bluuebunny/crossref_metadata_2025 huggingface dataset:
ACE-Breast-02: a randomized phase III trial of ARX788 versus lapatinib plus capecitabine for HER2-positive advanced breast cancer
Authors: Hu Xichun , Zhang Qingyuan , Wang Leiping , Zhang Jian , Ouyang Quchang , Wang Xiaojia , Li Wei , Xie Weimin , Tong Zhongsheng , Wang Shusen , Xu Faliang , Sun Tao , Liu Wei , Chen Zhendong , Wu Jinsheng , Wang Ying , Wang Haixia , Yan Min , Wang Xinshuai , Wang Jingfen , Cao Feilin , Du Yingying , Zhang Yongqiang , Chen Lilin , Lu Ping , Sun Sanyuan , Zhang Ruiwen , Zang Aimin , Nie Xiuqing , Lei Yuan
Published: February 2025

This phase III trial aimed to compare ARX788, a site-specific, construct-homogeneous antibody-drug conjugate, with lapatinib plus capecitabine in patients with human epidermal growth factor receptor 2 (HER2)-positive advanced breast cancer (ABC) who had progressed on one line of trastuzumab based regimen. Eligible patients were randomized (1:1) to receive ARX788 (1.5 mg/kg, IV, Q3W) or lapatinib plus capecitabine (LC: lapatinib 1250 mg QD; capecitabine 1000 mg/m2 BID, days 1–14, Q3W) and stratified by prior chemotherapy lines (0-1 versus >1) and visceral metastasis (yes versus no). The primary outcome was progression-free survival (PFS) assessed by a blinded independent central review (BICR). A total of 441 patients were randomly assigned to receive either ARX788 (n = 221) or LC (n = 220). The median PFS was 11.3 (95% confidence interval [CI], 8.4–13.8) months with ARX788 compared with 8.2 (95% CI, 6.9–8.7) months with LC, as per BICR (hazard ratio [HR] 0.64, p = 0.0006). Frequencies of treatment-related adverse events (TRAEs) of any grade were 98.6% and 99.1% for ARX788 and LC, respectively. Grade ≥3 TRAEs were 41.4% and 40.0%, respectively, the most common adverse events were blurred vision (12.3%), dry eye (9.1%), keratopathy (5.9%), and interstitial lung disease (ILD, 5.9%) with ARX788; hand-foot syndrome (18.1%) and hypokalemia (5.1%) with LC; all the hematological and gastrointestinal events of grade ≥3 with ARX788 were less than 3%. Six treatment-related deaths occurred, with three cases possibly related to ILD. ARX788 significantly improved PFS compared with LC in patients with HER2-positive ABC with a distinct toxicity profile, supporting it as a potential treatment option.
Predicting visual field global and local parameters from OCT measurements using explainable machine learning
Authors: Hasan Md Mahmudul , Phu Jack , Wang Henrietta , Sowmya Arcot , Meijering Erik , Kalloniatis Michael
Published: February 2025

Glaucoma is characterised by progressive vision loss due to retinal ganglion cell deterioration, leading to gradual visual field (VF) impairment. The standard VF test may be impractical in some cases, where optical coherence tomography (OCT) can offer predictive insights into VF for multimodal diagnoses. However, predicting VF measures from OCT data remains challenging. To address this, five regression models were developed to predict VF measures from OCT, Shapley Additive exPlanations (SHAP) analysis was performed for interpretability, and a clinical software tool called OCT to VF Predictor was developed. To evaluate the models, a total of 268 glaucomatous eyes (86 early, 72 moderate, 110 advanced) and 226 normal eyes were included. The machine learning models outperformed recent OCT-based VF prediction deep learning studies, with correlation coefficients of 0.76, 0.80 and 0.76 for mean deviation, visual field index and pattern standard deviation, respectively. Introducing the pointwise normalisation and step-size concept, a mean absolute error of 2.51 dB was obtained in pointwise sensitivity prediction, and the grayscale prediction model yielded a mean structural similarity index of 77%. The SHAP-based analysis provided critical insights into the most relevant features for glaucoma diagnosis, showing promise in assisting eye care practitioners through an explainable AI tool.
Unraveling the causal association between inflammatory bowel diseases and uveitis through mendelian randomization analysis
Authors: Zhong Min , An Hongjin , Gan Huatian
Published: February 2025

To investigate the causal relationship between inflammatory bowel disease (IBD) and uveitis, we conducted a two-sample bidirectional Mendelian randomization (MR) analysis utilizing summary data from genome-wide association studies (GWAS). The primary statistical analysis was performed using the inverse-variance weighted (IVW) method. False discovery rate (FDR) correction was used to control for false positives in multiple testing. In addition, sensitivity analyses were carried out using the MR Egger intercept test and Cochran’s Q test. The MR analysis revealed that genetically determined IBD (OR = 1.141, 95% CI 1.080–1.205, P = 2.21 × 10−6, PFDR = 6.90 × 10−6), ulcerative colitis (UC) (OR = 1.113, 95% CI 1.032–1.201, P = 0.006, PFDR = 0.009), and Crohn’s diseases (CD) (OR = 1.073, 95% CI 1.017–1.133, P = 0.010, PFDR = 0.011) had a causal effect on uveitis. Conversely, the reverse MR analysis did not reveal significant causal link of uveitis on IBD, including its two subtypes. Furthermore, the results of the MR-Egger and weighted median methods were consistent with the IVW method. No evidence of heterogeneity or pleiotropy was detected by sensitivity analysis. Our findings confirm that IBD and its main subtypes had a causal connection with uveitis. Further research is needed to elucidate the underlying pathophysiological mechanisms driving this association.
The transcriptomic landscape of monosomy X (45,X) during early human fetal and placental development
Authors: Suntharalingham Jenifer P. , del Valle Ignacio , Buonocore Federica , McGlacken-Byrne Sinead M. , Brooks Tony , Ogunbiyi Olumide K. , Liptrot Danielle , Dunton Nathan , Madhan Gaganjit K. , Metcalfe Kate , Nel Lydia , Marshall Abigail R. , Ishida Miho , Sebire Neil J. , Moore Gudrun E. , Crespo Berta , Solanky Nita , Conway Gerard S. , Achermann John C.
Published: February 2025

Monosomy X (45,X) is associated with Turner syndrome and pregnancy loss in humans, but the underlying mechanisms remain unclear. We therefore undertook an exploratory study of the transcriptomic landscape of clinically relevant human fetal 45,X tissues (including pancreas, liver, kidney, skin, placenta) with matched 46,XX and 46,XY control samples between 11 and 15 weeks post conception (n = 78). Although most pseudoautosomal region 1 (PAR1) genes are lower in monosomy X tissues, we also found reduced expression of several key genes escaping X inactivation (e.g., KDM5C and KDM6A), several ancestral X-Y gene pairs, and potentially clinically important transcripts such as genes implicated in ascending aortic aneurysm. In contrast, higher expression of an autosomal, long non-coding RNA (OVCH1-AS1) is seen in all 45,X tissues. In the placenta, lower expression of CSF2RA is demonstrated, likely contributing to immune dysregulation. Taken together, these findings provide insights into the biological consequences of a single X chromosome during early human development and potential insights in genetic mechanisms in Turner syndrome.
Holding back the damage: strong political institutions and the effect of populism on business investment
Authors: Corina Margherita , Hartwell Christopher , Carballo Alfonso
Published: February 2025

Populism is a political phenomenon that attempts to harness existing institutions for populist ends, often leading to negative consequences for businesses. However, can national institutions resist this pressure and mitigate the damage to firms? This paper investigates how populist electoral success influences corporate investment, unraveling the intricate connection between a country’s political institutions and the investment behavior of companies. Through the lens of political uncertainty and transaction cost economics, we theorize that countries with fortified checks and balances—facilitated by electoral systems (situated at the entrance to power), judicial independence (supervising the exercise of power), and government accountability (serving as ex-post checks)—effectively mitigate populist impulses. However, these checks and balances are also often targeted by populist leaders, as they prevent full implementation of a populist agenda. Analyzing a dataset spanning over 36,000 firms across 42 countries from 1995 to 2021, we find that existing checks and balances shield firms from populist excesses. In line with our theory, the longer a ruler is in power, the weaker these checks and balances remain. Our study highlights populism’s harm to business and the role of robust political institutions as mitigating factors.
Intravenous amino acids for renal protection in patients receiving temporary mechanical circulatory support: a secondary subgroup analysis of the PROTECTION study
Authors: Belletti Alessandro , Pisano Antonio , Scandroglio Anna Mara , Garofalo Eugenio , Calabrò Maria Grazia , Ferrod Federica , Monaco Fabrizio , Brambillasca Claudio , Baiardo Redaelli Martina , Meroi Francesco , Fominskiy Evgeny , Vignale Rosaria , Ajello Silvia , Venditto Maria , Scquizzato Tommaso , Porta Sabrina , Losiggio Rosario , Suriano Paola , Pontillo Domenico , Orso Daniele , Tomasi Enrico , Paternoster Gianluca , Lomivorotov Vladimir , Longhini Federico , Landoni Giovanni , Zangrillo Alberto , Maisano Francesco , Bellomo Rinaldo , Pieri Marina ,   PROTECTION Study Group Collaborators, D’Amico Filippo , Manazza Marco , Marmiere Marilena , Marzaroli Matteo , Monti Giacomo , Oliva Federico Mattia , Pruna Alessandro , Turi Stefano , Veneziano Marta , Vietri Simone , Zaraca Luisa , Fraja Diana Di , Verniero Luigi , Bruni Andrea , Perrelli Giulia , Prezzi Laura , Massaro Cristiano , Ferrante Palma , Arangino Cristina , Angelini Filippo , Bacchetti Giacomo , Vitielli Michelangelo , Gallicchio Francesca , Bradic Nikola , Ti Lian Kah
Published: February 2025

OBJECTIVES

In cardiac surgery patients, acute kidney injury (AKI) frequently occurs in the setting of haemodynamic instability and treatment with temporary mechanical circulatory support (tMCS). Recent evidence suggests amino acids (AA) infusion may reduce AKI rate. However, the effect of AA infusion in patients requiring tMCS may be less effective.

METHODS

We performed a secondary analysis of the PROTECTION multicentre randomized controlled trial including all patients treated with tMCS. Patients undergoing elective cardiac surgery with cardiopulmonary bypass were randomized to receive 2 g/kg ideal body weight/day of intravenous AA to a maximum of 100 g/day or matching placebo from operating room admission until up to 3 days, receipt of renal-replacement therapy, discharge from ICU or death. The primary outcome of the PROTECTION study was the rate of AKI, as in this secondary analysis. A total of 3511 patients were randomized in the study.

RESULTS

We studied 232 patients who received tMCS, 112 randomized to AA infusion and 120 to placebo. The median preoperative serum creatinine value was significantly higher among AA group patients (AA: 1.08, interquartile range 0.90–1.26; placebo: 0.98, interquartile range 0.85–1.15; P = 0.02). The rate of AKI, however, was lower in patients randomized to AA (44.6% vs 60.8%; relative risk 0.73; 95% confidence interval (0.57–0.94); P = 0.01; number needed to treat = 6). We found no significant differences in secondary outcomes.

CONCLUSIONS

Short-term AA infusion appears to reduce rate of AKI among patients requiring tMCS. Use of AA in this population at high-risk for renal failure appears justified.

Clinical trial registration number

ClinicalTrials.gov NCT03709264.
Scaling the fitness effects of mutations with respect to differentially adapted Arabidopsis thaliana accessions under natural conditions
Authors: Stearns Frank W , Zhou Juannan , Fenster Charles B
Published: February 2025

Mutations are the ultimate source of genetic variation for natural selection to act upon. A major question in evolutionary biology is the extent to which new mutations can generate genetic variation under natural conditions to permit adaptive evolution over ecological time scales. Here we collected fitness data for chemically induced (ethylmethane sulfonate, EMS) mutant lines descended from two Arabidopsis thaliana ecotypes that show differential adaptation to the local environment of our common garden plot. Using a novel nonparametric Bayesian statistical approach, we found that both ecotypes accumulated substantial proportions of beneficial mutations. The poorly adapted ecotype exhibited higher mean mutational effects and higher variance in the fitness effects of mutations compared to the well-adapted ecotype. Furthermore, we predict that it takes less than 4000 generations for the fitness space of the two ecotypes to overlap through mutation accumulation, and that a single founder, through mutation accumulation, is able to achieve the species-wide genetic variation in less than 10,000 generations. Our results provide evidence for relatively rapid local adaptation of Arabidopsis thaliana in natural conditions through new mutations, as well as the utility of a nonparametric Bayesian method for modeling the distribution of fitness effects for field-collected data.
Phytoplankton recruitment of specific microbial assemblages and phylosymbiotic patterns
Authors: Kim Joo-Hwan , Kim Jin Ho , Li Zhun , Shin Hyeon Ho , Lim Young Kyun , Baek Seung Ho , Wang Pengbin , Park Ro Young , Jin Soo Hwan , Han Myung-Soo , Park Bum Soo
Published: February 2025

Phytoplankton and bacteria represent two major pillars of the carbon cycle in marine ecosystems. While their interactions are known to be tightly linked, the specific mechanisms underlying these interactions remain largely unexplored. Evidence of host-specific microbial assemblages could serve as a foundation for studies of detailed host-microbe interactions, yet such research remains limited in phytoplankton. Here, we not only investigate the microbial assemblages of six phytoplankton species, including multiple strains of dinoflagellates and diatoms, but also samples of phytoplankton blooms from the field. Our results reveal the presence of host-specific microbial assemblages in phytoplankton, with members of the core microbial lineages (MCGs) playing pivotal roles in shaping host-specific microbial assemblages and contributing to network structures. Deterministic processes, particularly host genotypes, were the dominant factors shaping microbial assemblages, overriding environmental influences. Consequently, microbial composition reflected the evolutionary relationships of the host species, demonstrating phylosymbiotic patterns. These findings suggest that studying MCGs will be a crucial foundation for investigating specific phytoplankton-microbe interactions and highlight the ecological and evolutionary importance of host-microbial specificity in phytoplankton.
LANTERN: Leveraging Large Language Models and Transformers for Enhanced Molecular Interactions
Authors: Nga Ha Cong , Pham Phuc , Hy Truong Son
Published: February 2025

Understanding molecular interactions such as Drug-Target Interaction (DTI), Protein-Protein Interaction (PPI), and Drug-Drug Interaction (DDI) is critical for advancing drug discovery and systems biology. However, existing methods often struggle with scalability due to the vast chemical and biological space and suffer from limited accuracy when capturing intricate biochemical relationships. To address these challenges, we introduceLANTERN(Leveraging LargeLANguage Models andTransformers forEnhanced moleculaRinteractioNs), a novel deep learning framework that integrates Large Language Models (LLMs) with Transformer-based architectures to model molecular interactions more effectively. LANTERN generates high-quality, context-aware embeddings for drug and protein sequences, enabling richer feature representations and improving predictive accuracy. By leveraging a Transformer-based fusion mechanism, our framework enhances scalability by efficiently integrating diverse interaction data while maintaining computational feasibility. Experimental results demonstrate that LANTERN achieves state-of-the-art performance on multiple DTI and DDI benchmarks, significantly outperforming traditional deep learning approaches. Additionally, LANTERN exhibits competitive performance on challenging PPI tasks, underscoring its versatility across diverse molecular interaction domains. The proposed framework offers a robust and adaptable solution for modeling molecular interactions, efficiently handling a diverse range of molecular entities without the need for 3D structural data and making it a promising framework for foundation models in molecular interaction. Our findings highlight the transformative potential of combining LLM-based embeddings with Transformer architectures, setting a new standard for molecular interaction prediction. The source code and relevant documentation are available at:https://github.com/HySonLab/LANTERN.
Robust Prediction of Enzyme Variant Kinetics with RealKcat
Authors: Sajeevan Karuna Anna , Osinuga Abraham , B Arunraj , Ferdous Sakib , Shahreen Nabia , Noor Mohammed , Koneru Shashank , Santa-Correa Laura Mariana , Salehi Rahil , Chowdhury Niaz Bahar , Calderon-Lopez Brisa , Mali Ankur , Saha Rajib , Chowdhury Ratul
Published: February 2025

Accurate prediction of kinetic parameters is crucial for understanding known and tailoring novel enzymes for biocatalysis. Current models fail to capture mutation effects on catalytically essential residues, limiting their utility in enzyme design. We grid-searched through ten model architectures (25,671 hyperparameter combinations) to identify a gradient-based additive framework called RealKcat, trained on 27,176 experimental entries curated manually (KinHub-27k) by screening 2,158 articles. Clustering catalytic turnover (𝑘𝑐𝑎𝑡) and substrate affinity (KM) by rational orders of magnitude, RealKcat achieves >85% test accuracy, demonstrating highest sensitivity to mutation-induced variability thus far, and is the first-of-its-kind-model to demonstrate complete loss of activity upon deletion of the catalytic apparatus. Finally, state-of-the-art 𝑘𝑐𝑎𝑡 validation accuracy (96%) on alkaline phosphatase (PafA) mutant industrial dataset confirms RealKcat's generalizability in learning per-residue catalytic relevance.
Genetic Modifiers Influencing the Acute and Long-Term Responses to Traumatic Brain injury inDrosophila
Authors: Molina Brandon , Rojas Jesse J. , El-Mecharrafie Nadja , Ratliff Eric P. , Lipinski Marta M. , Finley Kim D.
Published: February 2025

Worldwide, traumatic brain injury (TBI) represents a major cause of mortality and long-term disability, with even mild repetitive forms of TBI (mTBI) potentially having deleterious consequences for both the acute and long-term function of the nervous system. Understanding the key cellular and molecular processes that occur following TBI exposure and potential factors that influence individual injury responses has been limited in part by the lack of comprehensivein vivoscreening technique that directly compares stress sensitive and resistant genotypes involving conserved genes and functional pathways. In this report, we use a high throughput adultDrosophilatrauma model system to compare the impact modest insulin signaling (IRS/chico) and autophagic defects (Atg8a/MAPLC3, Ref(2)P/SQSM1)have on traumatic injury outcomes. Using both severe and mild repetitive injury conditions the acute mortality indexes, longevity profiles, molecular and behavioral changes (locomotor, sleep) for individual fly genotypes were assessed. Compared to control cohorts (w1118/+), heterozygouschicomutants (chico1/+) demonstrated resistance, while aged flies (+2-weeks) or autophagy mutants (Atg8a1,Ref(2)Pc/e,Ref(2)Pe/+) showed heightened trauma sensitivity. Alterations that promote or impair autophagic function, longevity and stress responses were examined. Overall, this injury paradigm illustrates the effectiveness of using model systems to characterize conserved genetic factors that influence neuronal autophagy during complex trauma response. It also raises the potential for developing unique screens and therapies for patients that have experienced TBI.
The kisspeptin analog C6 reverses reproductive dysfunction in a mouse model of hyperprolactinaemia
Authors: Beaudou Chloe , Sionneau Louise , Lomet Didier , Robert Vincent , Jarrier-Gaillard Peggy , Aucagne Vincent , Dardente Hugues , Beltramo Massimiliano , Hellier Vincent
Published: February 2025

Hyperprolactinaemia (HPRL), characterized by elevated prolactin levels, disrupts the hypothalamic-pituitary-gonadal axis, leading to reproductive dysfunctions such as menstrual irregularities, anovulation, and infertility. Current treatments rely on dopamine agonists but are limited by side effects and resistance. Kisspeptin (Kp), a key neuropeptide regulating the reproductive function, offers potential as an alternative therapy. However, Kp's short half-life requires impractical administration regimens. To address this, we developed a synthetic Kp analog, C6, with enhanced pharmacokinetics. This study evaluated the effects of C6 compared to Kp in a mouse model of HPRL. Mice received subcutaneous PRL injections for 21 days to induce HPRL, followed by daily or alternate-day intraperitoneal administration of Kp10, C6, or vehicle. Estrous cyclicity, luteinizing hormone (LH) secretion, ovarian histology, and hypothalamic gene expression were analyzed. As expected, the HPRL treatment blocked estrous activity, which was restored by both Kp10, the shortest bioactive isoform of Kp and C6. Histological analysis revealed increased corpora lutea in Kp10- and C6-treated groups, indicating restored ovulation. C6 demonstrated equivalent efficacy to Kp10 in mitigating HPRL-induced reproductive dysfunctions, offering a promising alternative therapy. Future investigations should further explore the mechanistic advantages of C6, particularly its role in LH regulation, to optimize treatment strategies for HPRL-related reproductive disorders.
Meta-analysis and experimental evidence reveal no impact ofNosema ceranaeinfection on honeybee carbohydrate consumption
Authors: Ostap-Chec Monika , Antoł Weronika , Bajorek Daniel , Berbeć Ewelina , Moroń Dawid , Rapacz Marcin , Miler Krzysztof
Published: February 2025

Honeybees (Apis mellifera) are indispensable pollinators, essential for ecosystem stability and agricultural productivity. However, they face numerous challenges, including pathogens that threaten their survival and ecosystem services. Among these pathogens,Nosema ceranae, a microsporidian parasite, causes significant damage to the intestinal tract and induces energetic imbalances in an organism, posing a major threat to both individual bees and entire colonies. In response to infections, bees often engage in behavioural defenses, such as selecting foods with higher antibiotic properties. We hypothesized that bees infected withN. ceranaemight compensate behaviourally by increasing their carbohydrate consumption. To test this hypothesis, we conducted a meta-analysis of existing studies comparing sugar consumption in healthy and infected bees, complemented by an experimental study. In our experiment, we measured sugar intake and quantified trehalose levels in the hemolymph, a key indicator of energy reserves. Both the meta-analysis and experimental results consistently showed no significant differences in sugar consumption between healthy and infected bees. Similarly, trehalose levels in the hemolymph remained comparable between the two groups. Our findings suggest that the infection caused byN. ceranaedoes not elicit compensatory feeding behavior in honeybees. Moreover, the meta-analysis revealed significant gaps in current research, particularly a lack of studies focusing on forager bees, which face the highest energetic demands among colony members. Our findings call for future studies on the energetic effects of nosemosis and studies conducted under natural or semi-natural conditions.
Bacterial population dynamics during colonization of solid tumors
Authors: Sayin Serkan , ElGamel Motasem , Rosener Brittany , Brehm Michael , Mugler Andrew , Mitchell Amir
Published: February 2025

Bacterial colonization of cancer tumors is widespread. While the clinical significance of intratumor bacteria is widely investigated, the dynamics of tumor colonization remain underexplored. We monitored bacterial population dynamics in murine tumors after introducing genetically barcoded Escherichia coli cells by intravenous or intratumor injections. Barcode sequencing from resected tumors after intravenous injection suggested that narrow bottlenecks dominate infection and are followed by rapid, yet highly nonuniform growth. Within a day, bacteria reached a steady state and subsequently sustained load and clone diversity. Results from intratumor injections, circumventing the infection bottleneck, revealed that sizes of bacterial progenies followed a scale-free distribution matching Zipf's law. Theory suggested that our observations are compatible with a growth model constrained by a local niche load, competition for a global resource, and noise. Our work provides the first dynamical model of tumor colonization and suggests that descriptive statistics may allow distinguishing genuine tumor microbiomes from contamination.
APV-Sankey: A Comprehensive Toolbox for Aptamer Screening and Visualization
Authors: Zhang Yu , Wang Yashan , Gao Yajing , Hu Keyi , Gong Hao , Jia Haijing , Zhang Xin , Lou Xinhui
Published: February 2025

Aptamers, short single-stranded DNA or RNA molecules, have gained prominence as molecular recognition elements in diagnostics and therapeutics. Screening high-performance aptamers from SELEX process is tough due to limited library diversity, PCR bias, and low library enrichment efficiency. The enriched highest frequency sequences often do not have the highest affinity or specificity. Thus, we developed APV-Sankey, a novel and versatile toolbox designed for the rapid aptamer screening and visualization of the enrichment process. Its key feature is the innovative use of Sankey charts for interactive and informative visualizations. These charts facilitate tracing the evolution of K-mers (K-mer is just a sequence of k characters in a string across SELEX rounds, aiding in the identification and selection of high-affinity sequences containing K-mers while excluding high-frequency sequences without affinity. Besides integrating essential functions for aptamer analysis, we also developed advanced methods including K-mer concatenation and K-mer evolution, combined with Sankey chart visualizations. Using this toolbox to analyze experimentally screened sequences, we successfully identified high-performance candidate aptamers of rapamycin and thrombin.
Iron-deplete diet enhancesCaenorhabditis eleganslifespan via oxidative stress response pathways
Authors: Das Priyanka , Ravi  , Singh Jogender
Published: February 2025

Gut microbes play a crucial role in modulating host lifespan. However, the microbial factors that influence host longevity and their mechanisms of action remain poorly understood. Using the expression ofCaenorhabditis elegansFAT-7, a stearoyl-CoA 9-desaturase, as a proxy for lifespan modulation, we conduct a genome-wide bacterial mutant screen and identify 26Escherichia colimutants that enhance host lifespan. Transcriptomic and biochemical analyses reveal that these mutant diets induce oxidative stress and activate the mitochondrial unfolded protein response (UPRmt). Lifespan extension requires the oxidative stress response regulators SKN-1, SEK-1, and HLH-30. Mechanistically, these effects are linked to reduced iron availability, as iron supplementation restores FAT-7 expression, suppresses UPRmt activation, and abolishes lifespan extension. Iron chelation mimics the pro-longevity effects of the mutant diets, highlighting dietary iron as a key modulator of aging. Our findings reveal a bacterial-host metabolic axis that links iron homeostasis, oxidative stress, and longevity inC. elegans.
Integrating multi-modal transcriptomics identifies cellular subtypes with distinct roles in PDAC progression
Authors: Wu Jun , Dai Tenghui , Li Ziyue , Pan Meng , Zhang Wei , Chen Hao , Zheng Guansheng , Qiao Li , Lian Qizhou , Liu Yang , Chen Jierong
Published: February 2025

Background

Pancreatic ductal adenocarcinoma (PDAC) features a complex tumor microenvironment (TME) that significantly influences patient outcomes. Understanding the TME’s cellular composition and interactions is crucial for identifying therapeutic targets to improve treatment.

Methods

We performed an integrative analysis combining 88 single-cell RNA sequencing (scRNA-seq) samples with 187,520 cells, 20 Visium spatial transcriptomics (ST-seq) samples with 67,933 spots, and 1383 bulk RNA-seq samples and 2 Xenium high-resolution ST-seq samples with 307,679 cells, to delineate and characterize distinct subpopulations of fibroblasts, macrophages, T/NK cells, and B/plasma cells within the PDAC microenvironment. Correlations among major cell types across 12 PDAC datasets were assessed through gene set variation analysis (GSVA). Kaplan-Meier survival analysis was used to evaluate the prognostic significance of cell subtypes. Furthermore, multiplex immunohistochemistry (mIHC) and the Xenium platform was utilized to validate cellular interactions in human PDAC tissues at both protein and RNA levels.

Results

Six fibroblast subtypes and eight macrophage/monocyte subtypes were identified. POSTNhighfibroblasts and SPP1highmacrophages highly infiltrated tumor tissues and were associated with poor prognosis. Most immune cell subtypes mediate adverse prognoses, except for CCL4highCD8+ TEFFcells and IGHG1highplasma cells, which are linked to favorable outcomes. ST-seq revealed spatial colocalization of POSTNhighFibro and SPP1highMacro cells, as well as CCL4highCD8+ TEFFand IGHG1highplasma cells. These findings were corroborated by mIHC and validated using Xenium spatial transcriptomics with single-cell resolution, which confirmed the expression and spatial proximity of these markers at both the gene and protein levels.

Conclusion

This integrative analysis of the PDAC TME underscores the prognostic importance of POSTNhighfibroblasts and SPP1highmacrophages, while also highlighting the protective roles of CCL4highCD8+ TEFFcells and IGHG1highplasma cells. These insights could improve PDAC treatment strategies.
Compensatory Mechanisms in γδ T Cell-Deficient Chickens FollowingSalmonellainfection
Authors: Tetzlaff Felix , Methner Ulrich , von Heyl Theresa , Menge Christian , Schusser Benjamin , Berndt Angela
Published: February 2025

Avian γδ T lymphocytes are highly abundant in the intestinal mucosa and play a critical role in immune defense against infectious diseases in chickens. However, their specific contributions to infection control remain poorly understood. To investigate the role of γδ T cells and their possible compensation, we studied wild-type and γδ T cell knockout chickens following infection withSalmonellaEnteritidis. Bacterial loads in the liver, cecal content, and cecal wall were quantified. Immune cell populations in blood, spleen, and cecum were analyzed using flow cytometry. Immune gene transcription in sorted T cell subsets and cecal tissue was measured by RT-qPCR.

Strikingly, chickens lacking γδ T cells had significantly higher bacterial loads in the liver and more extensiveSalmonellainvasion in the cecal wall during the early stages of infection compared to wild-type birds. In the blood, infected γδ T cell knockout chickens displayed a significantly increased percentage of CD25+NK-like cells. In both blood and tissue, infected wild-type chickens demonstrated an increased absolute number of CD8αα++γδ T cells. Conversely, γδ T cell knockout chickens exhibited an augmented cell count of a CD8αα++CD4-non-γδ T cell population after infection, which might include αβ T cells. At 7 days post infection (dpi), gene expression analysis revealed elevated transcription of the activation marker IL-2Rα and proinflammatory cytokines (IL-17A, IFN-γ) in CD8αα++CD4-non-γδ T cells from γδ T cell knockout chickens compared to CD8αα++γδ T cells from wild-type birds. By 12 dpi, these differences diminished as transcription levels increased in γδ T cells of wild-type animals.

Our findings demonstrate that γδ T cells play a role in early immune protection againstSalmonellaEnteritidis infection in chickens. In later stages of the infection, the γδ T cells and their functions appear to be replaced by other cells.
Splenic MARCO+marginal zone macrophages regulate rapid production of MCP-1 and KC but are dispensable for alloantibody generation in response to stored RBCs in a murine model
Authors: Arneja Abhinav , Salazar Juan E. , Medved Jelena , Ratcliffe Sarah J. , Smolkin Mark E. , Santhanakrishnan Manjula , Stowell Sean R. , Hudson Krystalyn E. , Zimring James C. , Hendrickson Jeanne E. , Luckey Chance John
Published: February 2025

BACKGROUND

Alloimmunization to transfused red blood cells (RBCs) remains a significant clinical problem. However, the cells that initiate immune responses to transfused RBCs remain incompletely characterized.

Recently published work has identified splenic marginal zone B (MZB) cells as being critically required for the production of anti-RBC alloantibodies in response to RBCs. In infectious models, MZB cell activation has been shown to depend on a unique population of marginal zone macrophages (MZMs). We hypothesized that MZMs would capture stored RBCs and present them to MZBs, and ultimately MZMs would be required for generation of anti-RBC alloantibodies in response to stored RBC transfusion.

STUDY DESIGN AND METHODS

Stored GFP+murine RBCs were utilized to determine the splenic localization and erythrophagocytosis by splenic macrophage populations. To determine the functional impact of MZMs, we compared LXRα-KO mice, which have been reported to lack MZMs, with wild type mice. Both innate and adaptive immune responses to stored HOD allogenic RBC transfusion were measured in LXRα-KO and wild type mice.

RESULTS

RBC storage leads to a significant increase in the phagocytosis of transfused RBCs by splenic MZMs. LXRα-KO mice demonstrated a lack of MZMs and had significantly decreased rapid phase production of cytokines MCP-1 and KC, but similar levels of IL-6. Surprisingly, anti-RBC alloantibody levels were unaffected by the absence of splenic MZMs.

CONCLUSIONS

Splenic MZMs are involved in the innate response to transfused stored HOD RBCs, contributing to both MCP-1 and KC cytokine production. However, MZMs are dispensable for anti-RBC alloantibody production.
Swiprosin-1/EFhd2 promotes mitochondrial spare capacity in response to immobilized antigen in B cells via microtubule stabilization
Authors: Weckwerth Leonie , Tripal Philipp , Schmid Benjamin , Thomas Jana , Himmelreich Ann-Kathrin , Pracht Katharina , Urbanczyk Sophia , Allnach Hannah , Gottwald Anna , Palmisano Ralph , Mielenz Dirk
Published: February 2025

B cells can recognize soluble and membrane bound antigens, enabling them to initiate and execute versatile immune responses. This study examines Swiprosin-1/EFhd2 (EFhd2) in regulating mitochondrial function and organization in B cells during B cell receptor (BCR) activation and immune synapse formation. Using EFhd2 knockout (KO) and wild-type (WT) murine B cells, we assessed mitochondrial abundance, membrane potential, and respiratory capacity using soluble anti-IgM and anti-CD40/IL-4 stimulation. EFhd2KO B cells exhibit more functional mitochondria and mitochondrial spare capacity selectively in activated but not in resting cells. This phenotype changed absolutely upon BCR synapse formation: While activated WT B cells enhance basal mitochondrial respiration, ATP production and maximal respiration, with large increments of spare capacity, EFhd2KO B cells fail completely to do so. Actin depolymerization and microtubule destabilization impair functional mitochondrial upregulation in WT but not in EFhd2KO B cells, while microtubule stabilization restores full spare capacity in EFhd2KO B cells at the BCR synapse. Live-cell imaging reveals that EFhd2KO B cells fail to organize mitochondria, microtubules, and BCRs symmetrically. Super-resolution 3D imaging shows that WT B cells condense mitochondria at the synapse, whereas EFhd2KO B cells display dispersed, unorganized mitochondria and BCR clusters. EFhd2 re-expression restores mitochondrial polarization in EFhd2KO B cells, confirming its role in coordinating mitochondrial positioning. These findings highlight EFhd2 as a key integrator of cytoskeletal and mitochondrial functions for optimal B cell responses to membrane bound antigens.

Graphical Abstract
CAR-T cells locally delivered in porcine decellularized matrix hydrogels enhance survival in post-resection glioblastoma
Authors: Logun Meghan , Begley Sabrina L , Hicks Kelly , Park Jungmin , Zhang Logan , Binder Zev A , O'Rourke Donald M
Published: February 2025

Patients diagnosed with glioblastoma (GBM) receive a devastating prognosis of less than 15 months, and recurrence of GBM is most often local, suggesting that regional therapies would serve both immediate and long-term needs of patients. Here, we investigate a biomaterials-based approach for local delivery of chimeric antigen receptor (CAR) T cells using a murine model of partial GBM resection that mimics patient recurrence. We demonstrate that hydrogel delivery of CAR T cells directly into the intracranial resection cavity can stably implant cellular immunotherapies against CNS solid tumors, and significantly prolongs survival in recurrent GBM-bearing mice compared to those receiving resection alone.
Refining sequence-to-expression modelling with chromatin accessibility
Authors: Lapohos Orsolya , Fonseca Gregory J. , Emad Amin
Published: February 2025

Sequence-to-expression models have gained popularity in the past decade, enabling prediction of gene expression from genomic sequence alone. However, these models typically do not take into account chromatin accessibility, a major factor limiting gene regulation. We hypothesized that supplying accessibility as an input feature would allow a sequence-to-expression model to focus on important open regions of the genome. Using single-nucleus multiome RNA- and ATAC-sequencing data, we found that the predictive performance of such an augmented model was significantly greater than that of sequence-only or accessibility-only models with similar architectures. Specifically, its ability to predict the expression of highly variable genes and gene expression in other cell types improved, which we attribute to a reduction in bias originating from lowly variable genes. Moreover, post-hoc analyses revealed that higher attribution scores in the input DNA sequences of the augmented model conformed to accessibility, whereas those in the sequence-only model were scattered. Additionally, we show that fine-tuning a pre-trained sequence-only model with both sequence and accessibility can boost performance even further. We also highlight the importance of sequencing depth in sequence-to-expression prediction. Altogether, the results of this study provide a compelling argument for the inclusion of chromatin accessibility in sequence-to-expression models, as this strategy can be implemented easily and may improve downstream applications.
Neutrophil KLF2 regulates inflammasome-dependent neonatal mortality from endotoxemia
Authors: Mukherjee Devashis , Satyavolu Sriram , Thomas Asha , Cioffi Sarah , Li Yuexin , Chan E. Ricky , Wen Katherine , Huang Alex Y. , Jain Mukesh K. , Dubyak George R. , Nayak Lalitha
Published: February 2025

Preterm neonates die at a significantly higher rate from sepsis than full-term neonates, attributable to their dysregulated immune response. In addition to tissue destruction caused directly by bacterial invasion, an overwhelming cytokine response by the immune cells to bacterial antigens also results in collateral damage. Sepsis leads to decreased gene expression of a critical transcription factor, Krüppel-like factor-2 (KLF2), a tonic repressor of myeloid cell activation. Using a murine model of myeloid-Klf2deletion, we show that loss of KLF2 is associated with decreased survival after endotoxemia in a developmentally dependent manner, with increased mortality at postnatal day 4 (P4) compared to P12 pups. This survival is significantly increased by neutrophil depletion. P4 knockout pups have increased pro-inflammatory cytokine levels after endotoxemia compared to P4 controls or P12 pups, with significantly increased levels of IL-1β, a product of the activation of the NLRP3 inflammasome complex. Loss of myeloid-KLF2 at an earlier postnatal age leads to a greater increase in NLRP3 priming and activation and greater IL-1β release by BMNs. Inhibition of NLRP3 inflammasome activation by MCC950 significantly increased survival after endotoxemia in P4 pups. Transcriptomic analysis of bone marrow neutrophils showed that loss of myeloid-KLF2 is associated with gene enrichment of pro-inflammatory pathways in a developmentally dependent manner. These data suggest that targeting KLF2 could be a novel strategy to decrease the pro-inflammatory cytokine storm in neonatal sepsis and improve survival in neonates with sepsis.

Summary sentence

KLF2 regulates the developmental response to endotoxin in neonatal mice through the NLRP3 inflammasome signaling pathway.
Beyond the Hype: The Complexity of Automated Cell Type Annotations with GPT-4
Authors: Kazmi Arman , Singh Deepshikha , Jatav Shashank , Luthra Soumya
Published: February 2025

Recent research has shown the impressive capability of large language models like GPT-4 in various downstream tasks in single-cell data analysis. Among these tasks, cell type annotation remains particularly challenging, with researchers exploring various methods to improve accuracy and efficiency. While recent studies on GPT-like models have demonstrated annotation performance comparable to manual annotations, a significant gap remains in understanding their limitations and generalizability. In this work, we compare and evaluate the annotation performance of the GPT-4 model against traditional methods on nine randomly selected public single-cell RNA seq datasets from cellxgene, covering diverse tissue types. Our evaluation highlights the complexity of annotating cell types in single-cell data, revealing key differences between automated and manual approaches. We found specific cases where GPT-4 underperforms, demonstrating its limitations in certain contexts. We further introduce an automated approach to incorporate literature search using a RAG approach which enhances and outperforms GPT-4 cell type annotation when compared to traditional methods. We also introduce metrics based on taxonomic distance in the ontology tree to evaluate the granularity of the cell type annotations. To support future research, we also release an open-source Python package1that enables fully automated cell-type annotation of single-cell data using GPT-4 alongside other methods. The pipeline can take paper as an input and do cell type annotations on its own.
ABCG5 ABCG8-independent mechanisms fail to maintain sterol balance in mice fed a high cholesterol diet
Authors: Anspach Garrett B. , Chauhan Isha , Savage Erika L. , Poole Brittney , Noffsinger Victoria P. , Fu Xiaoming , Wang Zeneng , Temel Ryan E. , Gordon Scott R. , Helsley Robert N. , Graf Gregory A.
Published: February 2025

The ABCG5 ABCG8 (G5G8) sterol transporter opposes the accumulation of dietary xenosterols, but is also the primary mediator of biliary cholesterol secretion in the cholesterol elimination pathway. In humans and in mouse models of disrupted biliary cholesterol secretion, fecal neutral sterols remain constant, indicating the presence of a G5G8-independent mechanism for cholesterol excretion. Transintestinal cholesterol elimination (TICE) is thought to compensate for biliary G5G8 insufficiency. We sought to measure the compensatory increase in intestinal cholesterol secretion and provide mechanistic insight for how TICE maintains sterol balance in the absence of G5G8. Differences were not observed in fecal neutral sterols between control, acute, and chronic liver-specific G5G8 deficient mice (G5G8LKO). Cholesterol content did not differ at any point along the intestinal tract between genotypes. We also observed no change in the expression of apical or basolateral sterol transporting enzymes in the proximal small intestine. We then measured biliary and intestinal cholesterol secretion rates using cholesterol free and cholesterol enriched bile acid micelles as acceptors. While biliary cholesterol secretion was reduced, the intrinsic rate of intestinal cholesterol secretion did not differ between genotypes. G5G8LKOand whole-body G5G8-deficient mice were challenged with a cholesterol-containing diet. While control mice upregulate fecal neutral sterol excretion, G5G8LKOand G5G8-/-mice fail to do so and accumulate sterol in the liver and plasma. These studies indicate that while G5G8-independent mechanisms can mediate cholesterol excretion, TICE is not upregulated in response to a loss of hepatic G5G8 and is unable to compensate for hepatic or whole-body G5G8-deficiency in response to dietary cholesterol in mice.
Lymph nodes link sex-biased immune aging to compromised antigen recognition
Authors: Menzel Lutz , Zschummel Maria , O’Melia Meghan J. , Zhou Hengbo , Lei Pin-Ji , Liu Lingshan , Sen Debattama R. , Munn Lance L. , Padera Timothy P.
Published: February 2025

A diverse naive CD8 T cell repertoire is essential to provide broad protection against infection and cancer. Aging diminishes naive T cells, reducing potential diversity and leading to lymph node contraction. Here, we revealed that this decline occurs earlier in males, resulting in significant sex differences in immunity during middle age. Earlier in life, naive CD8 T cells in males become virtual memory cells prone to premature senescence. Due to androgen-driven thymic atrophy in males, naïve CD8 T cells are insufficiently replenished. Therapeutic thymus rejuvenation via testosterone ablation restored naive CD8 T cells in lymph nodes of middle-aged male mice, leading to enhanced tumor recognition. These findings show the crucial role of sex and age on lymph node T cell repertoires and suggest potential strategies to restore immune function in males during aging.
Deconvolution of Sample Identity in Single-Cell RNA SequencingviaGenome Imputation
Authors: Ghosh Rohit , Hugh-White Rupert , Nassiri Farshad , Zadeh Gelareh , Boutros Paul C.
Published: February 2025

Background

Droplet based single-cell RNA sequencing (scRNA-seq) is a powerful tool for measuring RNA abundance profiles at cell-specific resolution. Droplet-based barcoding technology allows sample multiplexing, thereby facilitating high-scale of single cell sequencing. The resulting processing complexity, sample contamination and the underlying chemistries can all contribute to cell mis-labelling and consequent spurious cell-to-sample assignment. Approaches for barcode-free de-multiplexing which leverage natural genetic variation have been developed, but generally require an external source of genotype information.

Results

We propose a novel method to exploit genome imputation and clustering to assign cells to inferred donor groups in the absence of a priori genetic information. Using tumor-derived single-cell RNA-sequencing (scRNA-seq) data, our workflow successfully assigned individual cells to donor-of-origin with high concordance.

Conclusions

This imputation-clustering approach represents a quality-assessment and quality-control strategy for barcode-free single cell donor-origin deconvolution with the capacity to resolve cases of sample cross-contamination.