Genome Biol. 2025 May 28;26(1):145. doi: 10.1186/s13059-025-03613-7.

ABSTRACT

BACKGROUND: Transcriptome sequencing (RNA-seq) is a powerful technology for gene expression profiling. Selection of optimal parameters for cDNA library generation is crucial for acquisition of high-quality data. In this study, we investigate the impact of the amount of RNA and the number of PCR cycles used for sample amplification on the rate of PCR duplication and, in consequence, on the RNA-seq data quality.

RESULTS: For broader applicability, we sequenced the data on four short-read sequencing platforms: Illumina NovaSeq 6000, Illumina NovaSeq X, Element Biosciences AVITI, and Singular Genomics G4. The native Illumina libraries were converted for sequencing on AVITI and G4 to assess the effect of library conversion, containing additional PCR cycles. We find that the rate of PCR duplicates depends on the combined effect of RNA input material and the number of PCR cycles used for amplification. For input amounts lower than 125 ng, 34-96% of reads were discarded via deduplication with the percentage increasing with lower input amount and decreasing with increasing PCR cycles. The reduced read diversity for low input amounts leads to fewer genes detected and increased noise in expression counts.

CONCLUSIONS: Data generated with each of the four sequencing platforms presents similar associations between starting material amount and the number of PCR cycles on PCR duplicates, a similar number of detected genes, and comparable gene expression profiles.

PMID:40437619 | DOI:10.1186/s13059-025-03613-7

BMC Womens Health. 2025 May 29;25(1):263. doi: 10.1186/s12905-025-03758-4.

ABSTRACT

BACKGROUND: This study aims to analyze the changes in inflammatory cytokines and state fatigue after exposure to a mental or physical fatiguing activity in breast cancer survivors (BCS).

METHODS: A total of 46 BCS women (age: 58.9 ± 9.1) were recruited for this study and randomly assigned to one of three groups: exposure to physical fatigue (n = 16), mental fatigue (n = 15), or control (n = 15). Participants exposed to physical fatigue performed a 6-minute walk/run test. Participants exposed to mental fatigue performed a version of a dual 2-back task on a computer. Participants in the control group watched a video for 6 min. Clinically significant fatigue was defined by the FACIT-F. Analytes in serum were profiled using the Bio-Plex 200 Suspension Array System, specifically IL-1β, IL-4, IL-5, IL-6, IL-8, IL-10, eotaxin, TNF-α, TGF-β1, and VEGF.

RESULTS: Changes in inflammatory factors in response to the assigned fatigue-inducing tasks were mainly not statistically significant. The presence of clinically significant fatigue reported at baseline was, however, related to reactions to fatigue-inducing stimuli. Levels of TGF-β and eotaxin were consistently altered in reactions to fatigue-inducing tasks, particularly in those with clinical fatigue.

CONCLUSIONS: Clinically significant fatigue is related to increased inflammatory reactions to mentally or physically fatiguing tasks, highlighting the consistent impact that fatigue has across various challenges of daily activities. Acute fatigue challenges, the kind that BCS would be exposed to in everyday circumstances, does increase inflammatory responses, and those with clinically significant levels of fatigue at baseline are more likely to show these effects.

PMID:40437526 | DOI:10.1186/s12905-025-03758-4

BMC Bioinformatics. 2025 May 28;26(1):140. doi: 10.1186/s12859-025-06159-4.

ABSTRACT

BACKGROUND: The exponential growth of scientific publications poses a formidable challenge for researchers seeking to validate emerging hypotheses or synthesize existing evidence. In this paper, we introduce Valsci, an open-source, self-hostable utility that automates large-batch scientific claim verification using any OpenAI-compatible large language model. Valsci unites retrieval-augmented generation with structured bibliometric scoring and chain-of-thought prompting, enabling users to efficiently search, evaluate, and summarize evidence from the Semantic Scholar database and other academic sources. Unlike conventional standalone LLMs, which often suffer from hallucinations and unreliable citations, Valsci grounds its analyses in verifiable published findings. A guided prompt-flow approach is employed to generate query expansions, retrieve relevant excerpts, and synthesize coherent, evidence-based reports.

RESULTS: Preliminary evaluations across claims from the SciFact benchmark dataset reveal that Valsci significantly outperforms base GPT-4o outputs in citation hallucination rate while maintaining a low misclassification rate. The system is highly scalable, processing hundreds of claims per hour through asynchronous parallelization.

CONCLUSIONS: By providing an open and transparent platform for large-batch literature verification, Valsci substantially lowers the barrier to comprehensive evidence-based reviews and fosters a more reproducible research ecosystem.

PMID:40437377 | DOI:10.1186/s12859-025-06159-4

Nat Aging. 2025 May 28. doi: 10.1038/s43587-025-00876-4. Online ahead of print.

ABSTRACT

Suppression of the insulin-IGF-mTORC1-Ras network ameliorates aging in animals. Many drugs have targets in the network because of its roles in cancer and metabolic disease and are candidates for repurposing as geroprotectors. Rapamycin, an established geroprotective drug, blocks mTORC1 signaling, and trametinib inhibits the Ras-MEK-ERK pathway. In this study, we assessed survival and health of male and female mice treated with trametinib, rapamycin or their combination. We show here that trametinib treatment extended lifespan in both sexes and that its combination with rapamycin was additive. Combination treatment reduced liver tumors in both sexes and spleen tumors in male mice, blocked the age-related increase in brain glucose uptake and strongly reduced inflammation in brain, kidney, spleen and muscle and circulating levels of pro-inflammatory cytokines. We conclude that trametinib is a geroprotector in mice and that its combination with rapamycin is more effective than either drug alone, making the combination a candidate for repurposing as a gerotherapy in humans.

PMID:40437307 | DOI:10.1038/s43587-025-00876-4

Mol Syst Biol. 2025 May 28. doi: 10.1038/s44320-025-00122-4. Online ahead of print.

ABSTRACT

Proteins operate within dense interconnected networks, with interactions necessary both for stabilising proteins and enabling them to execute their molecular functions. Remarkably, protein-protein interaction networks operating within tumour cells continue to function despite widespread genetic perturbations. Previous work has demonstrated that tumour cells tolerate perturbations of paralogs better than perturbations of singleton genes, but the underlying mechanisms remain poorly understood. Here, we systematically profile the proteomic response of tumours and cell lines to gene loss. We find many examples of proteomic compensation, where loss of one gene causes increased abundance of a paralog, and collateral loss, where gene loss causes reduced paralog abundance. Compensation is enriched among paralog pairs that are central in the protein-protein interaction network and whose interaction partners perform essential functions. Compensation is also significantly more likely to be observed between synthetic lethal pairs. Our results support a model whereby loss of one gene results in increased protein abundance of its paralog, stabilising the protein-protein interaction network. Consequently, tumour cells may become dependent on the paralog for survival, creating potentially targetable vulnerabilities.

PMID:40437196 | DOI:10.1038/s44320-025-00122-4

Nature. 2025 May 28. doi: 10.1038/s41586-025-09013-y. Online ahead of print.

ABSTRACT

Self-recognition is a fundamental cellular process across evolution and forms the basis of neuronal self-avoidance1-4. Clustered protocadherin (cPcdh) proteins, which comprise a large family of isoform-specific homophilic recognition molecules, have a pivotal role in the neuronal self-avoidance that is required for mammalian brain development5-7. The probabilistic expression of different cPcdh isoforms confers unique identities on neurons and forms the basis for neuronal processes to discriminate between self and non-self5,6,8. Whether this self-recognition mechanism also exists in astrocytes remains unknown. Here we report that γC3, a specific isoform in the Pcdhγ family, is enriched in human and mouse astrocytes. Using genetic manipulation, we demonstrate that γC3 acts autonomously to regulate astrocyte morphogenesis in the mouse visual cortex. To determine whether γC3 proteins act by promoting recognition between processes of the same astrocyte, we generated pairs of γC3 chimeric proteins that are capable of heterophilic binding to each other, but incapable of homophilic binding. Co-expression of complementary heterophilic binding isoform pairs in the same γC3-null astrocyte restored normal morphology. By contrast, chimeric γC3 proteins individually expressed in single γC3-null mutant astrocytes did not. These data establish that self-recognition mediated by γC3 contributes to astrocyte development in the mammalian brain.

PMID:40437095 | DOI:10.1038/s41586-025-09013-y

Nat Neurosci. 2025 May 28. doi: 10.1038/s41593-025-01972-9. Online ahead of print.

ABSTRACT

The choroid plexus (ChP) regulates cerebrospinal fluid (CSF) composition, providing essential molecular cues for brain development; yet, embryonic ChP secretory mechanisms remain poorly defined. Here we identify apocrine secretion by embryonic ChP epithelial cells as a key regulator of the CSF proteome and neurodevelopment in male and female mice. We demonstrate that the activation of serotonergic 5-HT2C receptors (by WAY-161503) triggers sustained Ca2+ signaling, driving high-volume apocrine secretion in mouse and human ChP. This secretion alters the CSF proteome, stimulating neural progenitors lining the brain's ventricles and shifting their developmental trajectory. Inducing ChP secretion in utero in mice disrupts neural progenitor dynamics, cerebral cortical architecture and offspring behavior. Additionally, illness or lysergic acid diethylamide exposure during pregnancy provokes coordinated ChP secretion in the mouse embryo. Our findings reveal a fundamental secretory pathway in the ChP that shapes brain development, highlighting how its disruption can have lasting consequences for brain health.

PMID:40437054 | DOI:10.1038/s41593-025-01972-9

Sci Rep. 2025 May 28;15(1):18708. doi: 10.1038/s41598-025-03168-4.

NO ABSTRACT

PMID:40437007 | DOI:10.1038/s41598-025-03168-4

Nat Commun. 2025 May 29;16(1):4967. doi: 10.1038/s41467-025-60208-3.

ABSTRACT

B-cell receptor (BCR) signaling plays an important role in the pathogenesis of mantle cell lymphoma (MCL), but the detailed mechanisms are not fully understood. In this study, through a genome-wide loss-of-function screen, we identify carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) as an essential factor in a subset of MCL tumors. Our signal transduction studies reveal that CEACAM1 plays a critical role in BCR activation through involvement in two dynamic processes. First, following BCR engagement, CEACAM1 co-localizes to the membrane microdomains (lipid rafts) by anchoring to the F-actin cytoskeleton through the adaptor protein filamin A. Second, CEACAM1 recruits and increases the abundance of SYK in the BCR complex leading to BCR activation. These activities of CEACAM1 require its cytoplasmic tail and the N-terminal ectodomain. Considering that previous studies have extensively characterized CEACAM1 as an ITIM-bearing inhibitory receptor, our findings regarding its activating role are both surprising and context-dependent, which may have implications for BCR-targeting therapies.

PMID:40436855 | DOI:10.1038/s41467-025-60208-3

BMJ Open. 2025 May 27;15(5):e097732. doi: 10.1136/bmjopen-2024-097732.

ABSTRACT

PURPOSE: We are conducting a longitudinal cohort study-the Community Burden of Acute Respiratory Infections in Shanghai-to assess age-stratified incidence, healthcare utilisation and risk factors of influenza virus, respiratory syncytial virus (RSV) and SARS-CoV-2 associated acute respiratory infections (ARIs) in Shanghai, China.

PARTICIPANTS: Study participants were enrolled by family doctors in all 47 community health services centres in Pudong New Area District, Shanghai, China. All permanent residents 6 months and older living in Pudong for at least 6 months were eligible for enrolment; residents who planned to leave Pudong for more than 1 month in the first study year were excluded. During enrolment, study staff conducted baseline assessments of sociodemographics, underlying medical conditions, vaccination history and household and self-rated health status. Study participants are being followed for ARIs for 3 years. Nasopharyngeal and oropharyngeal swab specimens are being obtained from suspected ARI cases. Influenza virus, RSV, SARS-CoV-2 and other respiratory pathogens are tested for by multiplex respiratory pathogen real-time quantitative PCR assays. Illness courses and clinical recoveries of ARI cases are assessed through weekly contact with ARI cases for 28 days post ascertainment.

FINDINGS TO DATE: Between 14 October 2024 and 22 November 2024, we enrolled 5387 community residents into the cohort, including 233 children aged from 6 months to 2 years, 278 preschool children aged 3-6 years, 575 school-age children aged 7-18 years, 2150 adults aged 19-64 years and 2151 older adults aged 65+years. All finished baseline assessment and started follow-up. Surveillance of ARI symptoms, collection of specimens and laboratory testing are ongoing.

FUTURE PLANS: Findings from this study will be used to provide valuable scientific data to inform ongoing control efforts and future pandemic preparedness for respiratory diseases in China. Planned analyses include analysis of annual pathogen-specific incidence by age group and exploration of healthcare seeking behaviour and factors associated with ARIs and severe ARIs. We will also assess transmission dynamics of common respiratory pathogens in a household transmission subcohort.

PMID:40436446 | DOI:10.1136/bmjopen-2024-097732

Environ Res. 2025 May 26:121970. doi: 10.1016/j.envres.2025.121970. Online ahead of print.

ABSTRACT

Respiratory tract infections have been linked to air pollution exposure, and both are known exogenous risk factors of asthma exacerbations. The current frontline therapy used to minimize exacerbations are inhaled corticosteroids (ICS), but these medications increase the risk of respiratory tract infections in patients due to immunosuppressive side-effects. Virally-triggered exacerbations are most commonly associated with rhinovirus, and the ICS fluticasone propionate (FP) has been demonstrated to increase rhinovirus viral load by 2.5-fold in infected epithelial cells. We hypothesized that air pollution exposure combined with ICS would magnify effects on host-defence antiviral responses and viral replication. Using rhinovirus (RV16), we infected human bronchial epithelial (BEAS-2B) cells that were pre-treated with FP (250 nM) and exposed to diesel exhaust particles (DEP) SRM2975 (50 μg/cm2). We show that DEP exposure significantly increased RV16 viral RNA by 12-fold over untreated cells 24 hours post-infection, while FP alone induced a 2-fold rise. However, when combined, FP and DEP induced a significant supra-additive 17-fold increase in RV16 RNA. In addition, we demonstrate that DEP induces the expression of the RV16 entry receptor ICAM-1 through the canonical NF-κB pathway and that suppression of this pathway results in attenuation of RV16 viral expression. Our findings suggest a mechanism through which combined epithelial exposure to DEP and ICS increases RV16 infectivity, through the suppression of innate antiviral immune responses and induction of the RV16 entry receptor ICAM-1. These findings suggest a need for caution during periods of high air pollution by those managing chronic lung diseases with corticosteroids.

PMID:40436198 | DOI:10.1016/j.envres.2025.121970

Int J Biol Macromol. 2025 May 26:144698. doi: 10.1016/j.ijbiomac.2025.144698. Online ahead of print.

ABSTRACT

DbpA, a DEAD-box RNA helicase, is known to bind helix 92 (H92) of the peptidyl transferase center (PTC) during 50S ribosomal subunit maturation. The presence of H92 and ss/dsRNA junction is essential for its ATP-dependent unwinding activity. However, the precise role of DbpA in 50S precursors (pre50S) and its underlying mechanism remain unclear. In this study, we used cryo-electron microscopy to characterize a series of pre50S intermediates isolated from Escherichia coli cells expressing a catalytically inactive mutant, DbpA(R331A). Pull-down assays revealed that DbpA recognizes only a small subset of pre50S particles in which the central protuberance (CP) is folded, while the PTC remains unfolded. Structural analysis uncovered a series of late-stage intermediates along a progressive assembly pathway, revealing an alternative route for 50S subunit maturation in the presence of non-functional DbpA. In summary, our study provides mechanistic insights into how DbpA facilitates 50S subunit maturation and how the ribosome assembles in its absence.

PMID:40436157 | DOI:10.1016/j.ijbiomac.2025.144698

Environ Pollut. 2025 May 26:126543. doi: 10.1016/j.envpol.2025.126543. Online ahead of print.

ABSTRACT

Lead (Pb), cadmium (Cd), and perfluorooctanoic acid (PFOA) are environmental pollutants with bioaccumulative properties, posing risks to embryonic development, particularly through cephalic region malformations. Despite their significance, few studies have investigated their effects at realistic concentrations or in mixtures. This study assessed the individual and combined effects of Pb, Cd, and PFOA on Gallus gallus embryos at relevant concentrations, focusing on the cephalic region at stages HH10 and HH14. Exposure to contaminant mixtures, particularly Pb+Cd, Pb+PFOA, and the full combination, resulted in a higher incidence of cranial malformations compared to single-compound exposures. Cd induced dose-dependent changes in cell morphology and significantly reduced proliferation in the head region. PFOA contributed additively to mixture toxicity, markedly impairing cell proliferation and modifying the expression of key adhesion molecules such as β-catenin and N-cadherin. Both embryonic stages exhibited aberrant cellular delamination from the neural tube, with HH10 embryos displaying heightened vulnerability. Systems biology analysis revealed distinct molecular responses to each contaminant, with Pb and Cd primarily affecting immune-related pathways, including complement activation, while PFOA operated through separate regulatory mechanisms. Integrative network analyses using STITCH 5 and the Comparative Toxicogenomics Database identified candidate genes potentially involved in developmental disruption. These findings underscore the complex interactions between pollutants, which may not be predicted solely by examining individual exposures and highlight the need for stricter environmental regulations to address the risks posed by contaminant mixtures.

PMID:40436095 | DOI:10.1016/j.envpol.2025.126543

Cell Rep Methods. 2025 May 22:101053. doi: 10.1016/j.crmeth.2025.101053. Online ahead of print.

ABSTRACT

Accurate relatedness estimation is essential in biobank-scale genetic studies. We present deepKin, a method-of-moments framework that accounts for sampling variance to enable statistical inference and classification of relatedness. Unlike traditional methods using fixed thresholds, deepKin computes data-specific significance thresholds, determines the minimum effective number of markers, and estimates the statistical power to detect distant relatives. Through simulations, we demonstrate that deepKin accurately infers both unrelated pairs and relatives by leveraging sampling variance. In the UK Biobank (UKB), analysis of the 3K Oxford subset showed that SNP sets with a larger effective number of markers provided greater power for detecting distant relatives. In the White British subset, deepKin identified over 212,000 significant relative pairs, categorized into six degrees, and revealed their geographic patterns across 19 UKB assessment centers through within-cohort and cross-cohort relatedness estimation. An R package (deepKin) is available at GitHub.

PMID:40436020 | DOI:10.1016/j.crmeth.2025.101053

Bioorg Med Chem. 2025 May 23;128:118258. doi: 10.1016/j.bmc.2025.118258. Online ahead of print.

ABSTRACT

The experience of the SARS-CoV-2 pandemic has highlighted the urgent need to develop broad-spectrum antivirals (BSA) agents capable of targeting viral and/or host factors essential for infection as undeniable weapons against future coronavirus threats with potential pandemic perspectives. In this study, we report the synthesis and biological evaluation of a novel series of indole-based ethyl cinnamate derivatives designed as multitarget inhibitors of both SARS-CoV-2 Main Protease (Mpro) and human cathepsin, namely CatL and CatS, key enzymes involved in viral replication and entry. Enzymatic assays showed that several compounds exert significant inhibition on multiple targets. Structure-activity relationship (SAR) studies highlighted the critical role of the tert-leucine (Tle) residue at P2 position of these (pseudo)dipeptides, which proved to be essential for multitarged enzyme inhibition and antiviral activity. In antiviral assays against representative α- (hCoV-229E) and β-coronavirus (hCoV-OC43), 12 (EC50 = 4.09 µM for hCoV-OC43, 0.77 µM for hCoV-229E), 20 (EC50 = 6.68 µM for hCoV-OC43, 0.62 µM for hCoV-229E), and 3 (EC50 = 2.96 µM for hCoV-OC43, 0.64 µM for hCoV-229E) restricted viral replication with high selectivity values (SI = 98, 56, and 101, respectively). Time-of-drug-addition experiments then revealed that 12 primarily inhibited viral entry by targeting CatL, whereas 20 affected both entry and post-entry stages of hCoV replication cycle likely thanks to its dual-inhibitory activity against both CatL and Mpro. These findings support the development of multitarget inhibitors as promising antivirals able to inhibit both α- and β-coronavirus, so as to reduce the risk of resistance associated with single-target agents. Furthermore, the demonstrated effectiveness of Tle-containing indole-based cinnamates as BSA highlights their potential in the context of the strategic framework for pandemic preparedness.

PMID:40435714 | DOI:10.1016/j.bmc.2025.118258

J Pharm Biomed Anal. 2025 May 21;264:116976. doi: 10.1016/j.jpba.2025.116976. Online ahead of print.

ABSTRACT

The plasma and urinary metabolite profiles of the 2-thiophene-based H1-receptor antagonist methapyrilene (N,N-dimethyl-N'-pyridin-2-yl-N'-(thiophen-2-ylmethyl)ethane-1,2-diamine) were investigated in the rat following the oral administration of 0, 50 or 150 mg/kg/day of the drug for 5 days. The systemic exposure and metabolic fate of methapyrilene were investigated initially using a rapid "fit for purpose" reversed-phase (RP) UHPLC-MS/MS assay followed by a more in-depth characterization of its metabolites using RP-UHPLC coupled to a high resolution multi reflecting time of flight mass spectrometer. No detectable methapyrilene was present in plasma when measured on days 1, 3 and 5, at any dose, using samples obtained 24 h post administration. However, methapyrilene-derived metabolites were detected, in increasing amounts, in these plasma samples on days 3 and 5 of the study. Both methapyrilene and large numbers of metabolites were present in the urines collected 24 h after dosing on days 3 and 5. The profiles of these metabolites were both dose and time dependent. From the urine and plasma profiles obtained using both +ve and -ve ESI HRMS some 24 metabolites were characterized showing functionalization by aliphatic and aromatic hydroxylation, N-oxidation, N-demethylation and loss of the thiophene ring. Glucuronic acid, glycine and glutathione-derived conjugates were also detected.

PMID:40435660 | DOI:10.1016/j.jpba.2025.116976

Sci Adv. 2025 May 30;11(22):eads7269. doi: 10.1126/sciadv.ads7269. Epub 2025 May 28.

ABSTRACT

Modules represent fundamental building blocks of cellular networks and are thought to facilitate robustness of phenotypes against perturbations. While reaction kinetic shapes the concentration of components and reaction rates, its use in identification of modules entails knowledge of parameter values. Here, we demonstrate that kinetic modules can be efficiently identified on the basis of steady-state reaction rate couplings in large-scale biochemical networks endowed with mass action kinetics without knowledge of parameter values. We then link the kinetic modules of metabolic networks with robustness of metabolite concentrations to perturbations. Analyzing 34 metabolic network models of 26 organisms, we demonstrate that the ordered binding enzyme mechanism leads to increased concentration robustness compared to random binding. Our findings pave the way for usage of modules in synthetic biology and biotechnological applications.

PMID:40435256 | DOI:10.1126/sciadv.ads7269

Sci Adv. 2025 May 30;11(22):eadt5833. doi: 10.1126/sciadv.adt5833. Epub 2025 May 28.

ABSTRACT

Linezolid, an oxazolidinone antibiotic, is widely used to treat multidrug-resistant tuberculosis and drug-resistant Gram-positive infections. However, prolonged use is associated with severe hematologic toxicity, the underlying mechanisms of which remain incompletely understood, particularly regarding the role of linezolid metabolites. Our clinical study indicates that elevated exposure to PNU142586, a primary metabolite of linezolid, is associated with an increased risk of linezolid-induced toxicity, even in the absence of renal impairment. To elucidate its mechanism, we identify DNA topoisomerase 2-α (TOP2A) and DNA topoisomerase 2-β (TOP2B) as primary targets of PNU142586 at molecular, cellular, and in vivo levels. PNU142586 disrupts replication and transcription by impeding DNA binding to TOP2A and TOP2B with a favorable conformation for cleavage and by inhibiting adenosine 5'-triphosphate hydrolysis, ultimately leading to antiproliferative and cytotoxic effects, including mitochondrial dysfunction. The present study thus provides mechanistic insight into linezolid-induced hematologic toxicity and offers a foundation for safer antibiotic development and improved clinical monitoring through biomarker identification.

PMID:40435237 | DOI:10.1126/sciadv.adt5833

Sci Transl Med. 2025 May 28;17(800):eado2622. doi: 10.1126/scitranslmed.ado2622. Epub 2025 May 28.

ABSTRACT

Severe injury accompanied by hemorrhagic shock triggers an early release of cell constituents into the circulation, referred to as the systemic storm. The systemic storm drives the systemic inflammatory response and is associated with increased mortality. The role of programmed cell death (PCD) in the systemic storm was investigated in mice that underwent hemorrhagic shock with tissue trauma (HS/T) followed by crystalloid resuscitation. Wild-type (WT) mice were treated with inhibitors, including z-VAD, necrostatin-1, ferrostatin-1, or disulfiram (DSF), to block the different forms of PCD. Gasdermin D (GSDMD)-dependent PCD was further targeted using Gsdmd-/- mice. Untargeted metabolomics and proteomics were used as the primary end point to gain a comprehensive view of the composition changes in the circulation. Although all inhibitor strategies partially reversed the systemic storm, the largest reversal occurred in Gsdmd-/- mice and WT mice treated with DSF, a nonspecific inhibitor of GSDMD pore formation. Weighted correlation network analysis and machine learning identified a subset of omics features increased in the circulation in a GSDMD-dependent manner. Linear regression analysis using a GSDMD-specific omics score (GSOS) in a published multiomic dataset from patients with trauma showed correlation of the GSOS with outcomes and inflammation. Female sex emerged as the variable with the strongest relationship to the GSOS in injured humans, a finding confirmed in mice. Last, DSF treatment or GSDMD deletion led to improvement in blood pressure recovery and increased survival in both sexes. These protective effects of DSF were observed when administered after HS/T, underscoring its potential as a therapeutic intervention.

PMID:40435214 | DOI:10.1126/scitranslmed.ado2622

Cell Rep. 2025 May 26;44(6):115748. doi: 10.1016/j.celrep.2025.115748. Online ahead of print.

ABSTRACT

Dissecting host factors critical for viral infection and understanding their mechanisms of action is critical for identifying drug targets. Here, we leverage a genome-wide CRISPR base-editing screen to identify functional lysine residues in host factors required for influenza A virus (IAV) replication. Multiple host genes, including GSTM4, FLNC, HMGB1, ZNF236, GRIP1, and PXN, along with regulatory lysine codons, are identified. Among these, paxillin (encoded by PXN) is identified as an important host entry factor. Depletion of paxillin significantly reduces IAV infection in both cell cultures and mice. Further analysis suggests that the δ isoform of paxillin, rather than the canonical β isoform, plays the key role. Additionally, our data indicate that lysine 68 of paxillin δ undergoes K6-linked ubiquitination and regulates influenza virus replication via modulating endosome-dependent viral entry. These observations contribute to understanding how influenza viruses interact with host factors and may inform therapeutic development.

PMID:40434888 | DOI:10.1016/j.celrep.2025.115748