bogdan , Bortsov Andrey , Ware Mark , Perez Jordi , Roy Mathieu , Diatchenko Luda , Vachon-Presseau Etienne
Published: April 2024

Chronic pain is a multifactorial condition presenting significant diagnostic and prognostic challenges. Biomarkers for the classification and the prediction of chronic pain are therefore critically needed. In this multi-dataset study of over 523,000 participants, we applied machine learning to multi-dimensional biological data from the UK Biobank to identify biomarkers for 35 medical conditions associated with pain (e.g., clinical diagnosis of rheumatoid arthritis, fibromyalgia, stroke, gout, etc.) or self-reported chronic pain (e.g., back pain, knee pain, etc). Biomarkers derived from blood immunoassays, brain and bone imaging, and genetics were effective in predicting medical conditions associated with chronic pain (area under the curve (AUC) 0.62-0.87) but not self-reported pain (AUC 0.50-0.62). Among the biomarkers identified was a composite blood-based signature that predicted the onset of various medical conditions approximately nine years in advance (AUC 0.59-0.72). Notably, all biomarkers worked in synergy with psychosocial factors, accurately predicting both medical conditions (AUC 0.69– 0.91) and self-report pain (AUC 0.71–0.92). Over a period of 15 years, individuals scoring high on both biomarkers and psychosocial risk factors had twice the cumulative incidence of diagnoses for pain-associated medical conditions (Hazard Ratio (HR): 2.26) compared to individuals scoring high on biomarkers but low on psychosocial risk factors (HR: 1.06). In summary, we identified various biomarkers for chronic pain conditions and showed that their predictive efficacy heavily depended on psychological and social influences. These findings underscore the necessity of adopting a holistic approach in the development of biomarkers to enhance their clinical utility.
Role of Thromboinflammation Interaction in the Serious-Critical COVID-19 Pneumonia: A Single-center Retrospective Study
Authors: Li Jiatao , Liu Shimeng
Published: April 2024

Aim

To describe the potential role of thromboinflammation in thromboembolism and the progress of coronavirus disease 2019 (COVID-19).

Methods

The retrospective study included sequentially hospitalized patients with the diagnosis of COVID-19 pneumonia during the first pandemic (December 1, 2022, to January 31, 2023) at a medical center in Beijing, China. Risks of critical medical support requirements, thrombosis events, and death were valued in the multivariate logistic regression models, where age (≥ 80 vs. < 80 years old), nadir platelets level (≤100 vs. > 100 10^9/L), C-reactive protein (CRP) level at admission (≥ 80 vs. < 80 mg/L), D-dimer level at admission (≥ 1.0 vs. < 1.0 mg/L) were dichotomized.

Results

A total of 88 patients were included (median age 77 years, 72% male). During hospitalization, 35 (40%) patients required critical medical support, 22 (29%) had disseminated intravascular coagulation (DIC), 11 (13%) had radiologically supported thrombosis events, and 26 (30%) died. Increased age (odds ratio [OR]: 5.22,95% confidence interval [CI]: 1.27-21.53;p=0.02), elevated CRP levels (OR: 9.26, 95% CI: 2.24-38.37;p<0.01), decreased nadir platelet level (OR: 13.47, 95% CI: 1.91-94.84;p<0.01), elevated D-dimer level (OR: 5.21, 95 CI%: 0.96-28.21;p=0.06) were associated with the requirements of critical care. Increased age (OR: 10.87, 95% CI: 3.05-38.80;p<0.01), elevated CRP levels (OR: 6.14, 95% CI:1.68-22.47;p<0.01), decreased nadir platelet levels (OR: 5.96, 95% CI: 1.34-26.47;p=0.02) and D-dimers (≥1.0 vs. <1.0 mg/L, OR: 2.26, 95% CI: 0.68-7.44;p=0.18) were associated with death. Increased age (OR: 2.40,95% CI: 0.60-9.67;p=0.22), decreased nadir platelet levels (OR: 1.31, 95% CI: 0.22-7.96;p=0.77), inflmmation status, including D-dimers (≥1.0 vs. <1.0 mg/L, OR:4.62, 95% CI: 0.89-24.04;p=0.07) and CRP (≥80 vs. <80 mg/mL, OR:5.44, 95% CI: 1.05-28.27;p=0.04) were significantly associated with the risks of thromboembolism.

Conclusions

The retrospective study indicated thromboinflammation promoted thromboembolism and was associated with the outcomes of COVID-19 pneumonia.
Patient preferences for features associated with leadless versus conventional transvenous cardiac pacemakers
Authors: Reed Shelby D. , Yang Jui-Chen , Wallace Matthew J. , Sutphin Jessie , Johnson F. Reed , Ozdemir Semra , Delgado Stephanie , Goates Scott , Harbert Nicole , Lo Monica , Rajagopalan Bharath , Ip James E. , Al-Khatib Sana M.
Published: April 2024

Background

Regulatory approval of the first dual-chamber leadless pacemaker (PM) system provides patients an alternative to conventional transvenous pacemakers.

Objective

To quantify patients’ preferences for pacemaker features.

Methods

Patients with a de-novo PM indication were recruited from 7 US sites to complete a discrete-choice experiment (DCE) survey. Patients chose between pairs of experimentally designed, hypothetical PMs that varied according to PM type (removable leadless, non-removable leadless, conventional transvenous); battery life (5, 8, 12, 15 years); time since regulatory approval (2, 10 years); discomfort for 6 months (none, discomfort); complication risk and infection risk (1%, 5%, 10%/20% for each). Patients with a de-novo pacemaker indication were recruited to complete a web-based survey from seven US sites between May 11, 2022 to May 24, 2023.

Results

Choice data from 117 patients indicated that complication risks and infection risks were the most influential. On average, patients preferred removable leadless pacemakers over both non-removable leadless pacemakers (p=0.001) and conventional transvenous pacemakers (p=0.031). However, latent-class analysis revealed two distinct preference classes. One class preferred leadless pacemakers (50.5%) and the other class preferred conventional transvenous pacemakers (49.5%). The conventional PM class prioritized pacemakers with ten rather than two years since regulatory approval (p<0.001) whereas the leadless PM class was insensitive to years since regulatory approval (p=0.83). All else equal, patients would accept maximum risks of complications or infections ranging about 5% to 18% to receive their preferred pacemaker type.

Conclusion

Latent-class analysis revealed strong patient preferences for the type of PM, with a nearly equal split between recent leadless PM technology and conventional transvenous PMs.

These findings can inform shared decision making between healthcare providers and patients.
The Glycolytic Metabolite Methylglyoxal Covalently Inactivates the NLRP3 Inflammasome
Authors: Stanton Caroline , Buasakdi Chavin , Sun Jie , Levitan Ian , Bora Prerona , Kutseikin Sergei , Wiseman R. Luke , Bollong Michael J.
Published: April 2024

The NLRP3 inflammasome promotes inflammation in disease, yet the full repertoire of mechanisms regulating its activity are not well delineated. Among established regulatory mechanisms, covalent modification of NLRP3 has emerged as a common route for pharmacological inactivation of this protein. Here, we show that inhibition of the glycolytic enzyme PGK1 results in the accumulation of methylglyoxal, a reactive metabolite whose increased levels decrease NLRP3 assembly and inflammatory signaling in cells. We find that methylglyoxal inactivates NLRP3 via a non-enzymatic, covalent crosslinking-based mechanism, promoting inter- and intra-protein MICA posttranslational linkages within NLRP3. This work establishes NLRP3 as capable of sensing a host of electrophilic chemicals, both exogenous small molecules and endogenous reactive metabolites, and suggests a mechanism by which glycolytic flux can moderate the activation status of a central inflammatory signaling pathway.
Multiplexed, multimodal profiling of the intracellular activity, interactions, and druggability of protein variants using LABEL-seq
Authors: Simon Jessica J. , Fowler Douglas M. , Maly Dustin J.
Published: April 2024

Multiplexed assays of variant effect are powerful tools for assessing the impact of protein sequence variation, but are limited to measuring a single protein property and often rely on indirect readouts of intracellular protein function. Here, we developed LAbeling with Barcodes and Enrichment for biochemicaL analysis by sequencing (LABEL-seq), a platform for the multimodal profiling of thousands of protein variants in cultured human cells. Multimodal measurement of ∼20,000 variant effects for ∼1,600 BRaf variants using LABEL-seq revealed that variation at positions that are frequently mutated in cancer had minimal effects on folding and intracellular abundance but could dramatically alter activity, protein-protein interactions, and druggability. Integrative analysis of our multimodal measurements identified networks of positions with similar roles in regulating BRaf’s signaling properties and enabled predictive modeling of variant effects on complex processes such as cell proliferation and small molecule-promoted degradation. LABEL-seq provides a scalable approach for the direct measurement of multiple biochemical effects of protein variants in their native cellular context, yielding insight into protein function, disease mechanisms, and druggability.
Cross-family transfer of the Arabidopsis cell-surface immune receptor LORE to tomato confers sensing of 3-hydroxylated fatty acids and enhanced disease resistance
Authors: Eschrig Sabine , Kahlon Parvinderdeep S. , Agius Carlos , Holzer Andrea , Hückelhoven Ralph , Schwechheimer Claus , Ranf Stefanie
Published: April 2024

Plant pathogens pose a high risk of yield losses and threaten food security. Technological and scientific advances have improved our understanding of the molecular processes underlying host-pathogen interactions, which paves the way for new strategies in crop disease management beyond the limits of conventional breeding. Cross-family transfer of immune receptor genes is one such strategy that takes advantage of common plant immune signaling pathways to improve disease resistance in crops. Sensing of microbe- or host damage-associated molecular patterns (MAMPs/DAMPs) by plasma membrane-resident pattern recognition receptors (PRR) activates pattern-triggered immunity (PTI) and restricts the spread of a broad spectrum of pathogens in the host plant. In the model plantArabidopsis thaliana, the S-domain receptor-like kinase LIPOOLIGOSACCHARIDE-SPECIFIC REDUCED ELICITATION (AtLORE, SD1-29) functions as PRR, which senses medium chain-length 3-hydroxylated fatty acids (mc-3-OH-FAs), such as 3-OH-C10:0, and 3-hydroxyalkanoates (HAAs) of microbial origin to activate PTI. In this study, we show that ectopic expression of the Brassicaceae-specific PRRAtLORE in the solanaceous crop speciesSolanum lycopersicumcv. M82 leads to the gain of 3-OH-C10:0 immune sensing without altering plant development.AtLORE-transgenic tomato shows enhanced resistance againstPseudomonas syringaepv.tomatoDC3000 andAlternaria solaniNL03003. Applying 3-OH-C10:0 to the soil before infection induces resistance against the oomycete pathogenPhytophthora infestansPi100 and further enhances resistance toA. solaniNL03003. Our study proposes a potential application ofAtLORE-transgenic crop plants and mc-3-OH-FAs as resistance-inducing bio-stimulants in disease management.
Glycogen phase separation drives macromolecular rearrangement and asymmetric division inE. coli
Authors: Thappeta Yashna , Cañas-Duarte Silvia J. , Kallem Till , Fragasso Alessio , Xiang Yingjie , Gray William , Lee Cheyenne , Cegelski Lynette , Jacobs-Wagner Christine
Published: April 2024

Bacteria often experience nutrient limitation in nature and the laboratory. While exponential and stationary growth phases are well characterized in the model bacteriumEscherichia coli, little is known about what transpires inside individual cells during the transition between these two phases. Through quantitative cell imaging, we found that the position of nucleoids and cell division sites becomes increasingly asymmetric during transition phase. These asymmetries were coupled with spatial reorganization of proteins, ribosomes, and RNAs to nucleoid-centric localizations. Results from live-cell imaging experiments, complemented with genetic and13C whole-cell nuclear magnetic resonance spectroscopy studies, show that preferential accumulation of the storage polymer glycogen at the old cell pole leads to the observed rearrangements and asymmetric divisions. In vitro experiments suggest that these phenotypes are likely due to the propensity of glycogen to phase separate in crowded environments, as glycogen condensates exclude fluorescent proteins under physiological crowding conditions. Glycogen-associated differences in cell sizes between strains and future daughter cells suggest that glycogen phase separation allows cells to store large glucose reserves without counting them as cytoplasmic space.
Transcriptomic Profiling of Thyroid Eye Disease Orbital Fat Demonstrates Differences in Adipogenicity and IGF-1R Pathway
Authors: Kim Dong Won , Kim Soohyun , Han Jeong , Belday Karan , Li Emily , Mahoney Nicholas , Blackshaw Seth , Rajaii Fatemeh
Published: April 2024

Despite recent advances in the treatment of thyroid eye disease (TED), significant gaps remain in our understanding of the underlying molecular mechanisms, particularly concerning the insulin-like growth factor-1 receptor (IGF-1R) pathway. To dissect the pathophysiology of TED, we utilized single nucleus RNA-Seq to analyze orbital fat specimens from both TED patients and matched controls. The analysis demonstrated a marked increase in the proportion of fibroblasts transitioning to adipogenesis in the orbital fat of TED patients compared to controls. This was associated with diverse alterations in immune cell composition. Significant alterations in the IGF-1R signaling pathway were noted between TED specimens and controls, indicating a potential pathological mechanism driven by IGF-1R signaling abnormalities. Additionally, our data show that linsitinib, a small molecule inhibitor of IGF-1R, effectively reduces adipogenesis in TED orbital fibroblastsin vitro, suggesting its potential utility as a therapeutic agent. Our findings reveal that beyond immune dysfunction, abnormal IGF-1R signaling leading to enhanced adipogenesis is a crucial pathogenic mechanism in TED.
VezA/vezatin facilitates proper assembly of the dynactin complex in vivo
Authors: Zhang Jun , Qiu Rongde , Xie Sean , Rasmussen Megan , Xiang Xin
Published: April 2024

Cytoplasmic dynein-mediated intracellular transport needs the multi-component dynactin complex for cargo binding and motor activation. However, cellular factors involved in dynactin assembly remain unexplored. Here we found inAspergillus nidulansthat the vezatin homolog VezA is important for dynactin assembly. VezA affects the microtubule plus-end accumulation of dynein before cargo binding and cargo adapter-mediated dynein activation, two processes that both need dynactin. The dynactin complex contains multiple components including an Arp1 (actin-related protein 1) mini-filament associated with a pointed-end sub-complex. VezA physically interacts with dynactin either directly or indirectly via the Arp1 mini-filament and its pointed-end sub-complex. Loss of VezA causes a defect in dynactin integrity, most likely by affecting the connection between the Arp1 mini-filament and its pointed-end sub-complex. Using various dynactin mutants, we further revealed that assembly of the dynactin complex must be highly coordinated. Together, these results shed important new light on dynactin assembly in vivo.
A novel iPSC-based model of ICF syndrome subtype 2 recapitulates the molecular phenotype of ZBTB24 deficiency
Authors: Lullo Vincenzo , Cecere Francesco , Batti Saveria , Allegretti Sara , Morone Barbara , Fioriniello Salvatore , Pisapia Laura , Genesio Rita , Ragione Floriana Della , Giardino Giuliana , Pignata Claudio , Riccio Andrea , Matarazzo Maria R. , Strazzullo Maria
Published: April 2024

Immunodeficiency, Centromeric instability and Facial anomalies (ICF) syndrome is a rare genetic disorder characterized by variable immunodeficiency. More than half of the affected individuals show mild to severe intellectual disability at early onset. This disorder is genetically heterogeneous andZBTB24is the causative gene of the subtype 2, accounting for about 30% of the ICF cases. ZBTB24 is a multifaceted transcription factor belonging to the Zinc-finger and BTB domain-containing protein family, which are key regulators of developmental processes. Aberrant DNA methylation is the main molecular hallmark of ICF syndrome. The functional link between ZBTB24 deficiency and DNA methylation errors is still elusive. Here, we generated a novel ICF2 disease model by deriving induced pluripotent stem cells (iPSCs) from peripheral CD34+-blood cells of a patient homozygous for the p.Cys408Gly mutation, the most frequent missense mutation in ICF2 patients and which is associated with a broad clinical spectrum. The mutation affects a conserved cysteine of the ZBTB24 zinc-finger domain, perturbing its function as transcriptional activator.

ICF2-iPSCs recapitulate the methylation defects associated with ZBTB24 deficiency, including centromeric hypomethylation. We validated that the mutated ZBTB24 protein loses its ability to directly activate expression ofCDCA7and other target genes in the patient-derived iPSCs. Upon hematopoietic differentiation, ICF2-iPSCs showed decreased vitality and a lower percentage of CD34+/CD43+/CD45+progenitors. Overall, the ICF2-iPSC model is highly relevant to explore the role of ZBTB24 in DNA methylation homeostasis and provides a tool to investigate the early molecular events linking ZBTB24 deficiency to the ICF2 clinical phenotype.
BNST GluN2D-containing NMDARs contribute to ethanol intake but not negative affective behaviors in female mice
Authors: Doyle Marie A. , Salimando Gregory J. , Altemus Megan E. , Badt Justin K. , Bedenbaugh Michelle N. , Vardy Alexander S. , Adank Danielle N. , Park Anika S. , Winder Danny G.
Published: April 2024

Alcohol use disorder (AUD) is a chronic, relapsing disease, highly comorbid with anxiety and depression. The bed nucleus of the stria terminalis (BNST), andCrh+ neurons in this region are thought to play a key role in chronic ethanol-induced increases in volitional ethanol intake. This role has been hypothesized to be driven by emergent BNST-dependent negative affective behaviors. Indeed, we report here that in female mice undergoing a home cage chronic drinking forced abstinence model (CDFA), excitatory transmission undergoes time-dependent upregulation in BNSTCrh+ cells. Excitatory NMDA receptors (NMDARs) are a major target of ethanol, and chronic ethanol exposure has been shown to regulate NMDAR function and expression. GluN2D subunit-containing NMDARs have emerged as a target of interest due to their limited distribution and potential roles in affective behavior. We find that knockdown of dorsal BNST (dBNST) GluN2D expression significantly decreases ethanol intake in female, but not male, mice. While BNSTGrin2bexpression was significantly increased in protracted abstinence following CDFA, no differences inGrin2dexpression were observed in dBNST or specifically in dBNSTCrh+ neurons. Finally, to determine the impact of GluN2D expression on negative affective behaviors, open field, elevated zero maze, and forced swim tasks were used to measure anxiety- and depressive-like behaviors in constitutive and conditional BNST GluN2D knockout mice. Surprisingly, we find that deletion of GluN2D fails to alter negative affect in ethanol-naïve female mice. Together, these data suggest a role for BNST GluN2D-containing NMDARs in ethanol drinking behaviors but not abstinence from ethanol, highlighting potential sex differences and behavioral specificity in the context of AUD behaviors. Overall, these data further suggest roles for BNST synaptic signaling in volitional ethanol intake that are partially independent of actions on affective behavior.
N-terminal tags impair the ability of Lamin A to provide structural support to the nucleus
Authors: Odell Jacob , Lammerding Jan
Published: April 2024

Lamins are intermediate filament proteins that contribute to numerous cellular functions, including nuclear morphology and mechanical stability. The N-terminal head domain of lamin is critical for higher order filament assembly and function, yet the effects of commonly used N-terminal tags on lamin function remain largely unexplored. Here, we systematically studied the effect of two differently sized tags on Lamin A (LaA) function in a mammalian cell model engineered to allow for precise control of expression of tagged lamin proteins. Untagged, FLAG-tagged, and GFP-tagged LaA completely rescued nuclear shape defects when expressed at similar levels in lamin A/C-deficient (Lmna−/−) MEFs, and all LaA constructs prevented increased nuclear envelope (NE) ruptures in these cells. N-terminal tags, however, altered the nuclear localization of LaA and impaired the ability of LaA to restore nuclear deformability and to recruit Emerin to the nuclear membrane inLmna−/−MEFs. Our finding that tags impede some LaA functions but not others may explain the partial loss of function phenotypes when tagged lamins are expressed in model organisms and should caution researchers using tagged lamins to study the nucleus.
Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists
Authors: Hollingsworth L. Robert , Veeraraghavan Priya , Paulo Joao A. , Harper J. Wade
Published: April 2024

Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 3 (NLRP3) is an innate immune sensor that forms an inflammasome in response to various cellular stressors. Gain-of-function mutations in NLRP3 cause autoinflammatory diseases and NLRP3 signalling itself exacerbates the pathogenesis of many other human diseases. Despite considerable therapeutic interest, the primary drivers of NLRP3 activation remain controversial due to the diverse array of signals that are integrated through NLRP3. Here, we mapped subcellular proteome changes to lysosomes, mitochondrion, EEA1-positive endosomes, and Golgi caused by the NLRP3 inflammasome agonists nigericin and CL097. We identified several common disruptions to retrograde trafficking pathways, including COPI and Shiga toxin-related transport, in line with recent studies. We further characterized mouse NLRP3 trafficking throughout its activation using temporal proximity proteomics, which supports a recent model of NLRP3 recruitment to endosomes during inflammasome activation. Collectively, these findings provide additional granularity to our understanding of the molecular events driving NLRP3 activation and serve as a valuable resource for cell biological research. We have made our proteomics data accessible through an open-access Shiny browser to facilitate future research within the community, available at:https://harperlab.connect.hms.harvard.edu/inflame/. We will display anonymous peer review for this manuscript onpubpub.org(https://harperlab.pubpub.org/pub/nlrp3/) rather than a traditional journal. Moreover, we invite community feedback on the pubpub version of this manuscript, and we will address criticisms accordingly.
Two dynamic, N-terminal regions are required for function in Ribosomal RNA Adenine Dimethylase family members
Authors: McGaha Danielle A. , Collins Alexandrea , Ajisafe Luqman O. , Perdigao Calvin C. , Bondrowski Jordan L. , Fetsch Karen , Dunkle Jack A.
Published: April 2024

The Ribosomal RNA Adenine Dimethylase (RRAD) family of enzymes facilitate ribosome maturation in all organisms by dimethylating two nucleotides of small subunit rRNA. Prominent members of this family are the human DIMT1 and bacterial KsgA enzymes. A sub-group of RRAD enzymes, named erythromycin resistance methyltransferases (Erm) dimethylate a specific nucleotide in large subunit rRNA to confer antibiotic resistance. How these enzymes regulate methylation so that it only occurs on the specific substrate is not fully understood. While performing random mutagenesis on the catalytic domain of ErmE, we discovered that mutants in an N-terminal region of the protein that is disordered in the ErmE crystal structure are associated with a loss of antibiotic resistance. By subjecting site-directed mutants of ErmE and KsgA to phenotypic and in vitro assays we found that the N-terminal region is critical for activity in RRAD enzymes: the N-terminal basic region promotes rRNA binding and the conserved motif likely assists in juxtaposing the adenosine substrate and the SAM cofactor. Our results and emerging structural data suggest this dynamic, N-terminal region of RRAD enzymes becomes ordered upon rRNA binding forming a cap on the active site required for methylation.
Roles of Tubulin Concentration during Prometaphase and Ran-GTP during Anaphase ofC. elegansmeiosis
Authors: Gong Ting , McNally Karen L. , Konanoor Siri , Peraza Alma , Bailey Cynthia , Redemann Stefanie , McNally Francis J.
Published: April 2024

In many animal species, the oocyte meiotic spindle, which is required for chromosome segregation, forms without centrosomes. In some systems, Ran-GEF on chromatin initiates spindle assembly. We found that inC. elegansoocytes, endogenously-tagged Ran-GEF dissociates from chromatin during spindle assembly but re-associates during meiotic anaphase. Meiotic spindle assembly occurred after auxin-induced degradation of Ran-GEF but anaphase I was faster than controls and extrusion of the first polar body frequently failed. In search of a possible alternative pathway for spindle assembly, we found that soluble tubulin concentrates in the nuclear volume during germinal vesicle breakdown. We found that the concentration of soluble tubulin in the metaphase spindle region is enclosed by ER sheets which exclude cytoplasmic organelles including mitochondria and yolk granules. Measurement of the volume occupied by yolk granules and mitochondria indicated that volume exclusion would be sufficient to explain the concentration of tubulin in the spindle volume. We suggest that this concentration of soluble tubulin may be a redundant mechanism promoting spindle assembly near chromosomes.
Parallel pheromone, metabolite, and lipid analyses reveal patterns associated with early life transitions and ovary activation in honey bee (Apis mellifera) queens
Authors: McAfee Alison , Magaña Armando Alcazar , Foster Leonard J. , Hoover Shelley E.
Published: April 2024

Eusocial insects exist in a state of reproductive conflict in which workers forgo reproduction in favor of helping relatives, typically queens, rear offspring. The honest signal hypothesis posits that queens emit pheromonal signals that convey information about their fecundity, which workers use to make decisions around investing in direct vs. indirect fitness and queen acceptance. We evaluated this idea using liquid chromatography-tandem mass spectrometry to measure honey bee queen retinue pheromone (QRP) components in relation to queen age, laying status, and likelihood of acceptance using a protocol that enables QRP to be measured concurrently with metabolomic and lipidomic analyses. We found that older mated queens (>1 month) were more readily accepted by colonies than younger queens (10-12 d), regardless of the queen’s prior laying status. This is despite non-laying queens having significantly smaller ovaries at the time of introduction. Older queens produced higher levels of the QRP components 9(R)-HDA, LEA, and HVA compared to younger queens, with HVA also positively correlating with ovary mass. However, these data suggest that ovary mass is not an influential fertility metric for worker decision-making; therefore, the relationship between HVA and ovary mass is merely an honest signal of a non-influential metric. Metabolomic and lipidomic analyses showed that samples cluster strongly according to queen age and mating status, but not ovary mass. These data also reveal some of the first hints of the importance of prostanoids in queen maturation, along with many other physiological changes that occur in the first month of a queen’s life.

Significance statement

Insect pheromones have historically been evaluated using gas chromatography-mass spectrometry, a technique that is incompatible with parallel lipidomics and metabolomics inquests. Here, we repurposed an established two-phase extraction protocol and optimized a liquid chromatography-tandem mass spectrometry method to acquire pheromone, metabolite, and lipid data concurrently from a single sample. We applied this technique to interrogate the honest signal hypothesis, which relates queen pheromone profiles to reproductive quality, but the approach is broadly applicable to any question in which simultaneous determination of complex pheromone profiles and lipidomics or metabolomics data is asset. Such applications may help uncover new pheromones and reveal relationships between pheromones, hormones, and physiology in diverse biological systems.
Point contact-restricted cAMP signaling control ephrin-A5-induced axon repulsion
Authors: Bécret J , Michaud C , Assali A , Chenais NAL , Kankadze I , Gomez-Bravo C , Roche F , Couvet S , Fassier C , Nicol X
Published: April 2024

Signal transduction downstream of axon guidance molecules is essential to steer developing axons. Second messengers including cAMP are key molecules shared by a multitude of signaling pathways and are required for a wide range of cellular processes including axon pathfinding. Yet, how these signaling molecules achieve specificity for each of their downstream pathways remains elusive. Subcellular compartmentation emerged as a flexible strategy to reach such a specificity. Here, we show that point contact-restricted cAMP signals control ephrin-A5-evoked axon repulsion in vitro by modulating Focal Adhesion Kinase phosphorylation and the assembly and disassembly rate of point contacts. Consistently, preventing point contact-specific cAMP signals, in developing retinal ganglion cells in vivo alters the refinement of their terminal axonal arbor in the brain. Altogether, our study identifies point contacts as a compartment containing a local cAMP signal required for ephrin-A5-dependent axon guidance and highlights the crucial role of such subcellularly restricted second messenger signals in the wiring of neuronal circuits.
Structures of influenza A and B replication complexes explain avian to human host adaption and reveal a role of ANP32 as an electrostatic chaperone for the apo-polymerase
Authors: Arragain Benoit , Krischuns Tim , Pelosse Martin , Drncova Petra , Blackledge Martin , Naffakh Nadia , Cusack Stephen
Published: April 2024

Replication of influenza viral RNA depends on at least two viral polymerases, a parental replicase and an encapsidase, and cellular factor ANP32. ANP32 comprises an LRR domain and a long C-terminal low complexity acidic region (LCAR). Here we show that ANP32 is recruited to the replication complex (replicase-ANP32-encapsidase) by first acting as an electrostatic chaperone to stabilise the encapsidase moiety within apo-polymerase symmetric dimers that are distinct for influenza A and B polymerases. The encapsidase, with ANP32, then forms an asymmetric complex with the replicase. Cryo-EM structures of the influenza A and B replication complexes give new insight into the mutations known to adapt avian strain polymerases to use the distinct ANP32 in mammalian cells. The cryo-EM map of the FluPolB complex shows extra density attributable to the ANP32 LCAR wrapping around and stabilising the apo-encapsidase conformation. These results suggest a functional requirement for three polymerases for replication.
A chimeric viral platform for directed evolution in mammalian cells
Authors: Cole Alexander J. , Denes Christopher E. , Moreno Cesar L. , Dobson Thomas , Hesselson Daniel , Neely G. Gregory
Published: April 2024

Directed evolution (DE) is a process of mutation and artificial selection to breed biomolecules with new or improved activity1,2. DE platforms are primarily prokaryotic or yeast-based, and stable mutagenic mammalian systems have been challenging to establish and apply3. To this end, we developed PROTein Evolution Using Selection (PROTEUS), a new platform that uses chimeric virus-like vesicles (VLVs) to enable extended mammalian DE campaigns without loss of system integrity. This platform is stable and can generate sufficient diversity for DE in mammalian systems. Using PROTEUS, we altered the doxycycline responsiveness of tetracycline-controlled transactivators, generating a more sensitive TetON-4G tool for gene regulation. PROTEUS is also compatible with intracellular nanobody evolution, and we use it to design a DNA damage-responsive anti-p53 nanobody. Overall, PROTEUS is an efficient and stable platform to direct evolution of biomolecules within mammalian cells.
Supervisor bottom-line mentality and employee workplace well-being: a multiple mediation model
Authors: Guo Linyi , Du Jing , Zhang Juncheng
Published: April 2024

Purpose

This study is intended to investigate the relationship between supervisor bottom-line mentality (BLM) and employee workplace well-being. In addition, this study discusses the mediating roles of perception of organizational politics and job anxiety in this relationship.

Design/methodology/approach

Data were gathered from a two-wave survey of 301 full-time employees in southern China. The PROCESS macro in SPSS was applied to test the hypotheses.

Findings

Results showed that supervisor BLM was negatively related to employee workplace well-being. Moreover, perceptions of organizational politics and job anxiety played multiple mediating roles in the relationship between supervisor BLM and employee workplace well-being.

Originality/value

Drawing on the conservation of resource (COR) theory and cognitive-affective personality system (CAPS) theory, this study proposes a multiple mediation model to advance our understanding of how supervisor BLM affects employee workplace well-being.
Top management team social capital and business model innovation: moderating role of business ecosystem health
Authors: Zhang Suping , Hu Baoliang , Zhou Minfei
Published: April 2024

Purpose

This study explores the influence of the Top Management Team (TMT) social capital on business model innovation in business ecosystems.

Design/methodology/approach

This study examines the impact of internal and external TMT social capital on enterprises’ business model innovation, explores the relationship between internal and external TMT social capital, and investigates how business ecosystem health moderates the relationship between external TMT social capital and enterprises’ business model innovation. These hypotheses are proposed and tested using a hierarchical regression analysis with data from 168 Chinese firms.

Findings

First, both internal and external TMT social capital exert a significantly positive influence on an enterprise’s business model innovation. Second, internal TMT social capital positively contributes to the development of external TMT social capital, affecting business model innovation. Finally, the moderating effect of business ecosystem health on the relationship between external TMT social capital and business model innovation depends on the dimensions. Specifically, the productivity of the business ecosystem negatively moderates this relationship, whereas the niche creation capability of the business ecosystem has a positive moderating effect.

Originality/value

These findings enrich prior research on business model innovation within the business ecosystem, thoroughly exploring the critical role of TMT social capital. This study reveals the diverse impacts of internal and external TMT social capital on business model innovation and the intricate relationship between these elements. Furthermore, it emphasizes that the success of enterprise’s business model innovation within a business ecosystem depends on the alignment and adaptation to dynamic ecosystem conditions. By presenting these insights, this study provides valuable practical implications for enterprises aiming to cultivate social capital within business ecosystem to facilitate business model innovation.
Augmented reality characteristics as drivers of consumers’ purchase intention
Authors: Konstantoulaki Kleopatra , Rizomyliotis Ioannis , Ang Eunice , Quynh Nguyen Thu
Published: April 2024

Purpose

The purpose of this study is to investigate the influence of augmented reality (AR) media characteristics on consumers’ purchase intention (PI) for fashion goods within the fashion industry context.

Design/methodology/approach

This study establishes five independent variables of salient AR media characteristics derived from existing studies which includes interactivity, vividness, augmentation, simulated physical control and environmental embedding. A quantitative online survey method is conducted with a sample of 172 respondents.

Findings

The findings suggest that all five AR media characteristics have a positive and significant influence on consumers’ PI for fashion goods. Among these five characteristics, interactivity and simulated physical control have the strongest positive impact on PI, followed by vividness, environmental embedding and augmentation.

Originality/value

This study provides valuable insights for fashion brands to better understand the media characteristics that consumers may be looking out for in AR experiences that could have an influence on their PI for fashion goods. This study also contributes to the literature by identifying the most influential AR media characteristics in the context of the fashion industry.
Incorporating pragmatism in a behaviour change-led climate adaptation project: a collaborative reflection
Authors: Nguyen-Trung Kien , Saeri Alexander K. , Kaufman Stefan
Published: April 2024

Purpose

This article argues the value of integrating pragmatism in applying behavioural science to complex challenges. We describe a behaviour change-led knowledge co-production process in the specific context of climate change in Australia. This process was led by an interdisciplinary research team who struggled with the limitations of the prevailing deterministic behaviour change paradigms, such as the “test, learn, adapt” model, which often focuses narrowly on individual behaviours and fails to integrate multiple interpretations from diverse stakeholders into their knowledge co-production process.

Design/methodology/approach

This article uses collaborative reflection as a method of inquiry. We document the team’s experience of a recent challenge-led, programatic research initiative that applied behaviour change strategies to reduce climate vulnerabilities. We demonstrate the necessity of critical reflection and abductive reasoning in the face of the complexities inherent in knowledge co-production addressing complex problems. It underscores the importance of accommodating diverse perspectives and contextual nuances over a one-size-fits-all method.

Findings

The article shares lessons learnt about integrating collaborative and critical reflection throughout a project cycle and demonstrates the capacity of abductive reasoning to ease the challenges arising from the tension between behaviour change paradigms and knowledge co-production principles. This approach allows for a more adaptable and context-sensitive application, acknowledging the multiplicity of understandings and the dynamic nature of behavioural change in relation to climate adaptation.

Originality/value

This reflection contributes original insights into the fusion of pragmatism with behaviour change strategies, proposing a novel framework that prioritises flexibility, context-specificity and the recognition of various stakeholder perspectives in the co-production of knowledge.
Association between dietary inflammation index and inflammatory bowel disease in adults: Results from National Health and Nutrition Examination Survey 2009–2010
Authors: Zhu Jing‐yi , Sun Xiao‐ru , Liu Mu‐yun , Sun Chang
Published: April 2024

Previous study has demonstrated that the Dietary Inflammation Index (DII) played a role in the risk of inflammatory bowel disease (IBD), however, the prevalence and risk factors for IBD are distinct across locations and groups, and therefore, the findings are debatable and warrant further investigation. A total of 4363 participants were calculated in the National Health and Nutrition Examination Survey (NHANES) 2009 to 2010, of whom 1.21% self‐reported a history of IBD. DII values were performed as a good predictor of dietary inflammation based on data from two 24‐h dietary reviews in the NHANES database. Comparing the multifarious effects along with variations of the whole population by grouping populations according to DII quartiles, dietary inflammation levels increased progressively from DII quartile 1(Q1) to quartile 4(Q4). The association between DII and IBD was tested with multi‐variable logistic regression models, subgroup analyses and weighted generalized additive models. Participants in the Q4 group showed the highest levels of C‐reactive protein and reduced haemoglobin and albumin levels. Logistic regression confirmed the odds ratios (95% confidence intervals) of IBD for DII were 0.99 (0.86, 1.15), 0.97 (0.84, 1.13) and 0.80 (0.66, 0.98) in models 1, 2 and 3, respectively. The negative correlation between DII and IBD among United States adults from the NHANES database became increasingly apparent as covariates were adjusted. Subgroup analyses and smoothed curve fitting confirmed the inverse results. The study revealed that DII was correlated with the overall physical well‐being of participants. However, there was no significant association between DII and IBD.