bluuebunny/crossref_metadata_2025 huggingface dataset:
Pesticides and lifestyle factors are associated with disease severity of Parkinson’s disease: a longitudinal study
Authors: Lüth Theresa , Caliebe Amke , Gabbert Carolin , Sendel Sebastian , Laabs Björn-Hergen , König Inke R. , Klein Christine , Trinh Joanne
Published: September 2024

Objective

To longitudinally analyze the impact of the environment and lifestyle on PD motor sign severity in LRRK2 p. Gly2019Ser-related PD (LRRK2-PD) and idiopathic PD (iPD).

Background

There is increasing evidence that the environment impacts disease severity. Recent studies have shown that pesticide exposure is associated with a faster disease progression. However, the relationship between smoking, caffeine, and disease severity has not yet been investigated longitudinally.

Methods

In this longitudinal study, we included patients with iPD from the PPMI Online (N=2815) and Fox Insight (N=2319) cohorts, as well as patients withLRRK2-PD (N=81) from Fox Insight. Motor signs were assessed with the MDS-UPDRS Part II, and patients were assessed multiple times, followed up to 35 months or 60 months in the PPMI Online or Fox Insight cohort, respectively. The motor sign severity over time was analyzed by applying a linear mixed effects model. The outcome was the cumulative score of the MDS-UPDRS Part II questionnaire. Subsequently, we investigated the association between environmental exposure, lifestyle factors and motor signs. Pesticide exposure in a work setting, smoking, coffee, black tea, green tea, and caffeinated soda consumption were assessed using the validated PD-RFQ-U questionnaires. The mixed effects model included the environmental and lifestyle factors as binary (yes/no) variables.

Results

When comparingLRRK2-related PD and iPD, motor signs were less severe in patients withLRRK2-PD compared to iPD (β=-0.23,p=0.005). InLRRK2-PD, black tea consumption was associated with less severe motor signs (β=-0.51,p=0.028). In patients with iPD, we observed that pesticide exposure was associated with more severe motor signs over time in PPMI-Online (β=0.23,p=3.56×10-9). Smoking was associated with a higher motor signs score in PPMI-Online (β=0.13,p=0.001). Lastly, caffeinated soda was associated with more severe motor signs in patients with iPD from PPMI-Online (β=0.15,p=3.84×10-8) and Fox Insight (β=0.09,p=0.031).

Conclusions

Our results provide further evidence of the importance of environment and lifestyle in PD, even after the disease onset. We suggest that pesticide exposure and lifestyle factors may affect disease severity in patients withLRRK2-PD and iPD; still, further validation is necessary.
Deep Learning based CT-scan Coronary Artery Segmentation and Calcium Scoring
Authors: Upadhyayula Sai Koundinya
Published: September 2024

Coronary artery disease (CAD), primarily driven by atherosclerosis, poses significant health risks, contributing to a rising mortality rate globally. This study introduces a deep learning framework designed for the automated segmentation of coronary arteries and quantification of coronary artery calcium (CAC) from CT scans, facilitating improved risk stratification in patients. Leveraging data from the National Lung Screening Trial, we developed a three-step model that includes heart localization, coronary calcium segmentation, and calcium scoring. Various configurations of the UNet architecture were employed, with the Extended UNet utilizing an autoencoder achieving the highest validation performance, reflected by an Intersection over Union (IoU) score of 0.78 and an F1 score of 0.83.

The model’s efficacy was validated against manually segmented masks, showcasing its potential for accurate risk assessment based on CAC scores. This automated approach significantly reduces the time and expertise required for traditional calcium scoring, enabling rapid and reliable assessments in clinical settings. Our findings indicate that the deep learning system can effectively classify patients into risk categories, underscoring its potential utility in enhancing the management of CAD and improving patient outcomes. This research highlights the feasibility of integrating advanced computational techniques into routine clinical practice, paving the way for more efficient cardiovascular risk stratification.
Exposome-wide gene-environment interaction study of psychotic experiences in the UK Biobank
Authors: Lin Bochao Danae , Pries Lotta-Katrin , Arias-Magnasco Angelo , Klingenberg Boris , Linden David E. J. , Blokland Gabriella A. M. , van der Meer Dennis , Luykx Jurjen J. , Rutten Bart P. F. , Guloksuz Sinan
Published: September 2024

Background

A previous study successfully identified 148 out of 23,098 exposures associated with any psychotic experiences (PE) in the UK Biobank using an exposome-wide association study (XWAS). Research has shown that the polygenic risk score for schizophrenia (PRS-SCZ) is associated with PE. However, the interaction of these exposures and PRS-SCZ remains unknown.

Method

To systematically investigate gene-environment interaction underlying PE through data-driven agnostic analyses, we conducted 1) a conditional XWAS adjusting for PRS-SCZ to estimate the main effects of the exposures and PRS-SCZ, respectively; 2) exposome-wide interaction studies (XWIS) to estimate multiplicative and additive interactions between PRS-SCZ and exposures; and 3) the correlations between PRS-SCZ and exposures. The study included 148,502 participants from UK biobank.

Results

In the conditional XWAS models, the significant effects of PRS-SCZ and 148 exposures on PE remained statistically significant. In the XWIS model, we found a significant multiplicative (Ms, 1.23, 95%CI, 1.10-1.37; P=4.0×10-4) and additive (RERI, 0.55; 95%CI, 0.32-0.77; SI, 0.22; 95%CI, 0.14-0.30; AP, 1.59; 95%CI, 1.30-1.91; all P < 0.05/148) interaction between PRS-SCZ and variable “serious medical conditions or disability” on PE. There were six additive gene-environment interactions identified for mental distress, help/treatment-seeking behaviors, vitamin D and sleep problems. In the correlation test focused on seven exposures with significant interaction with PRS-SCZ, no significant or small (r2< 0.04) gene-environment correlations were estimated.

Conclusion

These findings reveal preliminary evidence for gene-environment interaction underlying PEs and suggest that genetic vulnerability and exposures might represent intertwined pathways leading to psychosis.
Impact of pre-exposure prophylaxis on HIV-1 drug resistance and phylogenetic cluster growth in British Columbia, Canada
Authors: McLaughlin Angela , Toy K. Junine , Montoya Vincent , Sereda Paul , Triggs Jason , Hull Mark , Brumme Chanson J. , Barrios Rolando , Montaner Julio S. G. , Joy Jeffrey B.
Published: September 2024

Oral HIV pre-exposure prophylaxis (PrEP) effectively prevents infection when taken during periods of risk, however, its population-level effectiveness is hindered by incomplete uptake, adherence, and retention. Since PrEP became available free-of-cost in British Columbia (BC), Canada, in January 2018, uptake has been rapid among gay, bisexual, and other men who have sex with men (GBM). Epidemiological evidence suggests adding PrEP onto a background of generalized access to free antiretroviral therapy, under the BC Treatment as Prevention (TasP) strategy, had a synergistic effect on reducing new infections. Here, we sought to evaluate the impact of PrEP on HIV transmission and drug resistance in phylogenetic clusters. In a retrospective cohort study, we evaluated whether baseline HIV drug resistance and phylogenetic clustering were more likely among newly diagnosed PrEP users in BC (n=39) compared to non-PrEP users (n=566) during the same diagnosis period from October 23, 2018 to December 5, 2022. Subsequently, we evaluated heterogeneity in PrEP-related reductions of the effective reproduction number (Re) across BC, key populations, and phylogenetic clusters. Stochastic branching processes of phylogenetic clusters informed by Repreceding PrEP were used to estimate diagnoses averted via PrEP. Newly HIV diagnosed PrEP users were significantly more likely than non-PrEP users to join phylogenetic clusters and carry baseline nucleoside-analogue reverse transcriptase inhibitor (NRTI) resistance-associated mutation M184I/V. Despite reductions in growth rate and Rein the GBM population overall and in 50% of active GBM-predominant clusters following PrEP availability, we highlight predominantly GBM and PWID clusters with high or increasing Re. Across active phylogenetic clusters and non-clustered new diagnoses, we estimate PrEP averted approximately 20 new HIV diagnoses per year in BC since 2018. These findings highlight how PrEP has reduced HIV burden, while illuminating groups that could benefit from prioritized PrEP education, access, and retention.
Uncertainty quantification in epigenetic clocks via conformalized quantile regression
Authors: Li Yanping , Goodrich Jaclyn M. , Peterson Karen E , Song Peter X-K , Luo Lan
Published: September 2024

DNA methylation (DNAm) is a chemical modification of DNA that can be influenced by various factors, including age, the environment, and lifestyle. An epigenetic clock is a predictive tool that measures biological age based on DNAm levels. It can provide insights into an individual’s biological age, which may differ from their chronological age. This difference, known as the epigenetic age acceleration, may reflect health status and the risk for age-related diseases. Moreover, epigenetic clocks are used in studies of aging to assess the effectiveness of anti-aging interventions and to understand the underlying mechanisms of aging and disease. Various epigenetic clocks have been developed using samples from different populations, tissues, and cell types, typically by training high-dimensional linear regression models with an elastic net penalty. While these models can predict mean biological age based on DNAm with high precision, there is a lack of uncertainty quantification which is important for interpreting the precision of age estimations and for clinical decision-making. To understand the distribution of a biological age clock beyond its mean, we propose a general pipeline for training epigenetic clocks, based on an integration of high-dimensional quantile regression and conformal prediction, to effectively reveal population heterogeneity and construct prediction intervals. Our approach produces adaptive prediction intervals not only achieving nominal coverage but also accounting for the inherent variability across individuals. By using the data collected from 728 blood samples in 11 DNAm datasets from children, we find that our quantile regression-based prediction intervals are narrower than those derived from conventional mean regression-based epigenetic clocks. This observation demonstrates an improved statistical efficiency over the existing pipeline for training epigenetic clocks. In addition, the resulting intervals have a synchronized varying pattern to age acceleration, effectively revealing cellular evolutionary heterogeneity in age patterns in different developmental stages during individual childhoods and adolescent cohort. Our findings suggest that conformalized high-dimensional quantile regression can produce valid prediction intervals and uncover underlying population heterogeneity. Although our methodology focuses on the distribution of measures of biological aging in children, it is applicable to a broader range of age groups to improve understanding of epigenetic age beyond the mean. This inference-based toolbox could provide valuable insights for future applications of epigenetic interventions for age-related diseases.
Evidence that extracellular HSPB1 contributes to inflammation in alcohol-associated hepatitis
Authors: Overstreet Anne-Marie C , Burge McKenzie , Bellar Annette , McMullen Megan , Czarnecki Douglas , Huang Emily , Pathak Vai , Finney Chelsea , Vij Raveena , Dasarathy Srinivasan , Dasarathy Jaividhya , Streem David , Welch Nicole , Rotroff Daniel , Schmitt Adam M , Nagy Laura E , Messer Jeannette S
Published: September 2024

Background and aims

Alcohol-associated hepatitis (AH) is the most life-threatening form of alcohol-associated liver disease (ALD). AH is characterized by severe inflammation attributed to increased levels of ethanol, microbes or microbial components, and damage-associated molecular pattern (DAMP) molecules in the liver. HSPB1 (Heat Shock Protein Family B (Small) Member 1; also known as Hsp25/27) is a DAMP that is rapidly increased in and released from cells experiencing stress, including hepatocytes. The goal of this study was to define the role of HSPB1 in AH pathophysiology.

Methods

Serum HSPB1 was measured in a retrospective study of 184 heathy controls (HC), heavy alcohol consumers (HA), patients with alcohol-associated cirrhosis (AC), and patients with AH recruited from major hospital centers. HSPB1 was also retrospectively evaluated in liver tissue from 10 HC and AH patients and an existing liver RNA-seq dataset. Finally, HSPB1 was investigated in a murine Lieber-DeCarli diet model of early ALD as well as cellular models of ethanol stress in hepatocytes and hepatocyte-macrophage communication during ethanol stress.

Results

Circulating HSPB1 was significantly increased in AH patients and levels positively correlated with disease-severity scores. Likewise, HSPB1 was increased in the liver of patients with severe AH and in the liver of ethanol-fed mice.In vitro, ethanol-stressed hepatocytes released HSPB1, which then triggered TNFα-mediated inflammation in macrophages. Anti-HSPB1 antibody prevented TNFα release from macrophages exposed to media conditioned by ethanol-stressed hepatocytes.

Conclusions

Our findings support investigation of HSPB1 as both a biomarker and therapeutic target in ALD. Furthermore, this work demonstrates that anti-HSPB1 antibody is a rational approach to targeting HSPB1 with the potential to block inflammation and protect hepatocytes, without inactivating host defense.

GRAPHICAL ABSTRACT

HIGHLIGHTS

HSPB1 is significantly increased in serum and liver of patients with alcohol-associated hepatitis.

Ethanol consumption leads to early increases in HSPB1 in the mouse liver.

Hepatocytes subjected to ethanol stress release HSPB1 into the extracellular environment where it activates TNFα-mediated inflammation in macrophages.

Anti-HSPB1 antibody blocks hepatocyte-triggered TNFα in a model of hepatocyte-macrophage communication during ethanol stress.
Associations between accurate measures of adiposity and fitness, blood proteins, and insulin sensitivity among South Asians and Europeans
Authors: Kho Pik Fang , Stell Laurel , Jimenez Shirin , Zanetti Daniela , Panyard Daniel J , Watson Kathleen L , Sarraju Ashish , Chen Ming-Li , Lind Lars , Petrie John R , Chan Khin N , Fonda Holly , Kent Kyla , Myers Jonathan N , Palaniappan Latha , Abbasi Fahim , Assimes Themistocles L.
Published: September 2024

Objective

South Asians (SAs) may possess a unique predisposition to insulin resistance (IR). We explored this possibility by investigating the relationship between ‘gold standard’ measures of adiposity, fitness, selected proteomic biomarkers, and insulin sensitivity among a cohort of SAs and Europeans (EURs).

Methods

A total of 46 SAs and 41 EURs completed ‘conventional’ (lifestyle questionnaires, standard physical exam) as well as ‘gold standard’ (dual energy X-ray absorptiometry scan, cardiopulmonary exercise test, and insulin suppression test) assessments of adiposity, fitness, and insulin sensitivity. In a subset of 28 SAs and 36 EURs, we also measured the blood-levels of eleven IR-related proteins. We conducted Spearman correlation to identify correlates of steady-state plasma glucose (SSPG) derived from the insulin suppression test, followed by multivariable linear regression analyses of SSPG, adjusting for age, sex and ancestral group.

Results

Sixteen of 30 measures significantly associated with SSPG, including one conventional and eight gold standard measures of adiposity, one conventional and one gold standard measure of fitness, and five proteins. Multivariable regressions revealed that gold standard measures and plasma proteins attenuated ancestral group differences in IR, suggesting their potential utility in assessing IR, especially among SAs.

Conclusion

Ancestral group differences in IR may be explained by accurate measures of adiposity and fitness, with specific proteins possibly serving as useful surrogates for these measures, particularly for SAs.
A multicenter study to assess the performance of the point-of-care RT-PCR Cobas SARS-CoV-2 & Influenza A/B nucleic acid test for use on the Cobas Liat system in comparison with centralized assays across healthcare facilities in the United States
Authors: Robbins Elissa M. , Bertuzis Rasa , Chiu Ho-Chen , Miller Lupe , Noutsios Christopher
Published: September 2024

Non-structured abstract

Respiratory diseases can share many of the same symptoms, highlighting the need for timely and accurate differentiation to facilitate effective clinical management and reduce transmission. Compared with centralized testing, molecular point-of-care tests (POCT) can provide a faster time to result.

We evaluated the RT-PCR POCT Cobas®SARS-CoV-2 & Influenza A/B qualitative assay for use on the Cobas Liat®system (the POC SARS-CoV-2 & Influenza A/B test) in nasal and nasopharyngeal swab samples from 10 diverse healthcare facilities in the US. A composite comparator design consisting of three centralized tests was used to analyze SARS-CoV-2, whilst performance versus a single centralized test was used for analysis of influenza A and B. Evaluations included performance stratified by sample type (prospective/retrospective and nasal/nasopharyngeal [paired by subject]), collection method (self/healthcare worker-collected [alternated and approximately balanced], symptom status (symptomatic/asymptomatic), and SARS-CoV-2 vaccination status, as well as assay inclusivity and system ease of use.

A total of 2,247 samples were tested. For SARS-CoV-2, the overall percent agreement (OPA) was 98.8% (95% CI: 97.9, 99.3) in nasal swab samples and 99.0% (95% CI: 98.2, 99.4) in nasopharyngeal swab samples. Regression analysis showed that Ct values from paired nasal and nasopharyngeal swab samples were highly correlated (correlation coefficient 0.83). The OPA was ≥99.5% (sample type dependent) and 100.0% for influenza A and B, respectively. The POC SARS-CoV-2 & Influenza A/B test was easy to use.

These results support the use of the POCT in various sample types and by various operators in the intended-use setting.

Summary statement/importance

This study highlights the benefits of RT-PCR POCT, namely comparable performance to centralized testing in multiple sample types and ease of use. Utilizing assays such as the POC SARS-CoV-2 & Influenza A/B test may improve timely differentiation of respiratory diseases that share similar symptoms.
Phenotypic presentation of family members of ATTRv probands and subsequent disease penetrance
Authors: Fazzini Luca , Castrichini Matteo , Li Yan , De Melo Jose , Figueiral Marta , Cao Jenny J. , Klee Eric W. , Dessalvi Christian Cadeddu , Grogan Martha , Dispenzieri Angela , Pereira Naveen L.
Published: September 2024

BACKGROUND

Hereditary transthyretin amyloid cardiomyopathy (ATTRv-CM) is being increasingly diagnosed due to enhanced awareness and availability of newer therapeutics. MultipleTTRvariants have been described worldwide, but with uncertain disease penetrance. The characteristics and outcomes of “previously undiagnosed” pathogenic-likely pathogenic (P/LP)TTRvariant (genotype or G+; cardiac phenotype or P-) carriers are unknown which has important prognostic and therapeutic implications, especially for affected family members. This descriptive study aimed to delineate phenotype and cardiac penetrance in “previously undiagnosed” G+P-family members of ATTRv probands.

METHODS

Demographic, electrocardiographic (ECG), genetic, and imaging (echocardiography, cardiac technetium-99m pyrophosphate (PYP) and magnetic resonance imaging) data were analyzed. The prediction effect of selected baseline characteristics for ATTRv-CM development was evaluated. Kaplan-Meier and Cox regression methods were used to describe risk and predictors of ATTRv-CM development in family members.

RESULTS

There were 85 G+P-family members identified. Mean age was 48.5±11.7 years, 39% were male, 18% had a diagnosis of peripheral neuropathy, 15% with a history of carpal tunnel syndrome, and 4% had atrioventricular block at baseline. Of these, 55 patients had follow-up imaging studies. After a median 6.8-year follow-up, 22% developed ATTR-CM with a 10-year estimated risk of 29.5% (95% CI 7.9-46.0). Cardiac penetrance increased with increasing family member’s age. Proband’s diagnosis age (p=0.0096) and artificial intelligence (AI)-ECG prediction (p=0.0091) were promising baseline predictors of time to ATTRv-CM development.

CONCLUSION

In previously undiagnosed G+P-ATTRv family members, the incidence of subsequent CM is high. Predictors for CM development such as proband’s diagnosis age and AI-determined ECG probability of ATTR-CM require further investigation.
SYNE1gene novel variant is associated with myocardial infarction in young people with a family history of premature atherosclerosis
Authors: Ambroziak Michał , Franke Jakub , Wójcicka Anna , Kolanowska Monika , Budaj Andrzej
Published: September 2024

Aim

The aim of the study was to investigate the role of genetic variants in young patients (aged <50 years) with myocardial infarction (MI) and a family history of premature atherosclerosis.

Methods and Results

The studied group consisted of 70 patients aged 26-49 (mean 43.1, SD ±4.3), 17 women and 53 men, with MI and with a family history of premature atherosclerosis, defined as MI or ischaemic stroke in first-degree relatives at age <65 years in women or <55 years in men. The total DNA was extracted from the peripheral blood samples. The targeted enrichment library was prepared and analyzed using the Next-Generation Sequencing method. Statistical analyses were performed using the R software package (http://www.r-project.org/). The results of sequencing were compared to data from the reference control population consisting of 597 people with no history of MI (418 women, 179 men) aged 18-83 (mean 40.5, SD ± 12.4) as a whole and after matching with a studied group by age and gender in a proportion 1:3 (210 people, 51 women, 159 men, aged 18-77, mean 42.1, SD ±10.6) using Propensity Score Matching. Risks associated with detected variants were evaluated using Fisher’s exact test based on the allelic frequencies of variants in both groups.

SYNE1gene variant rs36215567 (NM_182961.4: c.20396+22A>G) occurs with a significantly higher incidence in the studied group when compared to the control population with OR 4.80 95%CI 1.43-14.45 (p=0.005) as well as when compared to the control population matched by age and gender OR 9.31 95%CI 1.64-95.41 (p=0.004). There were no statistically significant differences in the incidence of variants related to familial hypercholesterolemia such asLDLRc.667G>A,PCSK9c.658-36G>A, andAPOBc.12382G>A between both cohorts.

Conclusion

A novel variant of theSYNE1gene is associated with myocardial infarction in young patients with a family history of premature atherosclerosis.

Lay summary

The wide use of genetic information to predict coronary artery disease (CAD) development and incidence, particularly important in young people, still requires investigation before clinical implementation.

A novel variant of theSYNE1gene is associated with myocardial infarction (MI) in young patients with a family history of premature atherosclerosis.

Although, the role of SYNE1 in the maintenance of proper function of the cardiac muscles and coronary arteries remains still under examination the result of this study open a new opportunity to use theSYNE1gene variant in genetic risks MI scores.
Correlates of COVID-19 conspiracy theory beliefs in Japan: A nationally-representative cross-sectional survey
Authors: Sato Yukihiro , Kawachi Ichiro , Saijo Yasuaki , Yoshioka Eiji , Osaka Ken , Tabuchi Takahiro
Published: September 2024

Background

The COVID-19 pandemic was associated with an increase in conspiracy theories worldwide. However, the prevalence of COVID-19 conspiracy beliefs among Japanese has remained unclear. This study aimed to estimate the prevalence and correlates of COVID-19 conspiracy beliefs in Japan using a nationwide survey of 28,175 residents aged 16–81 years old.

Methods

A nationally representative, cross-sectional self-administered survey was conducted from September to October 2021. To assess the number of COVID-19 conspiracy beliefs, we used three questions from the Oxford Coronavirus Explanations, Attitudes, and Narratives Survey. Independent variables included general vaccine conspiracy beliefs, sociodemographic variables, information sources for COVID-19, trust in authorities, and fear of COVID-19.

Results

After applying sampling weights and imputation, the estimated prevalence of holding at least one COVID-19 conspiracy belief was 24.4%. From a linear regression model, several factors were independently associated with conspiracy beliefs. Notably, people with the lowest level of education (lower secondary school) endorsed fewer COVID-19 conspiracy beliefs (B -0.089, vs. upper secondary school). Furthermore, higher socioeconomic backgrounds–such as higher income, higher wealth, and regular employment–were associated with endorsing conspiracy beliefs. Additionally, only 37.3% of respondents trusted the government of Japan, but paradoxically, trust in the government was positively associated with conspiracy beliefs (B 0.175, vs. distrust).

Conclusions

Conspiracy beliefs about COVID-19 were prevalent in about a quarter of the Japanese population. Certain groups are more likely to endorse conspiracy beliefs, and targeting interventions towards these groups might be efficient in stemming the spread of conspiracy beliefs.
Pangenome analysis ofClostridium scindens: a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains
Authors: Olivos-Caicedo Kelly Y. , Fernandez Francelys , Daniel Steven L. , Anantharaman Karthik , Ridlon Jason M. , Alves João M. P.
Published: September 2024

Clostridium scindensis a commensal gut bacterium capable of forming the secondary bile acids deoxycholic acid and lithocholic acid from the primary bile acids cholic acid and chenodeoxycholic acid, respectively, as well as converting glucocorticoids to androgens. Historically, only two strains,C. scindensATCC 35704 andC. scindensVPI 12708, have been characterizedin vitroandin vivoto any significant extent. The formation of secondary bile acids is important in maintaining normal gastrointestinal function, in regulating the structure of the gut microbiome, in the etiology of such diseases such as cancers of the GI tract, and in the prevention ofClostridium difficileinfection. We therefore wanted to determine the pangenome of 34 cultured strains ofC. scindensand a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the 34 strains ofC. scindenshave an open pangenome with 12,720 orthologous gene groups, and a core genome with 1,630 gene families, in addition to 7,051 and 4,039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The core genome contains 39% of the proteins with predicted metabolic function, and, in the unique genome, the function of storage and processing of information prevails, with 34% of the proteins being in that category. The pangenome profile including the MAGs also proved to be open. The presence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes was identified among groups of strains. The analysis reveals thatC. scindensstrains are distributed into two clades, indicating the possible onset ofC. scindensseparation into two species, confirmed by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of theC. scindenspangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.
Modulating NLRP3 splicing with antisense oligonucleotides to control pathological inflammation
Authors: Klein Roni , Onyuru Janset , Viera Estela M. , Putnam Christopher D. , Hoffman Hal M. , Hastings Michelle L.
Published: September 2024

Inflammation has an essential role in healing. However, over-active inflammation disrupts normal cellular functions and can be life-threatening when not resolved. The NLRP3 inflammasome, a component of the innate immune system, is an intracellular multiprotein complex that senses stress-associated signals, and, for this reason is a promising therapeutic target for treating unresolved, pathogenic inflammation. Alternative splicing ofNLRP3RNA has been suggested as a regulatory mechanism for inflammasome activation, as some spliced isoforms encode NLRP3 proteins with compromised function. Here, we take advantage of this natural regulatory mechanism and devise a way to control pathogenic inflammation using splice-switching antisense oligonucleotides (ASOs). To identify and induce NLRP3 spliced isoforms lacking inflammatory activity, we tested a series of ASOs, each targeting a different exon, to determine the most effective strategy for down-regulating NLRP3. We identify several ASOs that modulateNLRP3splicing, reduce NLRP3 protein, and decrease inflammasome signalingin vitro. The most effective ASO suppresses systemic inflammationin vivoin mouse models of acute inflammation and cryopyrin-associated periodic syndrome (CAPS). Our results demonstrate a systematic approach to protein engineering using splice-switching ASOs to generate isoforms with altered activity, and identify an ASO that can treat pathological inflammation in mice by reducing functional NLRP3.
USP24 is an ISG15 cross-reactive deubiquitinase that mediates IFN-I production by de-ISGylating the RNA helicase MOV10
Authors: Mukhopadhyay Rishov , Draganov Simeon D. , Akkermans Jimmy J. L. L. , Kikkert Marjolein , Knobeloch Klaus-Peter , Fritz Günter , Guzmán María , Zuñiga Sonia , Kim Robbert. Q. , Kessler Benedikt M. , Pinto-Fernández Adán , Geurink Paul P. , Sapmaz Aysegul
Published: September 2024

The interferon-stimulated gene 15 (ISG15) is a ubiquitin-like modifier induced by type I Interferon (IFN-I) and plays a crucial role in the innate immune response against viral infections. ISG15 is conjugated to target proteins by an enzymatic cascade through a process called ISGylation. While ubiquitin-specific protease 18 (USP18) is a well-defined deISGylase counteracting ISG15 conjugation, ISG15 cross-reactive deubiquitylating enzymes (DUBs) have also been reported. Our study reports USP24 as a novel ISG15 cross-reactive DUB identified through activity-based protein profiling (ABPP). We demonstrate that recombinant USP24 processed pro-ISG15 and ISG15-linked synthetic substratesin vitro. Moreover, the depletion of USP24 significantly increased the accumulation of ISG15 conjugates upon IFN-β stimulation. An extensive proteomic analysis of the USP24-dependent ISGylome, integrating total proteome, GG-peptidome, and ISG15 interactome data, identified the helicase Moloney leukemia virus 10 (MOV10) as a specific target of USP24 for deISGylation. Further validation in cells revealed that ISGylated MOV10 enhances IFN-β production/secretion, whereas USP24 deISGylates MOV10 to negatively regulate the innate immune response. This study showcases USP24’s novel roles in modulating ISGylation and modulation of the IFN-I-dependent immune responses, with potential therapeutic implications in infectious diseases, cancer, autoimmunity, and neuroinflammation.
GelGenie: an AI-powered framework for gel electrophoresis image analysis
Authors: Aquilina Matthew , Wu Nathan J.W. , Kwan Kiros , Bušić Filip , Dodd James , Nicolás-Sáenz Laura , O’Callaghan Alan , Bankhead Peter , Dunn Katherine E.
Published: September 2024

Gel electrophoresis is a ubiquitous laboratory method for the separation and semi-quantitative analysis of biomolecules. However, gel image analysis principles have barely advanced for decades, in stark contrast to other fields where AI has revolutionised data processing. Here, we show that an AI-based system can automatically identify gel bands in seconds for a wide range of experimental conditions, far surpassing the capabilities of current software. We used a dataset containing 500+ images of manually-labelled gels to train various U-Nets to accurately identify bands through segmentation, i.e. classifying pixels as ‘band’ or ‘background’. When applied to gel electrophoresis data from other laboratories, our system generated results that quantitatively matched those of the original authors. We have publicly released our models through GelGenie, an open-source application that allows users to extract bands from gel images on their own devices, with no expert knowledge or experience required.
The penta-EF-hand protein Pef1 ofCandida albicansfunctions at sites of membrane perturbation to support polarized growth and membrane integrity
Authors: Weichert Martin , Schumann Marcel René , Brandt Ulrike , Brand Alexandra C. , Fleißner André
Published: September 2024

The fungal plasma membrane is the target of fungicidal compounds, such as polyenes and saponins, that directly interact with fungus-specific ergosterol to cause deleterious membrane disruption. To counter membrane attack, diverse eukaryotic cells employ Ca2+-binding penta-EF (PEF)-hand proteins, including the human ortholog, ALG-2, to maintain membrane integrity.Candida albicansis a major fungal pathogen in humans, where increasing resistance to current antifungal drugs that target the plasma membrane is a serious cause of concern. Combinatorial treatments that additionally compromise the plasma membrane offer a way forward, but our mechanistic understanding of how fungi respond to direct membrane disruption remains limited. Here, we characterized the PEF-hand ortholog, Pef1, in this polymorphic species. GFP-tagged Pef1 localized at sites of polarized growth in yeast and hyphal cells ofC. albicans. On treatment of cells with the polyene drug, amphotericin B, or the saponin, tomatine, GFP-Pef1 appeared as punctate spots at the membrane. In a similar manner, loss of calcineurin, but not of its transcription factor, Crz1, caused a punctate localization pattern of GFP-Pef1, which correlated with the serum sensitivity of thecna1Δ mutant. While deletion ofPEF1impaired yeast cell separation, filamentation was not affected. Strikingly,pef1Δ hyphae could not maintain plasma membrane integrity in serum. Consistent with this, the mutant exhibited attenuated virulence in an insect larvae infection model. Taken together, these observations suggest that Pef1 localizes to sites of membrane perturbation in order to maintain cell integrity, including sites of dynamic polarized growth and fungicide-induced membrane disruption.
Macrophage-intrinsic MDA5-IRF5 axis drives HIV-1 icRNA-induced inflammatory responses
Authors: Ramaswamy Sita , Akiyama Hisashi , Berrigan Jacob , Quiñones Andrés , Olson Alex , Chen Yunhan , Liang Yan Mei , Henderson Andrew J. , Asundi Archana , Sagar Manish , Gummuluru Suryaram
Published: September 2024

Despite effective antiretroviral therapy (ART), transcriptionally competent HIV-1 reservoirs persist and contribute to persistent immune activation in people living with HIV (PWH). HIV-1-infected macrophages are important mediators of chronic innate immune activation, though mechanisms remain unclear. We previously reported that nuclear export and cytoplasmic expression of HIV-1 intron-containing RNA (icRNA) activates mitochondrial antiviral signaling protein (MAVS)-mediated type I interferon (IFN) responses in macrophages. In this study, we demonstrate an essential role of melanoma differentiation-associated protein 5 (MDA5) in sensing HIV-1 icRNA and promoting MAVS-dependent IRF5 activation in macrophages. Suppression of MDA5, but not RIG-I expression nor disruption of endosomal TLR pathway, abrogated HIV-1 icRNA-induced type I IFN responses and IP-10 expression in macrophages. Furthermore, induction of IP-10 in macrophages upon HIV-1 icRNA sensing by MDA5 was uniquely dependent on IRF5. Additionally, monocytes and MDMs from older (>50 years) individuals exhibit constitutively higher levels of IRF5 expression compared to younger (<35 years) individuals, and HIV-1 icRNA induced IP-10 expression was significantly enhanced in older macrophages, which was attenuated upon ablation of IRF5 expression suggesting that IRF5 functions as a major mediator of pro-inflammatory response downstream of MDA5-dependent HIV-1 icRNA sensing, dysregulation of which might contribute to chronic inflammation in older PWH.
CRISPRi with barcoded expression reporters dissects regulatory networks in human cells
Authors: Kim Jinyoung , Muller Ryan Y. , Bondra Eliana R. , Ingolia Nicholas T.
Published: September 2024

Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy of CiBER-seq and its potential for dissecting genetic networks in mammalian cells with superior time resolution.
Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth ofCampylobacterotaisolates
Authors: Heo Hokwan , Nguyen-Dinh Thanh , Jung Man-Young , Greening Chris , Yoon Sukhwan
Published: September 2024

Dissimilatory nitrate reduction to ammonium (DNRA) is a key process in global nitrogen cycling, supporting the energy conservation of diverse microbes. For a long time, DNRA has been thought to primarily depend on organic electron donors, and thus to be governed by carbon-to-nitrogen (C:N) ratios. However, recent studies suggest that inorganic electron donors, such as sulfur compounds and iron, may also facilitate DNRA. The coupling of DNRA with molecular hydrogen (H2) oxidation is theoretically feasible, but largely unexplored microbial process. Here, we report the isolation of twoCampylobacterotastrains,Aliarcobacter butzlerihDNRA1 andSulfurospirillumsp. hDNRA2, that grow by using H2as an electron donor for DNRA. In both batch and continuous cultures, DNRAsensu stricto, i.e., NO2−-to-NH+reduction, depended on the presence of H2and was stoichiometric with H2oxidation. The electrons for NO−reduction were clearly derived from H, and hydrogenotrophic DNRA was largely unaffected by the ratio of either carbon or electron donor to NO−/NO−. Genomic and transcriptomic analyses indicate that group 1b [NiFe]-hydrogenase and cytochromec552nitrite reductase are the key enzymes catalyzing hydrogenotrophic DNRA. These findings reveal novel physiological mechanisms enabling anaerobic bacterial growth, challenge the traditional C:N ratio paradigm, and uncover new biogeochemical processes and mediators controlling the global nitrogen and hydrogen cycles.
Genome scale identification of new genes using saturated reporter transposon mutagenesis
Authors: Goodall Emily C. A. , Hodges Freya , Kok Weine , Permana Budi , Cuddihy Thom , Yang Zihao , Kahler Nicole , Shires Kenneth , Pullela Karthik , Torres Von Vergel L. , Rooke Jessica L. , Delhaye Antoine , Collet Jean-François , Bryant Jack A. , Forde Brian M. , Hemm Matthew , Henderson Ian R.
Published: September 2024

Small or overlapping genes are prevalent across all domains of life but are often overlooked for annotation and function because of challenges in their detection. The advent of high-density mutagenesis and data-mining studies suggest the existence of further coding potential within bacterial genomes. To overcome limitations in existing protein detection methods, we applied a genetics-based approach. We combined transposon insertion sequencing with a translation reporter to identify translated open reading frames throughout the genome at scale, independent of genome annotation. We applied our method to the well-characterised speciesEscherichia coliand identified ∼200 putative novel protein coding sequences (CDS). These are mostly short CDSs (<50 amino acids) and in some cases highly conserved. We validated the expression of selected CDSs demonstrating the utility of this approach. Despite the extensive study ofE. coli, this method revealed proteins that have not been described previously, including proteins that are conserved and neighbour functionally important genes, suggesting significant functional roles of these small proteins. We present this as a complementary method to whole cell proteomics and ribosome trapping for condition-dependent identification of protein CDSs, and as a high-throughput method for testing conditional gene expression. We anticipate this technique will be a starting point for future high-throughput genetics investigations to determine the existence of unannotated genes in multiple bacterial species.
Integrative Multi-Omics Analysis of IFNγ-induced Macrophages and Atherosclerotic Plaques Reveals Macrophage-dependent STAT1-Driven Transcription in Atherosclerosis
Authors: Boroujeni Mahdi Eskandarian , Lopacinska Natalia , Antonczyk Aleksandra , Kluzek Katarzyna , Wesoly Joanna , Bluyssen Hans AR
Published: September 2024

This study investigates the role of STAT1-mediated IFNγ signaling in atherosclerosis progression through multi-omics integration and analysis of human and mouse models of atherosclerotic lesions. By integrating ATAC-seq, ChIP-seq, and RNA-seq data from IFNγ-treated bone marrow-derived macrophages, we identified 1139 STAT1-dependent integrative genes that show chromatin accessibility, differential epigenetic marks (H3K27ac, H3K4me1, H3K4me3), prominent transcription factor binding patterns (STAT1 and PU.1), and active transcription. These genes were also enriched for lipid metabolism and atherosclerosis-related pathways. We then validated our findings by tracing the expression of these genes in human atherosclerotic lesions and in ApoE-/- and LDLr-/-mouse models, revealing significant correlations with LDL cholesterol and diseased vessel traits. Single-cell RNA-seq of human and mouse atherosclerotic samples showed dynamic changes in macrophage subtypes, with foamy and tissue-resident macrophages displaying increased STAT1 activity. This comprehensive multi-omics approach provides new insights into the transcriptional regulation of atherosclerosis progression mediated by STAT1-PU.1 co-binding and IFNγ signaling. Moreover, our data delineates a STAT1-dependent gene signature, highlighting the potential of these integrative genes as biomarkers and therapeutic targets in atherosclerosis.
ER stress relief drives ß-cell proliferation
Authors: Bourgeois Stephanie , Van Mulders Annelore , Heremans Yves , Leuckx Gunter , Willems Lien , Coenen Sophie , Degroote Laure , Pierreux Julie , Kancheva Daliya , Scheyltjens Isabelle , Movahedi Kiavash , Carlotti Françoise , de Koning Eelco , Yi Xiaoyan , Vinci Chiara , Tong Yue , Cnop Miriam , Heimberg Harry , Leu Nico De , Staels Willem
Published: September 2024

Regenerating endogenous pancreatic ß-cells is a potentially curative yet currently elusive strategy for diabetes therapy. Mimicking the microenvironment of the developing pancreas and leveraging vascular signals that support pancreatic endocrinogenesis may promote ß-cell regeneration. We aimed to investigate whether recovery from experimental hypovascularization of the endocrine pancreas, achieved by modulating the transgenic production of a VEGF-A blocker in ß-cells, could trigger mouse ß-cell proliferation. Serendipitously, we found that transgene overexpression in ß-cells induces endoplasmic reticulum (ER) stress and that subsequent relief from this stress stimulates ß-cell proliferation independent of vessel recovery. TransientGFPoverexpressionin vivoand chemical induction of ER stressin vitroreplicated this ß-cell cycling response. Our findings highlight the potential side effects of ER stress due to transgene overexpression in ß-cells and assert that ER stress relief serves as a potent regenerative stimulus.
Uukuniemi virus infection causes a pervasive remodelling of the RNA-binding proteome in tick cells
Authors: Wilson Alexandra , Kamel Wael , Davies Kelsey , De Laurent Zaydah R. , Arif Rozeena , Bell-Sakyi Lesley , Lamont Douglas , Demyanenko Yana , Noerenberg Marko , Kohl Alain , Mohammed Shabaz , Castello Alfredo , Brennan Benjamin
Published: September 2024

Cellular RNA-binding proteins (RBPs) are pivotal for the viral lifecycle, mediating key host-virus interactions that promote or repress virus infection. While these interactions have been largely studied in the vertebrate host, no comprehensive analyses of protein-RNA interactions occurring in cells of arbovirus vectors, in particular ticks, have been performed to date. Here we systematically identified the responses of the RNA-binding proteome (RBPome) to infection with a prototype bunyavirus (Uukuniemi virus; UUKV) in tick cells and discovered changes in RNA-binding activity for 283 proteins. In an orthogonal approach, we analysed the composition of the viral ribonucleoprotein by immunoprecipitation of UUKV nucleocapsid protein (N) in infected cells. We found many tick RBPs that are regulated by UUKV infection and associate with viral nucleocapsid protein complexes. We confirmed experimentally that these RBPs impact UUKV infection. This includes the tick homolog of topoisomerase 3B (TOP3B), a protein able to manipulate the topology of RNA, which showed an effect on viral particle production. Our data thus reveals the first protein-RNA interaction map for infected tick cells.

Research highlights

UUKV RNAs interact with nearly three hundred tick cell RBPs.

Demonstrated an enrichment of N protein interactors within the upregulated RIC data suggesting a direct involvement in viral RNA metabolism and translation.

Developed a robust methodology to silence gene expression in tick cell cultures.

The TOP3B complex facilitates efficient packaging of UUKV virions.